mirror of
https://github.com/msberends/AMR.git
synced 2026-07-28 19:20:54 +02:00
(v1.4.0.9044) mo tibble printing, mo_shortname() fix
This commit is contained in:
@@ -1,6 +1,6 @@
|
||||
Package: AMR
|
||||
Version: 1.4.0.9043
|
||||
Date: 2020-12-22
|
||||
Version: 1.4.0.9044
|
||||
Date: 2020-12-24
|
||||
Title: Antimicrobial Resistance Analysis
|
||||
Authors@R: c(
|
||||
person(role = c("aut", "cre"),
|
||||
|
||||
8
NEWS.md
8
NEWS.md
@@ -1,5 +1,5 @@
|
||||
# AMR 1.4.0.9043
|
||||
## <small>Last updated: 22 December 2020</small>
|
||||
# AMR 1.4.0.9044
|
||||
## <small>Last updated: 24 December 2020</small>
|
||||
|
||||
### New
|
||||
* Function `is_new_episode()` to determine patient episodes which are not necessarily based on microorganisms. It also supports grouped variables with e.g. `mutate()`, `filter()` and `summarise()` of the `dplyr` package:
|
||||
@@ -45,12 +45,14 @@
|
||||
* Fix for plotting MIC values with `plot()`
|
||||
* Added `plot()` generic to class `<disk>`
|
||||
* LA-MRSA and CA-MRSA are now recognised as an abbreviation for *Staphylococcus aureus*, meaning that e.g. `mo_genus("LA-MRSA")` will return `"Staphylococcus"` and `mo_is_gram_positive("LA-MRSA")` will return `TRUE`.
|
||||
* Fix for printing class <mo> in tibbles when all values are `NA`
|
||||
* Fix for `mo_shortname()` when the input contains `NA`
|
||||
* If `as.mo()` takes more than 30 seconds, some suggestions will be done to improve speed
|
||||
|
||||
### Other
|
||||
* All messages and warnings thrown by this package now break sentences on whole words
|
||||
* More extensive unit tests
|
||||
* Internal calls to `options()` were all removed in favour of a new internal environment `mo_env`
|
||||
* Our website now also has a dark theme, that switches on automatically based on system settings (such as Night Mode in macOS)
|
||||
|
||||
# AMR 1.4.0
|
||||
|
||||
|
||||
@@ -187,13 +187,16 @@ search_type_in_df <- function(x, type, info = TRUE) {
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
if (!is.null(found) & info == TRUE) {
|
||||
msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.")
|
||||
if (type %in% c("keyantibiotics", "specimen")) {
|
||||
msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
|
||||
if (message_not_thrown_before(fn = paste0("search_", type))) {
|
||||
msg <- paste0("Using column '", font_bold(found), "' as input for `col_", type, "`.")
|
||||
if (type %in% c("keyantibiotics", "specimen")) {
|
||||
msg <- paste(msg, "Use", font_bold(paste0("col_", type), "= FALSE"), "to prevent this.")
|
||||
}
|
||||
message_(msg)
|
||||
remember_thrown_message(fn = paste0("search_", type))
|
||||
}
|
||||
message_(msg)
|
||||
}
|
||||
found
|
||||
}
|
||||
@@ -534,6 +537,20 @@ get_current_data <- function(arg_name, call) {
|
||||
call = call - 4))
|
||||
}
|
||||
|
||||
get_root_env_address <- function() {
|
||||
sub('<environment: (.*)>', '\\1', utils::capture.output(sys.frames()[[1]]))
|
||||
}
|
||||
|
||||
remember_thrown_message <- function(fn) {
|
||||
assign(x = paste0("address_", fn),
|
||||
value = get_root_env_address(),
|
||||
envir = mo_env)
|
||||
}
|
||||
|
||||
message_not_thrown_before <- function(fn) {
|
||||
is.null(mo_env[[paste0("address_", fn)]]) || !identical(mo_env[[paste0("address_", fn)]], get_root_env_address())
|
||||
}
|
||||
|
||||
has_colour <- function() {
|
||||
# this is a base R version of crayon::has_color
|
||||
enabled <- getOption("crayon.enabled")
|
||||
|
||||
10
R/count.R
10
R/count.R
@@ -134,7 +134,10 @@ count_R <- function(..., only_all_tested = FALSE) {
|
||||
#' @rdname count
|
||||
#' @export
|
||||
count_IR <- function(..., only_all_tested = FALSE) {
|
||||
warning_("Using 'count_IR' is discouraged; use 'count_resistant()' instead to not consider \"I\" being resistant.", call = FALSE)
|
||||
if (message_not_thrown_before("count_IR")) {
|
||||
warning_("Using count_IR() is discouraged; use count_resistant() instead to not consider \"I\" being resistant.", call = FALSE)
|
||||
remember_thrown_message("count_IR")
|
||||
}
|
||||
rsi_calc(...,
|
||||
ab_result = c("I", "R"),
|
||||
only_all_tested = only_all_tested,
|
||||
@@ -162,7 +165,10 @@ count_SI <- function(..., only_all_tested = FALSE) {
|
||||
#' @rdname count
|
||||
#' @export
|
||||
count_S <- function(..., only_all_tested = FALSE) {
|
||||
warning_("Using 'count_S' is discouraged; use 'count_susceptible()' instead to also consider \"I\" being susceptible.", call = FALSE)
|
||||
if (message_not_thrown_before("count_S")) {
|
||||
warning_("Using count_S() is discouraged; use count_susceptible() instead to also consider \"I\" being susceptible.", call = FALSE)
|
||||
remember_thrown_message("count_S")
|
||||
}
|
||||
rsi_calc(...,
|
||||
ab_result = "S",
|
||||
only_all_tested = only_all_tested,
|
||||
|
||||
@@ -87,7 +87,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
|
||||
#'
|
||||
#' The following antibiotics are used for the functions [eucast_rules()] and [mdro()]. These are shown below in the format 'name (`antimicrobial ID`, [ATC code](https://www.whocc.no/atc/structure_and_principles/))', sorted alphabetically:
|
||||
#'
|
||||
#' `r create_ab_documentation(c("AMC", "AMK", "AMP", "AMX", "ATM", "AVO", "AZL", "AZM", "BAM", "BPR", "CAC", "CAP", "CAT", "CAZ", "CCV", "CDR", "CDZ", "CEC", "CED", "CEI", "CEP", "CFM", "CFM1", "CFP", "CFR", "CFS", "CHL", "CID", "CIP", "CLI", "CLR", "CMX", "CMZ", "CND", "COL", "CPD", "CPM", "CPO", "CPR", "CPT", "CRB", "CRD", "CRN", "CRO", "CSL", "CTB", "CTF", "CTL", "CTT", "CTX", "CTZ", "CXM", "CYC", "CZD", "CZO", "CZX", "DAL", "DAP", "DIR", "DIT", "DIZ", "DKB", "DOR", "DOX", "ENX", "EPC", "ERV", "ERY", "ETH", "ETP", "FDX", "FEP", "FLC", "FLE", "FLR1", "FOS", "FOX", "FOX1", "FUS", "GAT", "GEH", "GEM", "GEN", "GRX", "HAP", "HET", "INH", "IPM", "ISE", "JOS", "KAN", "LEX", "LIN", "LNZ", "LOM", "LOR", "LTM", "LVX", "MAN", "MCM", "MEC", "MEM", "MEV", "MEZ", "MFX", "MID", "MNO", "MTM", "MTR", "NAL", "NEO", "NET", "NIT", "NOR", "NOV", "NVA", "OFX", "OLE", "OMC", "ORI", "OXA", "PAZ", "PEF", "PEN", "PHN", "PIP", "PLB", "PME", "PRI", "PRL", "PRU", "PVM", "PZA", "QDA", "RAM", "RFL", "RFP", "RIB", "RID", "RIF", "ROK", "RST", "RXT", "SAM", "SBC", "SDI", "SDM", "SIS", "SLF", "SLF1", "SLF10", "SLF11", "SLF12", "SLF13", "SLF2", "SLF3", "SLF4", "SLF5", "SLF6", "SLF7", "SLF8", "SLF9", "SLT1", "SLT2", "SLT3", "SLT4", "SLT5", "SMX", "SPI", "SPT", "SPX", "STH", "STR", "STR1", "SUD", "SUT", "SXT", "SZO", "TAL", "TCC", "TCM", "TCY", "TEC", "TEM", "TGC", "THA", "TIC", "TLT", "TLV", "TMP", "TMX", "TOB", "TRL", "TVA", "TZD", "TZP", "VAN"))`
|
||||
#' `r create_ab_documentation(c("AMC", "AMK", "AMP", "AMX", "ATM", "AVO", "AZL", "AZM", "BAM", "BPR", "CAC", "CAT", "CAZ", "CCP", "CCV", "CCX", "CDC", "CDR", "CDZ", "CEC", "CED", "CEI", "CEM", "CEP", "CFM", "CFM1", "CFP", "CFR", "CFS", "CFZ", "CHE", "CHL", "CID", "CIP", "CLI", "CLR", "CMX", "CMZ", "CND", "COL", "CPD", "CPI", "CPL", "CPM", "CPO", "CPR", "CPT", "CPX", "CRB", "CRD", "CRN", "CRO", "CSL", "CTB", "CTC", "CTF", "CTL", "CTS", "CTT", "CTX", "CTZ", "CXM", "CYC", "CZA", "CZD", "CZO", "CZP", "CZX", "DAL", "DAP", "DIR", "DIT", "DIX", "DIZ", "DKB", "DOR", "DOX", "ENX", "EPC", "ERY", "ETP", "FEP", "FLC", "FLE", "FLR1", "FOS", "FOV", "FOX", "FOX1", "FUS", "GAT", "GEM", "GEN", "GRX", "HAP", "HET", "IPM", "ISE", "JOS", "KAN", "LEX", "LIN", "LNZ", "LOM", "LOR", "LTM", "LVX", "MAN", "MCM", "MEC", "MEM", "MEV", "MEZ", "MFX", "MID", "MNO", "MTM", "NAL", "NEO", "NET", "NIT", "NOR", "NOV", "NVA", "OFX", "OLE", "ORI", "OXA", "PAZ", "PEF", "PEN", "PHN", "PIP", "PLB", "PME", "PRI", "PRL", "PRU", "PVM", "QDA", "RAM", "RFL", "RID", "RIF", "ROK", "RST", "RXT", "SAM", "SBC", "SDI", "SDM", "SIS", "SLF", "SLF1", "SLF10", "SLF11", "SLF12", "SLF13", "SLF2", "SLF3", "SLF4", "SLF5", "SLF6", "SLF7", "SLF8", "SLF9", "SLT1", "SLT2", "SLT3", "SLT4", "SLT5", "SMX", "SPI", "SPX", "STR", "STR1", "SUD", "SUT", "SXT", "SZO", "TAL", "TCC", "TCM", "TCY", "TEC", "TEM", "TGC", "THA", "TIC", "TIO", "TLT", "TLV", "TMP", "TMX", "TOB", "TRL", "TVA", "TZD", "TZP", "VAN"))`
|
||||
#' @aliases EUCAST
|
||||
#' @rdname eucast_rules
|
||||
#' @export
|
||||
@@ -278,53 +278,66 @@ eucast_rules <- function(x,
|
||||
CAC <- cols_ab["CAC"]
|
||||
CAT <- cols_ab["CAT"]
|
||||
CAZ <- cols_ab["CAZ"]
|
||||
CCP <- cols_ab["CCP"]
|
||||
CCV <- cols_ab["CCV"]
|
||||
CCX <- cols_ab["CCX"]
|
||||
CDC <- cols_ab["CDC"]
|
||||
CDR <- cols_ab["CDR"]
|
||||
CDZ <- cols_ab["CDZ"]
|
||||
CEC <- cols_ab["CEC"]
|
||||
CED <- cols_ab["CED"]
|
||||
CEI <- cols_ab["CEI"]
|
||||
CEM <- cols_ab["CEM"]
|
||||
CEP <- cols_ab["CEP"]
|
||||
CFM <- cols_ab["CFM"]
|
||||
CFM1 <- cols_ab["CFM1"]
|
||||
CFP <- cols_ab["CFP"]
|
||||
CFR <- cols_ab["CFR"]
|
||||
CFS <- cols_ab["CFS"]
|
||||
CFZ <- cols_ab["CFZ"]
|
||||
CHE <- cols_ab["CHE"]
|
||||
CHL <- cols_ab["CHL"]
|
||||
CID <- cols_ab["CID"]
|
||||
CIP <- cols_ab["CIP"]
|
||||
CLI <- cols_ab["CLI"]
|
||||
CLI <- cols_ab["CLI"]
|
||||
CLR <- cols_ab["CLR"]
|
||||
CMX <- cols_ab["CMX"]
|
||||
CMZ <- cols_ab["CMZ"]
|
||||
CND <- cols_ab["CND"]
|
||||
COL <- cols_ab["COL"]
|
||||
CPD <- cols_ab["CPD"]
|
||||
CPI <- cols_ab["CPI"]
|
||||
CPL <- cols_ab["CPL"]
|
||||
CPM <- cols_ab["CPM"]
|
||||
CPO <- cols_ab["CPO"]
|
||||
CPR <- cols_ab["CPR"]
|
||||
CPT <- cols_ab["CPT"]
|
||||
CPX <- cols_ab["CPX"]
|
||||
CRB <- cols_ab["CRB"]
|
||||
CRD <- cols_ab["CRD"]
|
||||
CRN <- cols_ab["CRN"]
|
||||
CRO <- cols_ab["CRO"]
|
||||
CSL <- cols_ab["CSL"]
|
||||
CTB <- cols_ab["CTB"]
|
||||
CTC <- cols_ab["CTC"]
|
||||
CTF <- cols_ab["CTF"]
|
||||
CTL <- cols_ab["CTL"]
|
||||
CTS <- cols_ab["CTS"]
|
||||
CTT <- cols_ab["CTT"]
|
||||
CTX <- cols_ab["CTX"]
|
||||
CTZ <- cols_ab["CTZ"]
|
||||
CXM <- cols_ab["CXM"]
|
||||
CYC <- cols_ab["CYC"]
|
||||
CZA <- cols_ab["CZA"]
|
||||
CZD <- cols_ab["CZD"]
|
||||
CZO <- cols_ab["CZO"]
|
||||
CZP <- cols_ab["CZP"]
|
||||
CZX <- cols_ab["CZX"]
|
||||
DAL <- cols_ab["DAL"]
|
||||
DAP <- cols_ab["DAP"]
|
||||
DIR <- cols_ab["DIR"]
|
||||
DIT <- cols_ab["DIT"]
|
||||
DIX <- cols_ab["DIX"]
|
||||
DIZ <- cols_ab["DIZ"]
|
||||
DKB <- cols_ab["DKB"]
|
||||
DOR <- cols_ab["DOR"]
|
||||
@@ -338,6 +351,7 @@ eucast_rules <- function(x,
|
||||
FLE <- cols_ab["FLE"]
|
||||
FLR1 <- cols_ab["FLR1"]
|
||||
FOS <- cols_ab["FOS"]
|
||||
FOV <- cols_ab["FOV"]
|
||||
FOX <- cols_ab["FOX"]
|
||||
FOX1 <- cols_ab["FOX1"]
|
||||
FUS <- cols_ab["FUS"]
|
||||
@@ -391,7 +405,6 @@ eucast_rules <- function(x,
|
||||
PRU <- cols_ab["PRU"]
|
||||
PVM <- cols_ab["PVM"]
|
||||
QDA <- cols_ab["QDA"]
|
||||
QDA <- cols_ab["QDA"]
|
||||
RAM <- cols_ab["RAM"]
|
||||
RFL <- cols_ab["RFL"]
|
||||
RID <- cols_ab["RID"]
|
||||
@@ -441,6 +454,7 @@ eucast_rules <- function(x,
|
||||
TGC <- cols_ab["TGC"]
|
||||
THA <- cols_ab["THA"]
|
||||
TIC <- cols_ab["TIC"]
|
||||
TIO <- cols_ab["TIO"]
|
||||
TLT <- cols_ab["TLT"]
|
||||
TLV <- cols_ab["TLV"]
|
||||
TMP <- cols_ab["TMP"]
|
||||
@@ -474,9 +488,10 @@ eucast_rules <- function(x,
|
||||
aminoglycosides <- c(AMK, DKB, GEN, ISE, KAN, NEO, NET, RST, SIS, STR, STR1, TOB)
|
||||
aminopenicillins <- c(AMP, AMX)
|
||||
carbapenems <- c(DOR, ETP, IPM, MEM, MEV)
|
||||
cephalosporins <- c(CDZ, CAC, CEC, CFR, RID, MAN, CTZ, CZD, CZO, CDR, DIT, FEP, CAT, CFM, CMX, CMZ, DIZ, CID, CFP, CSL, CND, CTX, CTT, CTF, FOX, CPM, CPO, CPD, CPR, CRD, CFS, CPT, CAZ, CCV, CTL, CTB, CZX, BPR, CFM1, CEI, CRO, CXM, LEX, CEP, HAP, CED, LTM, LOR)
|
||||
cephalosporins <- c(CDZ, CCP, CAC, CEC, CFR, RID, MAN, CTZ, CZD, CZO, CDR, DIT, FEP, CAT, CFM, CMX, CMZ, DIZ, CID, CFP, CSL, CND, CTX, CTT, CTF, FOX, CPM, CPO, CPD, CPR, CRD, CFS, CPT, CAZ, CCV, CTL, CTB, CZX, BPR, CFM1, CEI, CRO, CXM, LEX, CEP, HAP, CED, LTM, LOR)
|
||||
cephalosporins_1st <- c(CAC, CFR, RID, CTZ, CZD, CZO, CRD, CTL, LEX, CEP, HAP, CED)
|
||||
cephalosporins_2nd <- c(CEC, MAN, CMZ, CID, CND, CTT, CTF, FOX, CPR, CXM, LOR)
|
||||
cephalosporins_3rd <- c(CDZ, CCP, CCX, CDR, DIT, DIX, CAT, CPI, CFM, CMX, DIZ, CFP, CSL, CTX, CTC, CTS, CHE, FOV, CFZ, CPM, CPD, CPX, CDC, CFS, CAZ, CZA, CCV, CEM, CPL, CTB, TIO, CZX, CZP, CRO, LTM)
|
||||
cephalosporins_except_CAZ <- cephalosporins[cephalosporins != ifelse(is.null(CAZ), "", CAZ)]
|
||||
fluoroquinolones <- c(CIP, ENX, FLE, GAT, GEM, GRX, LVX, LOM, MFX, NOR, OFX, PAZ, PEF, PRU, RFL, SPX, TMX, TVA)
|
||||
glycopeptides <- c(AVO, NVA, RAM, TEC, TCM, VAN) # dalba/orita/tela are in lipoglycopeptides
|
||||
@@ -796,7 +811,7 @@ eucast_rules <- function(x,
|
||||
word_wrap(
|
||||
expertrules_info$title, " (",
|
||||
font_red(paste0(expertrules_info$version_txt, ", ", expertrules_info$year)), ")\n")),
|
||||
""))))
|
||||
""))), "\n")
|
||||
}
|
||||
# Print rule -------------------------------------------------------------
|
||||
if (rule_current != rule_previous) {
|
||||
|
||||
18
R/mdro.R
18
R/mdro.R
@@ -192,7 +192,7 @@ mdro <- function(x,
|
||||
if (guideline$code == "cmi2012") {
|
||||
guideline$name <- "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance."
|
||||
guideline$author <- "Magiorakos AP, Srinivasan A, Carey RB, ..., Vatopoulos A, Weber JT, Monnet DL"
|
||||
guideline$version <- "N/A"
|
||||
guideline$version <- NA
|
||||
guideline$source <- "Clinical Microbiology and Infection 18:3, 2012. DOI: 10.1111/j.1469-0691.2011.03570.x"
|
||||
guideline$type <- "MDRs/XDRs/PDRs"
|
||||
|
||||
@@ -221,7 +221,7 @@ mdro <- function(x,
|
||||
} else if (guideline$code == "mrgn") {
|
||||
guideline$name <- "Cross-border comparison of the Dutch and German guidelines on multidrug-resistant Gram-negative microorganisms"
|
||||
guideline$author <- "M\u00fcller J, Voss A, K\u00f6ck R, ..., Kern WV, Wendt C, Friedrich AW"
|
||||
guideline$version <- "N/A"
|
||||
guideline$version <- NA
|
||||
guideline$source <- "Antimicrobial Resistance and Infection Control 4:7, 2015. DOI: 10.1186/s13756-015-0047-6"
|
||||
guideline$type <- "MRGNs"
|
||||
|
||||
@@ -568,11 +568,13 @@ mdro <- function(x,
|
||||
} else {
|
||||
cat(font_red("\nResults with 'R' or 'I' are considered as resistance. Use `combine_SI = TRUE` to only consider 'R' as resistance.\n"))
|
||||
}
|
||||
cat("\nDetermining multidrug-resistant organisms (MDRO), according to:\n",
|
||||
font_bold("Guideline: "), font_italic(guideline$name), "\n",
|
||||
font_bold("Version: "), guideline$version, "\n",
|
||||
font_bold("Author: "), guideline$author, "\n",
|
||||
font_bold("Source: "), guideline$source, "\n",
|
||||
cat("\n", word_wrap("Determining multidrug-resistant organisms (MDRO), according to:"), "\n",
|
||||
word_wrap(paste0(font_bold("Guideline: "), font_italic(guideline$name)), extra_indent = 11, as_note = FALSE), "\n",
|
||||
word_wrap(paste0(font_bold("Author(s): "), guideline$author), extra_indent = 11, as_note = FALSE), "\n",
|
||||
ifelse(!is.na(guideline$version),
|
||||
paste0(word_wrap(paste0(font_bold("Version: "), guideline$version), extra_indent = 11, as_note = FALSE), "\n"),
|
||||
""),
|
||||
word_wrap(paste0(font_bold("Source: "), guideline$source), extra_indent = 11, as_note = FALSE), "\n",
|
||||
"\n", sep = "")
|
||||
}
|
||||
|
||||
@@ -1237,7 +1239,7 @@ mdro <- function(x,
|
||||
if (guideline$code == "cmi2012") {
|
||||
if (any(x$MDRO == -1, na.rm = TRUE)) {
|
||||
warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
|
||||
percentage(pct_required_classes), " (set with `pct_required_classes`)")
|
||||
percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
|
||||
# set these -1s to NA
|
||||
x[which(x$MDRO == -1), "MDRO"] <- NA_integer_
|
||||
}
|
||||
|
||||
29
R/mo.R
29
R/mo.R
@@ -276,7 +276,7 @@ exec_as.mo <- function(x,
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
check_dataset_integrity()
|
||||
|
||||
|
||||
lookup <- function(needle,
|
||||
column = property,
|
||||
haystack = reference_data_to_use,
|
||||
@@ -358,6 +358,9 @@ exec_as.mo <- function(x,
|
||||
x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
|
||||
|
||||
if (initial_search == TRUE) {
|
||||
# keep track of time - give some hints to improve speed if it takes a long time
|
||||
start_time <- Sys.time()
|
||||
|
||||
mo_env$mo_failures <- NULL
|
||||
mo_env$mo_uncertainties <- NULL
|
||||
mo_env$mo_renamed <- NULL
|
||||
@@ -1524,8 +1527,24 @@ exec_as.mo <- function(x,
|
||||
}
|
||||
# this will save the uncertain items as attribute, so they can be bound to `uncertainties` in the uncertain_fn() function
|
||||
x <- structure(x, uncertainties = uncertainties)
|
||||
} else {
|
||||
# keep track of time - give some hints to improve speed if it takes a long time
|
||||
end_time <- Sys.time()
|
||||
delta_time <- difftime(end_time, start_time, units = "secs")
|
||||
if (delta_time >= 30) {
|
||||
message_("Using `as.mo()` took ", delta_time, " seconds, which is a long time. Some suggestions to improve speed include:")
|
||||
message_(word_wrap("- Try to use as many valid taxonomic names as possible for your input.",
|
||||
extra_indent = 2),
|
||||
as_note = FALSE)
|
||||
message_(word_wrap("- Save the output and use it as input for future calculations, e.g. create a new variable to your data using `as.mo()`. All functions in this package that rely on microorganism codes will automatically use that new column where possible. All `mo_*()` functions also do not require you to set their `x` argument as long as you have the dplyr package installed and you have a column of class <mo>.",
|
||||
extra_indent = 2),
|
||||
as_note = FALSE)
|
||||
message_(word_wrap("- Use `set_mo_source()` to continually transform your organisation codes to microorganisms codes used by this package, please see `?mo_source`.",
|
||||
extra_indent = 2),
|
||||
as_note = FALSE)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
x
|
||||
}
|
||||
|
||||
@@ -1585,9 +1604,13 @@ pillar_shaft.mo <- function(x, ...) {
|
||||
out[x == "UNKNOWN"] <- font_na(" UNKNOWN")
|
||||
|
||||
# make it always fit exactly
|
||||
max_char <- max(nchar(x))
|
||||
if (is.na(max_char)) {
|
||||
max_char <- 7
|
||||
}
|
||||
create_pillar_column(out,
|
||||
align = "left",
|
||||
width = max(nchar(x)) + ifelse(any(x %in% c(NA, "UNKNOWN")), 2, 0))
|
||||
width = max_char + ifelse(any(x %in% c(NA, "UNKNOWN")), 2, 0))
|
||||
}
|
||||
|
||||
# will be exported using s3_register() in R/zzz.R
|
||||
|
||||
198
R/mo_property.R
198
R/mo_property.R
@@ -27,12 +27,12 @@
|
||||
#'
|
||||
#' Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with [as.mo()], which makes it possible to use microbial abbreviations, codes and names as input. Please see *Examples*.
|
||||
#' @inheritSection lifecycle Stable lifecycle
|
||||
#' @param x any character (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be omitted for auto-guessing in `mo_is_*()` functions when used inside `dplyr` verbs, such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()], please see *Examples*.
|
||||
#' @param x any character (vector) that can be coerced to a valid microorganism code with [as.mo()]. Can be omitted for auto-guessing the column containing microorganism codes when used inside `dplyr` verbs, such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()], please see *Examples*.
|
||||
#' @param property one of the column names of the [microorganisms] data set: `r paste0('"``', colnames(microorganisms), '\``"', collapse = ", ")`, or must be `"shortname"`
|
||||
#' @param language language of the returned text, defaults to system language (see [get_locale()]) and can be overwritten by setting the option `AMR_locale`, e.g. `options(AMR_locale = "de")`, see [translate]. Also used to translate text like "no growth". Use `language = NULL` or `language = ""` to prevent translation.
|
||||
#' @param ... other arguments passed on to [as.mo()], such as 'allow_uncertain' and 'ignore_pattern'
|
||||
#' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
|
||||
#' @param open browse the URL using [utils::browseURL()]
|
||||
#' @param open browse the URL using [`browseURL()`][utils::browseURL()]
|
||||
#' @details All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for [mo_ref()], [mo_authors()] and [mo_year()]. Please refer to this example, knowing that *Escherichia blattae* was renamed to *Shimwellia blattae* in 2010:
|
||||
#' - `mo_name("Escherichia blattae")` will return `"Shimwellia blattae"` (with a message about the renaming)
|
||||
#' - `mo_ref("Escherichia blattae")` will return `"Burgess et al., 1973"` (with a message about the renaming)
|
||||
@@ -161,9 +161,13 @@
|
||||
#' mo_info("E. coli")
|
||||
#' }
|
||||
mo_name <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_AMR(mo_validate(x = x, property = "fullname", language = language, ...), language = language, only_unknown = FALSE)
|
||||
}
|
||||
|
||||
@@ -174,22 +178,26 @@ mo_fullname <- mo_name
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_shortname <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
x.mo <- as.mo(x, language = language, ...)
|
||||
|
||||
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
|
||||
replace_empty <- function(x) {
|
||||
x[x == ""] <- "spp."
|
||||
x
|
||||
}
|
||||
|
||||
|
||||
# get first char of genus and complete species in English
|
||||
genera <- mo_genus(x.mo, language = NULL)
|
||||
shortnames <- paste0(substr(genera, 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL)))
|
||||
|
||||
|
||||
# exceptions for where no species is known
|
||||
shortnames[shortnames %like% ".[.] spp[.]"] <- genera[shortnames %like% ".[.] spp[.]"]
|
||||
# exceptions for staphylococci
|
||||
@@ -199,7 +207,8 @@ mo_shortname <- function(x, language = get_locale(), ...) {
|
||||
shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"]), "S")
|
||||
# unknown species etc.
|
||||
shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"])), ")")
|
||||
|
||||
|
||||
shortnames[is.na(x.mo)] <- NA_character_
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
translate_AMR(shortnames, language = language, only_unknown = FALSE)
|
||||
}
|
||||
@@ -207,72 +216,104 @@ mo_shortname <- function(x, language = get_locale(), ...) {
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_subspecies <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_AMR(mo_validate(x = x, property = "subspecies", language = language, ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_species <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_AMR(mo_validate(x = x, property = "species", language = language, ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_genus <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_AMR(mo_validate(x = x, property = "genus", language = language, ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_family <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_AMR(mo_validate(x = x, property = "family", language = language, ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_order <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_AMR(mo_validate(x = x, property = "order", language = language, ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_class <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_AMR(mo_validate(x = x, property = "class", language = language, ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_phylum <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_AMR(mo_validate(x = x, property = "phylum", language = language, ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_kingdom <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
@@ -283,21 +324,29 @@ mo_domain <- mo_kingdom
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_type <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_AMR(mo_validate(x = x, property = "kingdom", language = language, ...), language = language, only_unknown = FALSE)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_gramstain <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
x.mo <- as.mo(x, language = language, ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
|
||||
x.phylum <- mo_phylum(x.mo)
|
||||
# DETERMINE GRAM STAIN FOR BACTERIA
|
||||
# Source: https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097
|
||||
@@ -318,7 +367,7 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
|
||||
"Firmicutes",
|
||||
"Tenericutes")
|
||||
| x.mo == "B_GRAMP"] <- "Gram-positive"
|
||||
|
||||
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
translate_AMR(x, language = language, only_unknown = FALSE)
|
||||
}
|
||||
@@ -327,12 +376,12 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
|
||||
#' @export
|
||||
mo_is_gram_negative <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_gram_negative())
|
||||
x <- find_mo_col("mo_is_gram_negative")
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
x.mo <- as.mo(x, language = language, ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
grams <- mo_gramstain(x.mo, language = NULL)
|
||||
@@ -346,12 +395,12 @@ mo_is_gram_negative <- function(x, language = get_locale(), ...) {
|
||||
#' @export
|
||||
mo_is_gram_positive <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_gram_positive())
|
||||
x <- find_mo_col("mo_is_gram_positive")
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
x.mo <- as.mo(x, language = language, ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
grams <- mo_gramstain(x.mo, language = NULL)
|
||||
@@ -399,27 +448,39 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_snomed <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
mo_validate(x = x, property = "snomed", language = language, ...)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_ref <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
mo_validate(x = x, property = "ref", language = language, ...)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_authors <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
x <- mo_validate(x = x, property = "ref", language = language, ...)
|
||||
# remove last 4 digits and presumably the comma and space that preceed them
|
||||
x[!is.na(x)] <- gsub(",? ?[0-9]{4}", "", x[!is.na(x)])
|
||||
@@ -429,9 +490,13 @@ mo_authors <- function(x, language = get_locale(), ...) {
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_year <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
x <- mo_validate(x = x, property = "ref", language = language, ...)
|
||||
# get last 4 digits
|
||||
x[!is.na(x)] <- gsub(".*([0-9]{4})$", "\\1", x[!is.na(x)])
|
||||
@@ -441,21 +506,29 @@ mo_year <- function(x, language = get_locale(), ...) {
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_rank <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
mo_validate(x = x, property = "rank", language = language, ...)
|
||||
}
|
||||
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_taxonomy <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
x <- as.mo(x, language = language, ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
|
||||
result <- list(kingdom = mo_kingdom(x, language = language),
|
||||
phylum = mo_phylum(x, language = language),
|
||||
class = mo_class(x, language = language),
|
||||
@@ -464,7 +537,7 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
|
||||
genus = mo_genus(x, language = language),
|
||||
species = mo_species(x, language = language),
|
||||
subspecies = mo_subspecies(x, language = language))
|
||||
|
||||
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
result
|
||||
}
|
||||
@@ -472,12 +545,16 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_synonyms <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
x <- as.mo(x, language = language, ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
|
||||
IDs <- mo_name(x = x, language = NULL)
|
||||
syns <- lapply(IDs, function(newname) {
|
||||
res <- sort(microorganisms.old[which(microorganisms.old$fullname_new == newname), "fullname"])
|
||||
@@ -493,7 +570,7 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
|
||||
} else {
|
||||
result <- unlist(syns)
|
||||
}
|
||||
|
||||
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
result
|
||||
}
|
||||
@@ -501,12 +578,16 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_info <- function(x, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
x <- as.mo(x, language = language, ...)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
|
||||
info <- lapply(x, function(y)
|
||||
c(mo_taxonomy(y, language = language),
|
||||
list(synonyms = mo_synonyms(y),
|
||||
@@ -519,7 +600,7 @@ mo_info <- function(x, language = get_locale(), ...) {
|
||||
} else {
|
||||
result <- info[[1L]]
|
||||
}
|
||||
|
||||
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
result
|
||||
}
|
||||
@@ -527,14 +608,18 @@ mo_info <- function(x, language = get_locale(), ...) {
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(open, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
mo <- as.mo(x = x, language = language, ... = ...)
|
||||
mo_names <- mo_name(mo)
|
||||
metadata <- get_mo_failures_uncertainties_renamed()
|
||||
|
||||
|
||||
df <- data.frame(mo, stringsAsFactors = FALSE) %pm>%
|
||||
pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
|
||||
df$url <- ifelse(df$source == "CoL",
|
||||
@@ -544,14 +629,14 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
|
||||
NA_character_))
|
||||
u <- df$url
|
||||
names(u) <- mo_names
|
||||
|
||||
|
||||
if (open == TRUE) {
|
||||
if (length(u) > 1) {
|
||||
warning_("Only the first URL will be opened, as `browseURL()` only suports one string.")
|
||||
}
|
||||
utils::browseURL(u[1L])
|
||||
}
|
||||
|
||||
|
||||
load_mo_failures_uncertainties_renamed(metadata)
|
||||
u
|
||||
}
|
||||
@@ -560,21 +645,25 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
|
||||
#' @rdname mo_property
|
||||
#' @export
|
||||
mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
|
||||
if (missing(x)) {
|
||||
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
|
||||
x <- find_mo_col("mo_is_intrinsic_resistant")
|
||||
}
|
||||
meet_criteria(x, allow_NA = TRUE)
|
||||
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))
|
||||
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
|
||||
translate_AMR(mo_validate(x = x, property = property, language = language, ...), language = language, only_unknown = TRUE)
|
||||
}
|
||||
|
||||
mo_validate <- function(x, property, language, ...) {
|
||||
check_dataset_integrity()
|
||||
|
||||
|
||||
if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & length(list(...)) == 0, error = function(e) FALSE)) {
|
||||
# special case for mo_* functions where class is already <mo>
|
||||
return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE])
|
||||
}
|
||||
|
||||
|
||||
dots <- list(...)
|
||||
Becker <- dots$Becker
|
||||
if (is.null(Becker)) {
|
||||
@@ -584,12 +673,12 @@ mo_validate <- function(x, property, language, ...) {
|
||||
if (is.null(Lancefield)) {
|
||||
Lancefield <- FALSE
|
||||
}
|
||||
|
||||
|
||||
# try to catch an error when inputting an invalid argument
|
||||
# so the 'call.' can be set to FALSE
|
||||
tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
|
||||
error = function(e) stop(e$message, call. = FALSE))
|
||||
|
||||
|
||||
if (is.mo(x)
|
||||
& !Becker %in% c(TRUE, "all")
|
||||
& !Lancefield %in% c(TRUE, "all")) {
|
||||
@@ -601,7 +690,7 @@ mo_validate <- function(x, property, language, ...) {
|
||||
| Lancefield %in% c(TRUE, "all")) {
|
||||
x <- exec_as.mo(x, property = property, language = language, ...)
|
||||
}
|
||||
|
||||
|
||||
if (property == "mo") {
|
||||
return(set_clean_class(x, new_class = c("mo", "character")))
|
||||
} else if (property == "snomed") {
|
||||
@@ -614,13 +703,16 @@ mo_validate <- function(x, property, language, ...) {
|
||||
find_mo_col <- function(fn) {
|
||||
# this function tries to find an mo column using dplyr::cur_data_all() for mo_is_*() functions,
|
||||
# which is useful when functions are used within dplyr verbs
|
||||
df <- get_current_data("x", call = -3) # will return an error if not found
|
||||
df <- get_current_data(arg_name = "x", call = -3) # will return an error if not found
|
||||
mo <- NULL
|
||||
try({
|
||||
mo <- suppressMessages(search_type_in_df(df, "mo"))
|
||||
}, silent = TRUE)
|
||||
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
|
||||
message_("Using column '", font_bold(mo), "' as input for ", fn, "()")
|
||||
if (message_not_thrown_before(fn = fn)) {
|
||||
message_("Using column '", font_bold(mo), "' as input for ", fn, "()")
|
||||
remember_thrown_message(fn = fn)
|
||||
}
|
||||
return(df[, mo, drop = TRUE])
|
||||
} else {
|
||||
stop_("argument `x` is missing and no column with info about microorganisms could be found.", call = -2)
|
||||
|
||||
@@ -25,9 +25,9 @@
|
||||
|
||||
#' User-defined reference data set for microorganisms
|
||||
#'
|
||||
#' @description These functions can be used to predefine your own reference to be used in [as.mo()] and consequently all `mo_*` functions like [mo_genus()] and [mo_gramstain()].
|
||||
#' @description These functions can be used to predefine your own reference to be used in [as.mo()] and consequently all [`mo_*`][mo_property()] functions (such as [mo_genus()] and [mo_gramstain()]).
|
||||
#'
|
||||
#' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package.
|
||||
#' This is **the fastest way** to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.
|
||||
#' @inheritSection lifecycle Stable lifecycle
|
||||
#' @param path location of your reference file, see Details. Can be `""`, `NULL` or `FALSE` to delete the reference file.
|
||||
#' @param destination destination of the compressed data file, default to the user's home directory.
|
||||
@@ -103,7 +103,7 @@
|
||||
#' ```
|
||||
#' as.mo("lab_mo_ecoli")
|
||||
#' #> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
|
||||
#' #> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
|
||||
#' #> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
|
||||
#' #> "Organisation XYZ" and "mo"
|
||||
#' #> Class <mo>
|
||||
#' #> [1] B_ESCHR_COLI
|
||||
@@ -119,7 +119,7 @@
|
||||
#' #> Removed mo_source file '/Users/me/mo_source.rds'
|
||||
#' ```
|
||||
#'
|
||||
#' If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of [as.mo()].
|
||||
#' If the original file (in the previous case an Excel file) is moved or deleted, the `mo_source.rds` file will be removed upon the next use of [as.mo()] or any [`mo_*`][mo_property()] function.
|
||||
#' @export
|
||||
#' @inheritSection AMR Read more on our website!
|
||||
set_mo_source <- function(path, destination = getOption("AMR_mo_source", "~/mo_source.rds")) {
|
||||
|
||||
15
R/rsi.R
15
R/rsi.R
@@ -709,7 +709,10 @@ exec_as.rsi <- function(method,
|
||||
|
||||
guideline_coerced <- get_guideline(guideline, reference_data)
|
||||
if (guideline_coerced != guideline) {
|
||||
message_("Using guideline ", font_bold(guideline_coerced), " as input for `guideline`.")
|
||||
if (message_not_thrown_before("as.rsi")) {
|
||||
message_("Using guideline ", font_bold(guideline_coerced), " as input for `guideline`.")
|
||||
remember_thrown_message("as.rsi")
|
||||
}
|
||||
}
|
||||
|
||||
new_rsi <- rep(NA_character_, length(x))
|
||||
@@ -745,7 +748,10 @@ exec_as.rsi <- function(method,
|
||||
|
||||
if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) {
|
||||
if (!guideline_coerced %like% "EUCAST") {
|
||||
warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call = FALSE)
|
||||
if (message_not_thrown_before("as.rsi2")) {
|
||||
warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call = FALSE)
|
||||
remember_thrown_message("as.rsi2")
|
||||
}
|
||||
} else {
|
||||
new_rsi[i] <- "R"
|
||||
next
|
||||
@@ -811,7 +817,10 @@ exec_as.rsi <- function(method,
|
||||
if (any_is_intrinsic_resistant & guideline_coerced %like% "EUCAST" & !isTRUE(add_intrinsic_resistance)) {
|
||||
# found some intrinsic resistance, but was not applied
|
||||
message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
|
||||
warning_("Found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.", call = FALSE)
|
||||
if (message_not_thrown_before("as.rsi3")) {
|
||||
warning_("Found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.", call = FALSE)
|
||||
remember_thrown_message("as.rsi3")
|
||||
}
|
||||
warned <- TRUE
|
||||
}
|
||||
|
||||
|
||||
@@ -147,8 +147,11 @@ rsi_calc <- function(...,
|
||||
}
|
||||
|
||||
if (print_warning == TRUE) {
|
||||
warning_("Increase speed by transforming to class <rsi> on beforehand: your_data %pm>% mutate_if(is.rsi.eligible, as.rsi)",
|
||||
call = FALSE)
|
||||
if (message_not_thrown_before("rsi_calc")) {
|
||||
warning_("Increase speed by transforming to class <rsi> on beforehand: your_data %pm>% mutate_if(is.rsi.eligible, as.rsi)",
|
||||
call = FALSE)
|
||||
remember_thrown_message("rsi_calc")
|
||||
}
|
||||
}
|
||||
|
||||
if (only_count == TRUE) {
|
||||
|
||||
7
R/zzz.R
7
R/zzz.R
@@ -75,6 +75,13 @@
|
||||
s3_register("skimr::get_skimmers", "rsi")
|
||||
s3_register("skimr::get_skimmers", "mic")
|
||||
s3_register("skimr::get_skimmers", "disk")
|
||||
|
||||
# if mo source exists, fire it up (see mo_source())
|
||||
try({
|
||||
if (file.exists(getOption("AMR_mo_source", "~/mo_source.rds"))) {
|
||||
invisible(get_mo_source())
|
||||
}
|
||||
}, silent = TRUE)
|
||||
}
|
||||
|
||||
.onAttach <- function(...) {
|
||||
|
||||
@@ -213,7 +213,8 @@ authors:
|
||||
|
||||
template:
|
||||
# this requires the 'preferably' package, https://github.com/amirmasoudabdol/preferably/
|
||||
package: preferably
|
||||
# package: preferably
|
||||
assets: "pkgdown/logos" # use logos in this folder
|
||||
params:
|
||||
noindex: false
|
||||
template: "flatly"
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
# -------------------------------------------------------------------------------------------------------------------------------
|
||||
# For editing this EUCAST reference file, these values can all be used for targeting antibiotics:
|
||||
# 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_1st', 'cephalosporins_2nd', 'cephalosporins_except_CAZ',
|
||||
# 'all_betalactams', 'aminoglycosides', 'aminopenicillins', 'carbapenems', 'cephalosporins', 'cephalosporins_1st', 'cephalosporins_2nd', 'cephalosporins_3rd', 'cephalosporins_except_CAZ',
|
||||
# 'fluoroquinolones', 'glycopeptides', 'lincosamides', 'lipoglycopeptides', 'macrolides', 'oxazolidinones', 'polymyxins', 'streptogramins', 'tetracyclines', 'ureidopenicillins',
|
||||
# and all separate EARS-Net letter codes like 'AMC'. They can be separated by comma: 'AMC, fluoroquinolones'.
|
||||
# The 'if_mo_property' column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
|
||||
|
||||
|
Can't render this file because it contains an unexpected character in line 6 and column 96.
|
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Page not found (404) • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="https://msberends.github.io/AMR//preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="https://msberends.github.io/AMR//code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="https://msberends.github.io/AMR//code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="https://msberends.github.io/AMR//bootstrap-toc.css">
|
||||
<script src="https://msberends.github.io/AMR//bootstrap-toc.js"></script>
|
||||
@@ -85,9 +58,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -111,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -235,7 +205,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -286,7 +255,7 @@ Content not found. Please use links in the navbar.
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>License • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="bootstrap-toc.css">
|
||||
<script src="bootstrap-toc.js"></script>
|
||||
@@ -85,9 +58,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -111,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -235,7 +205,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -534,7 +503,7 @@ END OF TERMS AND CONDITIONS
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
Binary file not shown.
|
Before Width: | Height: | Size: 38 KiB After Width: | Height: | Size: 38 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 26 KiB After Width: | Height: | Size: 26 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 68 KiB After Width: | Height: | Size: 68 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 45 KiB After Width: | Height: | Size: 45 KiB |
@@ -5,32 +5,15 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. --><meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script><title>How to apply EUCAST rules • AMR (for R)</title>
|
||||
<title>How to apply EUCAST rules • AMR (for R)</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- Flatly Theme - Light --><link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<!-- Darkly Theme - Dark --><link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- preferably CSS --><link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -56,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -419,7 +402,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -5,32 +5,15 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. --><meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script><title>How to determine multi-drug resistance (MDR) • AMR (for R)</title>
|
||||
<title>How to determine multi-drug resistance (MDR) • AMR (for R)</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- Flatly Theme - Light --><link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<!-- Darkly Theme - Dark --><link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- preferably CSS --><link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -56,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -268,7 +251,7 @@
|
||||
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span>
|
||||
<span class="co"># Warning in warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ", : NA introduced for isolates where the available percentage of antimicrobial</span>
|
||||
<span class="co"># Warning: NA introduced for isolates where the available percentage of antimicrobial</span>
|
||||
<span class="co"># classes was below 50% (set with `pct_required_classes`)</span></code></pre></div>
|
||||
<p><strong>Frequency table</strong></p>
|
||||
<p>Class: factor > ordered (numeric)<br>
|
||||
@@ -306,48 +289,41 @@ Unique: 2</p>
|
||||
</table>
|
||||
<p>For another example, I will create a data set to determine multi-drug resistant TB:</p>
|
||||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="co"># a helper function to get a random vector with values S, I and R</span>
|
||||
<span class="co"># with the probabilities 50% - 10% - 40%</span>
|
||||
<span class="va">sample_rsi</span> <span class="op"><-</span> <span class="kw">function</span><span class="op">(</span><span class="op">)</span> <span class="op">{</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/base/sample.html">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"I"</span>, <span class="st">"R"</span><span class="op">)</span>,
|
||||
size <span class="op">=</span> <span class="fl">5000</span>,
|
||||
prob <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0.5</span>, <span class="fl">0.1</span>, <span class="fl">0.4</span><span class="op">)</span>,
|
||||
replace <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>
|
||||
<span class="op">}</span>
|
||||
|
||||
<span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
isoniazid <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
gatifloxacin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
ethambutol <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
pyrazinamide <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
moxifloxacin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
kanamycin <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<code class="sourceCode R"><span class="co"># random_rsi() is a helper function to generate</span>
|
||||
<span class="co"># a random vector with values S, I and R</span>
|
||||
<span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>rifampicin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
|
||||
isoniazid <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
|
||||
gatifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
|
||||
ethambutol <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
|
||||
pyrazinamide <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
|
||||
moxifloxacin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
|
||||
kanamycin <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<p>Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:</p>
|
||||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
INH <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
GAT <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
ETH <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
PZA <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
MFX <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span>,
|
||||
KAN <span class="op">=</span> <span class="fu">sample_rsi</span><span class="op">(</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<code class="sourceCode R"><span class="va">my_TB_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span>RIF <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
|
||||
INH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
|
||||
GAT <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
|
||||
ETH <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
|
||||
PZA <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
|
||||
MFX <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span>,
|
||||
KAN <span class="op">=</span> <span class="fu"><a href="../reference/random.html">random_rsi</a></span><span class="op">(</span><span class="fl">5000</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<p>The data set now looks like this:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span>
|
||||
<span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span>
|
||||
<span class="co"># 1 S R S R R S</span>
|
||||
<span class="co"># 2 S R S S S S</span>
|
||||
<span class="co"># 3 S S S S R S</span>
|
||||
<span class="co"># 4 S R S R S S</span>
|
||||
<span class="co"># 5 R S R S R S</span>
|
||||
<span class="co"># 6 S R R R S S</span>
|
||||
<span class="co"># 1 S S R I R S</span>
|
||||
<span class="co"># 2 I S R I I R</span>
|
||||
<span class="co"># 3 R R R S I R</span>
|
||||
<span class="co"># 4 I I R R S S</span>
|
||||
<span class="co"># 5 I R I S S R</span>
|
||||
<span class="co"># 6 I R I I S I</span>
|
||||
<span class="co"># kanamycin</span>
|
||||
<span class="co"># 1 S</span>
|
||||
<span class="co"># 1 R</span>
|
||||
<span class="co"># 2 S</span>
|
||||
<span class="co"># 3 S</span>
|
||||
<span class="co"># 4 S</span>
|
||||
<span class="co"># 5 R</span>
|
||||
<span class="co"># 6 S</span></code></pre></div>
|
||||
<span class="co"># 3 I</span>
|
||||
<span class="co"># 4 I</span>
|
||||
<span class="co"># 5 I</span>
|
||||
<span class="co"># 6 R</span></code></pre></div>
|
||||
<p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
|
||||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></code></pre></div>
|
||||
@@ -378,40 +354,40 @@ Unique: 5</p>
|
||||
<tr class="odd">
|
||||
<td align="left">1</td>
|
||||
<td align="left">Mono-resistant</td>
|
||||
<td align="right">3314</td>
|
||||
<td align="right">66.28%</td>
|
||||
<td align="right">3314</td>
|
||||
<td align="right">66.28%</td>
|
||||
<td align="right">3214</td>
|
||||
<td align="right">64.28%</td>
|
||||
<td align="right">3214</td>
|
||||
<td align="right">64.28%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">2</td>
|
||||
<td align="left">Negative</td>
|
||||
<td align="right">637</td>
|
||||
<td align="right">12.74%</td>
|
||||
<td align="right">3951</td>
|
||||
<td align="right">79.02%</td>
|
||||
<td align="right">997</td>
|
||||
<td align="right">19.94%</td>
|
||||
<td align="right">4211</td>
|
||||
<td align="right">84.22%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">3</td>
|
||||
<td align="left">Multi-drug-resistant</td>
|
||||
<td align="right">565</td>
|
||||
<td align="right">11.30%</td>
|
||||
<td align="right">4516</td>
|
||||
<td align="right">90.32%</td>
|
||||
<td align="right">442</td>
|
||||
<td align="right">8.84%</td>
|
||||
<td align="right">4653</td>
|
||||
<td align="right">93.06%</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td align="left">4</td>
|
||||
<td align="left">Poly-resistant</td>
|
||||
<td align="right">298</td>
|
||||
<td align="right">5.96%</td>
|
||||
<td align="right">4814</td>
|
||||
<td align="right">96.28%</td>
|
||||
<td align="right">239</td>
|
||||
<td align="right">4.78%</td>
|
||||
<td align="right">4892</td>
|
||||
<td align="right">97.84%</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td align="left">5</td>
|
||||
<td align="left">Extensively drug-resistant</td>
|
||||
<td align="right">186</td>
|
||||
<td align="right">3.72%</td>
|
||||
<td align="right">108</td>
|
||||
<td align="right">2.16%</td>
|
||||
<td align="right">5000</td>
|
||||
<td align="right">100.00%</td>
|
||||
</tr>
|
||||
@@ -433,7 +409,7 @@ Unique: 5</p>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -5,32 +5,15 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. --><meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script><title>How to conduct principal component analysis (PCA) for AMR • AMR (for R)</title>
|
||||
<title>How to conduct principal component analysis (PCA) for AMR • AMR (for R)</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- Flatly Theme - Light --><link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<!-- Darkly Theme - Dark --><link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- preferably CSS --><link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -56,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -353,7 +336,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -5,32 +5,15 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. --><meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script><title>How to import data from SPSS / SAS / Stata • AMR (for R)</title>
|
||||
<title>How to import data from SPSS / SAS / Stata • AMR (for R)</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- Flatly Theme - Light --><link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<!-- Darkly Theme - Dark --><link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- preferably CSS --><link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -56,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -210,7 +193,7 @@
|
||||
<h1 data-toc-skip>How to import data from SPSS / SAS / Stata</h1>
|
||||
<h4 class="author">Matthijs S. Berends</h4>
|
||||
|
||||
<h4 class="date">21 December 2020</h4>
|
||||
<h4 class="date">24 December 2020</h4>
|
||||
|
||||
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/SPSS.Rmd"><code>vignettes/SPSS.Rmd</code></a></small>
|
||||
<div class="hidden name"><code>SPSS.Rmd</code></div>
|
||||
@@ -431,7 +414,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -5,32 +5,15 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. --><meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script><title>How to work with WHONET data • AMR (for R)</title>
|
||||
<title>How to work with WHONET data • AMR (for R)</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- Flatly Theme - Light --><link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<!-- Darkly Theme - Dark --><link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- preferably CSS --><link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -56,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -430,7 +413,7 @@ Drug group: Beta-lactams/penicillins<br>
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -5,32 +5,15 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. --><meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script><title>Benchmarks • AMR (for R)</title>
|
||||
<title>Benchmarks • AMR (for R)</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- Flatly Theme - Light --><link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<!-- Darkly Theme - Dark --><link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- preferably CSS --><link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -56,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -244,20 +227,20 @@
|
||||
times <span class="op">=</span> <span class="fl">10</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">S.aureus</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">2</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max</span>
|
||||
<span class="co"># as.mo("sau") 10.0 11.0 20.0 13.0 38.0 41.0</span>
|
||||
<span class="co"># as.mo("stau") 100.0 110.0 120.0 110.0 140.0 140.0</span>
|
||||
<span class="co"># as.mo("STAU") 100.0 110.0 130.0 140.0 140.0 160.0</span>
|
||||
<span class="co"># as.mo("staaur") 10.0 12.0 23.0 14.0 38.0 58.0</span>
|
||||
<span class="co"># as.mo("STAAUR") 10.0 11.0 18.0 13.0 14.0 42.0</span>
|
||||
<span class="co"># as.mo("S. aureus") 26.0 30.0 46.0 44.0 58.0 78.0</span>
|
||||
<span class="co"># as.mo("S aureus") 26.0 27.0 32.0 31.0 31.0 56.0</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 2.0 2.4 2.6 2.7 2.8 3.1</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 890.0 910.0 920.0 920.0 930.0 960.0</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 380.0 390.0 400.0 390.0 400.0 430.0</span>
|
||||
<span class="co"># as.mo("MRSA") 9.9 11.0 16.0 14.0 14.0 41.0</span>
|
||||
<span class="co"># as.mo("VISA") 17.0 19.0 28.0 21.0 45.0 52.0</span>
|
||||
<span class="co"># as.mo("VRSA") 17.0 19.0 26.0 21.0 22.0 53.0</span>
|
||||
<span class="co"># expr min lq mean median uq max</span>
|
||||
<span class="co"># as.mo("sau") 9.9 12.0 15.0 13.0 13.0 42.0</span>
|
||||
<span class="co"># as.mo("stau") 100.0 100.0 130.0 120.0 140.0 190.0</span>
|
||||
<span class="co"># as.mo("STAU") 110.0 110.0 130.0 130.0 140.0 150.0</span>
|
||||
<span class="co"># as.mo("staaur") 9.8 12.0 26.0 13.0 41.0 60.0</span>
|
||||
<span class="co"># as.mo("STAAUR") 11.0 11.0 15.0 13.0 13.0 41.0</span>
|
||||
<span class="co"># as.mo("S. aureus") 26.0 28.0 50.0 58.0 63.0 75.0</span>
|
||||
<span class="co"># as.mo("S aureus") 26.0 27.0 46.0 51.0 60.0 67.0</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus") 1.9 2.2 2.5 2.5 2.8 3.1</span>
|
||||
<span class="co"># as.mo("Staphylococcus aureus (MRSA)") 870.0 880.0 1100.0 910.0 1000.0 2400.0</span>
|
||||
<span class="co"># as.mo("Sthafilokkockus aaureuz") 360.0 370.0 400.0 380.0 420.0 540.0</span>
|
||||
<span class="co"># as.mo("MRSA") 9.7 11.0 17.0 12.0 13.0 66.0</span>
|
||||
<span class="co"># as.mo("VISA") 19.0 19.0 36.0 35.0 53.0 56.0</span>
|
||||
<span class="co"># as.mo("VRSA") 17.0 20.0 20.0 21.0 21.0 23.0</span>
|
||||
<span class="co"># neval</span>
|
||||
<span class="co"># 10</span>
|
||||
<span class="co"># 10</span>
|
||||
@@ -301,8 +284,8 @@
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># mo_name(x) 128 167 205 195 232 298 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.195 seconds. You only lose time on your unique input values.</p>
|
||||
<span class="co"># mo_name(x) 134 167 201 179 207 310 10</span></code></pre></div>
|
||||
<p>So getting official taxonomic names of 2,000,000 (!!) items consisting of 90 unique values only takes 0.179 seconds. You only lose time on your unique input values.</p>
|
||||
</div>
|
||||
<div id="precalculated-results" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
@@ -316,10 +299,10 @@
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 7.35 7.70 8.15 8.11 8.68 8.96 10</span>
|
||||
<span class="co"># B 22.50 22.80 28.10 24.30 25.70 62.60 10</span>
|
||||
<span class="co"># C 1.84 1.98 2.13 2.13 2.17 2.43 10</span></code></pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0021 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<span class="co"># A 7.59 7.93 8.24 8.09 8.66 9.06 10</span>
|
||||
<span class="co"># B 23.60 23.70 29.20 24.30 27.10 66.10 10</span>
|
||||
<span class="co"># C 1.84 2.13 2.22 2.19 2.35 2.62 10</span></code></pre></div>
|
||||
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0022 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
|
||||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R"><span class="va">run_it</span> <span class="op"><-</span> <span class="fu">microbenchmark</span><span class="op">(</span>A <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"aureus"</span><span class="op">)</span>,
|
||||
B <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"Staphylococcus"</span><span class="op">)</span>,
|
||||
@@ -333,14 +316,14 @@
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># A 1.60 1.63 1.74 1.70 1.83 2.02 10</span>
|
||||
<span class="co"># B 1.37 1.40 1.62 1.54 1.74 2.07 10</span>
|
||||
<span class="co"># C 1.39 1.45 1.63 1.65 1.77 1.86 10</span>
|
||||
<span class="co"># D 1.37 1.40 1.58 1.51 1.62 2.27 10</span>
|
||||
<span class="co"># E 1.44 1.64 1.70 1.66 1.81 2.13 10</span>
|
||||
<span class="co"># F 1.38 1.42 1.57 1.58 1.67 1.81 10</span>
|
||||
<span class="co"># G 1.38 1.62 1.64 1.63 1.70 1.82 10</span>
|
||||
<span class="co"># H 1.44 1.65 1.84 1.82 1.99 2.60 10</span></code></pre></div>
|
||||
<span class="co"># A 1.69 1.77 1.82 1.83 1.86 1.92 10</span>
|
||||
<span class="co"># B 1.78 1.79 1.89 1.91 1.95 2.06 10</span>
|
||||
<span class="co"># C 1.74 1.79 1.88 1.87 1.94 2.06 10</span>
|
||||
<span class="co"># D 1.75 1.77 1.94 1.95 1.99 2.41 10</span>
|
||||
<span class="co"># E 1.70 1.75 1.84 1.81 1.87 2.08 10</span>
|
||||
<span class="co"># F 1.66 1.70 1.76 1.74 1.80 1.89 10</span>
|
||||
<span class="co"># G 1.68 1.70 1.82 1.75 1.93 2.09 10</span>
|
||||
<span class="co"># H 1.66 1.69 1.75 1.74 1.80 1.92 10</span></code></pre></div>
|
||||
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> anyway, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
|
||||
</div>
|
||||
<div id="results-in-other-languages" class="section level3">
|
||||
@@ -367,14 +350,14 @@
|
||||
times <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://docs.ropensci.org/skimr/reference/print.html">print</a></span><span class="op">(</span><span class="va">run_it</span>, unit <span class="op">=</span> <span class="st">"ms"</span>, signif <span class="op">=</span> <span class="fl">4</span><span class="op">)</span>
|
||||
<span class="co"># Unit: milliseconds</span>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># en 15.77 16.36 18.40 16.85 17.50 53.58 100</span>
|
||||
<span class="co"># de 19.03 19.70 24.60 20.14 21.06 59.83 100</span>
|
||||
<span class="co"># nl 30.93 32.03 36.58 32.80 33.78 85.59 100</span>
|
||||
<span class="co"># es 18.78 19.62 24.49 19.98 20.60 58.73 100</span>
|
||||
<span class="co"># it 18.80 19.50 22.68 19.92 20.89 63.99 100</span>
|
||||
<span class="co"># fr 18.78 19.59 21.99 19.90 20.75 58.87 100</span>
|
||||
<span class="co"># pt 18.79 19.65 23.04 20.08 20.82 59.30 100</span></code></pre></div>
|
||||
<span class="co"># expr min lq mean median uq max neval</span>
|
||||
<span class="co"># en 15.91 16.98 21.87 17.54 18.34 168.50 100</span>
|
||||
<span class="co"># de 18.98 20.14 26.30 20.74 22.64 66.68 100</span>
|
||||
<span class="co"># nl 31.02 32.71 37.56 33.84 35.81 82.77 100</span>
|
||||
<span class="co"># es 19.13 20.06 22.96 20.54 21.42 65.26 100</span>
|
||||
<span class="co"># it 18.90 19.84 24.26 20.59 22.80 60.30 100</span>
|
||||
<span class="co"># fr 18.89 19.92 23.46 20.49 21.72 62.85 100</span>
|
||||
<span class="co"># pt 18.90 19.99 23.80 20.70 22.17 61.42 100</span></code></pre></div>
|
||||
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
|
||||
</div>
|
||||
</div>
|
||||
@@ -392,7 +375,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 69 KiB After Width: | Height: | Size: 68 KiB |
@@ -5,32 +5,15 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. --><meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script><title>Data sets for download / own use • AMR (for R)</title>
|
||||
<title>Data sets for download / own use • AMR (for R)</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- Flatly Theme - Light --><link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<!-- Darkly Theme - Dark --><link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- preferably CSS --><link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -56,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -1163,7 +1146,7 @@ If you are reading this page from within R, please <a href="https://msberends.gi
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Articles • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -85,9 +58,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -111,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -235,7 +205,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -303,7 +272,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -5,32 +5,15 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. --><meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script><title>How to predict antimicrobial resistance • AMR (for R)</title>
|
||||
<title>How to predict antimicrobial resistance • AMR (for R)</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- Flatly Theme - Light --><link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<!-- Darkly Theme - Dark --><link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- preferably CSS --><link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -56,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -305,8 +288,7 @@
|
||||
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># NOTE: Using column 'date' as input for `col_date`.</span></code></pre></div>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
|
||||
<p>Vancomycin resistance could be 100% in ten years, but might also stay around 0%.</p>
|
||||
<p>You can define the model with the <code>model</code> parameter. The model chosen above is a generalised linear regression model using a binomial distribution, assuming that a period of zero resistance was followed by a period of increasing resistance leading slowly to more and more resistance.</p>
|
||||
@@ -351,8 +333,7 @@
|
||||
<code class="sourceCode R"><span class="va">example_isolates</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># NOTE: Using column 'date' as input for `col_date`.</span></code></pre></div>
|
||||
<span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
|
||||
<p>This seems more likely, doesn’t it?</p>
|
||||
<p>The model itself is also available from the object, as an <code>attribute</code>:</p>
|
||||
@@ -387,7 +368,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -5,32 +5,15 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. --><meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script><title>Welcome to the AMR package • AMR (for R)</title>
|
||||
<title>Welcome to the AMR package • AMR (for R)</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- Flatly Theme - Light --><link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<!-- Darkly Theme - Dark --><link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- preferably CSS --><link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
|
||||
@@ -56,7 +39,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -266,7 +249,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Citation and Authors • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="bootstrap-toc.css">
|
||||
<script src="bootstrap-toc.js"></script>
|
||||
@@ -85,9 +58,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -111,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -235,7 +205,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -356,7 +325,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -5,32 +5,15 @@
|
||||
<meta charset="utf-8">
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. --><meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script><title>Antimicrobial Resistance Analysis • AMR (for R)</title>
|
||||
<title>Antimicrobial Resistance Analysis • AMR (for R)</title>
|
||||
<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
|
||||
<link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
|
||||
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- Flatly Theme - Light --><link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<!-- Darkly Theme - Dark --><link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- preferably CSS --><link rel="stylesheet" href="preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
<!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css">
|
||||
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css">
|
||||
<script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
|
||||
<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
|
||||
@@ -60,7 +43,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -531,7 +514,7 @@ Since you are one of our users, we would like to know how you use the package an
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Changelog • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -85,9 +58,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -111,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -235,7 +205,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -267,13 +236,13 @@
|
||||
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
|
||||
</div>
|
||||
|
||||
<div id="amr-1409043" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.4.0.9043">
|
||||
<a href="#amr-1409043" class="anchor"></a>AMR 1.4.0.9043<small> Unreleased </small>
|
||||
<div id="amr-1409044" class="section level1">
|
||||
<h1 class="page-header" data-toc-text="1.4.0.9044">
|
||||
<a href="#amr-1409044" class="anchor"></a>AMR 1.4.0.9044<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-22-december-2020" class="section level2">
|
||||
<div id="last-updated-24-december-2020" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
<a href="#last-updated-22-december-2020" class="anchor"></a><small>Last updated: 22 December 2020</small>
|
||||
<a href="#last-updated-24-december-2020" class="anchor"></a><small>Last updated: 24 December 2020</small>
|
||||
</h2>
|
||||
<div id="new" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
@@ -333,6 +302,9 @@
|
||||
<li><p>Fix for plotting MIC values with <code><a href="../reference/plot.html">plot()</a></code></p></li>
|
||||
<li><p>Added <code><a href="../reference/plot.html">plot()</a></code> generic to class <code><disk></code></p></li>
|
||||
<li><p>LA-MRSA and CA-MRSA are now recognised as an abbreviation for <em>Staphylococcus aureus</em>, meaning that e.g. <code><a href="../reference/mo_property.html">mo_genus("LA-MRSA")</a></code> will return <code>"Staphylococcus"</code> and <code><a href="../reference/mo_property.html">mo_is_gram_positive("LA-MRSA")</a></code> will return <code>TRUE</code>.</p></li>
|
||||
<li><p>Fix for printing class <mo> in tibbles when all values are <code>NA</code></mo></p></li>
|
||||
<li><p>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> when the input contains <code>NA</code></p></li>
|
||||
<li><p>If <code><a href="../reference/as.mo.html">as.mo()</a></code> takes more than 30 seconds, some suggestions will be done to improve speed</p></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other" class="section level3">
|
||||
@@ -343,7 +315,6 @@
|
||||
<li>More extensive unit tests</li>
|
||||
<li>Internal calls to <code><a href="https://rdrr.io/r/base/options.html">options()</a></code> were all removed in favour of a new internal environment <code>mo_env</code>
|
||||
</li>
|
||||
<li>Our website now also has a dark theme, that switches on automatically based on system settings (such as Night Mode in macOS)</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
@@ -548,7 +519,7 @@
|
||||
<p>Making this package independent of especially the tidyverse (e.g. packages <code>dplyr</code> and <code>tidyr</code>) tremendously increases sustainability on the long term, since tidyverse functions change quite often. Good for users, but hard for package maintainers. Most of our functions are replaced with versions that only rely on base R, which keeps this package fully functional for many years to come, without requiring a lot of maintenance to keep up with other packages anymore. Another upside it that this package can now be used with all versions of R since R-3.0.0 (April 2013). Our package is being used in settings where the resources are very limited. Fewer dependencies on newer software is helpful for such settings.</p>
|
||||
<p>Negative effects of this change are:</p>
|
||||
<ul>
|
||||
<li>Function <code>freq()</code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code>freq()</code>.</li>
|
||||
<li>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> that was borrowed from the <code>cleaner</code> package was removed. Use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">cleaner::freq()</a></code>, or run <code><a href="https://github.com/msberends/cleaner">library("cleaner")</a></code> before you use <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>.</li>
|
||||
<li><del>Printing values of class <code>mo</code> or <code>rsi</code> in a tibble will no longer be in colour and printing <code>rsi</code> in a tibble will show the class <code><ord></code>, not <code><rsi></code> anymore. This is purely a visual effect.</del></li>
|
||||
<li><del>All functions from the <code>mo_*</code> family (like <code><a href="../reference/mo_property.html">mo_name()</a></code> and <code><a href="../reference/mo_property.html">mo_gramstain()</a></code>) are noticeably slower when running on hundreds of thousands of rows.</del></li>
|
||||
<li>For developers: classes <code>mo</code> and <code>ab</code> now both also inherit class <code>character</code>, to support any data transformation. This change invalidates code that checks for class length == 1.</li>
|
||||
@@ -885,7 +856,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<span class="co">#> invalid microorganism code, NA generated</span></code></pre></div>
|
||||
<p>This is important, because a value like <code>"testvalue"</code> could never be understood by e.g. <code><a href="../reference/mo_property.html">mo_name()</a></code>, although the class would suggest a valid microbial code.</p>
|
||||
</li>
|
||||
<li><p>Function <code>freq()</code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code>freq()</code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
|
||||
<li><p>Function <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> has moved to a new package, <a href="https://github.com/msberends/clean"><code>clean</code></a> (<a href="https://cran.r-project.org/package=clean">CRAN link</a>), since creating frequency tables actually does not fit the scope of this package. The <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function still works, since it is re-exported from the <code>clean</code> package (which will be installed automatically upon updating this <code>AMR</code> package).</p></li>
|
||||
<li><p>Renamed data set <code>septic_patients</code> to <code>example_isolates</code></p></li>
|
||||
</ul>
|
||||
</div>
|
||||
@@ -1154,7 +1125,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>The <code><a href="../reference/age.html">age()</a></code> function gained a new argument <code>exact</code> to determine ages with decimals</li>
|
||||
<li>Removed deprecated functions <code>guess_mo()</code>, <code>guess_atc()</code>, <code>EUCAST_rules()</code>, <code>interpretive_reading()</code>, <code><a href="../reference/as.rsi.html">rsi()</a></code>
|
||||
</li>
|
||||
<li>Frequency tables (<code>freq()</code>):
|
||||
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>):
|
||||
<ul>
|
||||
<li><p>speed improvement for microbial IDs</p></li>
|
||||
<li><p>fixed factor level names for R Markdown</p></li>
|
||||
@@ -1164,12 +1135,12 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span>
|
||||
<span class="co"># grouped boxplots:</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/r/graphics/boxplot.html">boxplot</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
@@ -1179,7 +1150,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li>Added ceftazidim intrinsic resistance to <em>Streptococci</em>
|
||||
</li>
|
||||
<li>Changed default settings for <code><a href="../reference/age_groups.html">age_groups()</a></code>, to let groups of fives and tens end with 100+ instead of 120+</li>
|
||||
<li>Fix for <code>freq()</code> for when all values are <code>NA</code>
|
||||
<li>Fix for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> for when all values are <code>NA</code>
|
||||
</li>
|
||||
<li>Fix for <code><a href="../reference/first_isolate.html">first_isolate()</a></code> for when dates are missing</li>
|
||||
<li>Improved speed of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>
|
||||
@@ -1420,7 +1391,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>Frequency tables (<code>freq()</code> function):
|
||||
<li>Frequency tables (<code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code> function):
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
|
||||
@@ -1430,15 +1401,15 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<span class="co"># OLD WAY</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span>
|
||||
<span class="co"># NEW WAY</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span>
|
||||
|
||||
<span class="co"># Even supports grouping variables:</span>
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Header info is now available as a list, with the <code>header</code> function</p></li>
|
||||
<li><p>The argument <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</p></li>
|
||||
@@ -1521,7 +1492,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>Using <code>portion_*</code> functions now throws a warning when total available isolate is below argument <code>minimum</code></p></li>
|
||||
<li><p>Functions <code>as.mo</code>, <code>as.rsi</code>, <code>as.mic</code>, <code>as.atc</code> and <code>freq</code> will not set package name as attribute anymore</p></li>
|
||||
<li>
|
||||
<p>Frequency tables - <code>freq()</code>:</p>
|
||||
<p>Frequency tables - <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq()</a></code>:</p>
|
||||
<ul>
|
||||
<li>
|
||||
<p>Support for grouping variables, test with:</p>
|
||||
@@ -1529,14 +1500,14 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
<li>
|
||||
<p>Support for (un)selecting columns:</p>
|
||||
<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">septic_patients</span> <span class="op">%>%</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">hospital_id</span><span class="op">)</span> <span class="op">%>%</span>
|
||||
<span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="op">-</span><span class="va">count</span>, <span class="op">-</span><span class="va">cum_count</span><span class="op">)</span> <span class="co"># only get item, percent, cum_percent</span></code></pre></div>
|
||||
</li>
|
||||
<li><p>Check for <code><a href="https://hms.tidyverse.org/reference/Deprecated.html">hms::is.hms</a></code></p></li>
|
||||
@@ -1554,7 +1525,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<li><p>Removed diacritics from all authors (columns <code>microorganisms$ref</code> and <code>microorganisms.old$ref</code>) to comply with CRAN policy to only allow ASCII characters</p></li>
|
||||
<li><p>Fix for <code>mo_property</code> not working properly</p></li>
|
||||
<li><p>Fix for <code>eucast_rules</code> where some Streptococci would become ceftazidime R in EUCAST rule 4.5</p></li>
|
||||
<li><p>Support for named vectors of class <code>mo</code>, useful for <code>top_freq()</code></p></li>
|
||||
<li><p>Support for named vectors of class <code>mo</code>, useful for <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">top_freq()</a></code></p></li>
|
||||
<li><p><code>ggplot_rsi</code> and <code>scale_y_percent</code> have <code>breaks</code> argument</p></li>
|
||||
<li>
|
||||
<p>AI improvements for <code>as.mo</code>:</p>
|
||||
@@ -1722,13 +1693,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">my_matrix</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/with.html">with</a></span><span class="op">(</span><span class="va">septic_patients</span>, <span class="fu"><a href="https://rdrr.io/r/base/matrix.html">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">age</span>, <span class="va">gender</span><span class="op">)</span>, ncol <span class="op">=</span> <span class="fl">2</span><span class="op">)</span><span class="op">)</span>
|
||||
<span class="fu">freq</span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
|
||||
<span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">my_matrix</span><span class="op">)</span></code></pre></div>
|
||||
<p>For lists, subsetting is possible:</p>
|
||||
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
|
||||
<code class="sourceCode R">
|
||||
<span class="va">my_list</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span><span class="op">(</span>age <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">age</span>, gender <span class="op">=</span> <span class="va">septic_patients</span><span class="op">$</span><span class="va">gender</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu">freq</span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">age</span><span class="op">)</span>
|
||||
<span class="va">my_list</span> <span class="op">%>%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">gender</span><span class="op">)</span></code></pre></div>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
@@ -1802,13 +1773,13 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
<ul>
|
||||
<li>A vignette to explain its usage</li>
|
||||
<li>Support for <code>rsi</code> (antimicrobial resistance) to use as input</li>
|
||||
<li>Support for <code>table</code> to use as input: <code>freq(table(x, y))</code>
|
||||
<li>Support for <code>table</code> to use as input: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(table(x, y))</a></code>
|
||||
</li>
|
||||
<li>Support for existing functions <code>hist</code> and <code>plot</code> to use a frequency table as input: <code><a href="https://rdrr.io/r/graphics/hist.html">hist(freq(df$age))</a></code>
|
||||
</li>
|
||||
<li>Support for <code>as.vector</code>, <code>as.data.frame</code>, <code>as_tibble</code> and <code>format</code>
|
||||
</li>
|
||||
<li>Support for quasiquotation: <code>freq(mydata, mycolumn)</code> is the same as <code>mydata %>% freq(mycolumn)</code>
|
||||
<li>Support for quasiquotation: <code><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq(mydata, mycolumn)</a></code> is the same as <code>mydata %>% freq(mycolumn)</code>
|
||||
</li>
|
||||
<li>Function <code>top_freq</code> function to return the top/below <em>n</em> items as vector</li>
|
||||
<li>Header of frequency tables now also show Mean Absolute Deviaton (MAD) and Interquartile Range (IQR)</li>
|
||||
@@ -1973,7 +1944,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -264,7 +264,50 @@ table {
|
||||
|
||||
/* Syntax highlighting ---------------------------------------------------- */
|
||||
|
||||
/* Moved to new files.*/
|
||||
pre {
|
||||
word-wrap: normal;
|
||||
word-break: normal;
|
||||
border: 1px solid #eee;
|
||||
}
|
||||
|
||||
pre, code {
|
||||
background-color: #f8f8f8;
|
||||
color: #333;
|
||||
}
|
||||
|
||||
pre code {
|
||||
overflow: auto;
|
||||
word-wrap: normal;
|
||||
white-space: pre;
|
||||
}
|
||||
|
||||
pre .img {
|
||||
margin: 5px 0;
|
||||
}
|
||||
|
||||
pre .img img {
|
||||
background-color: #fff;
|
||||
display: block;
|
||||
height: auto;
|
||||
}
|
||||
|
||||
code a, pre a {
|
||||
color: #375f84;
|
||||
}
|
||||
|
||||
a.sourceLine:hover {
|
||||
text-decoration: none;
|
||||
}
|
||||
|
||||
.fl {color: #1514b5;}
|
||||
.fu {color: #000000;} /* function */
|
||||
.ch,.st {color: #036a07;} /* string */
|
||||
.kw {color: #264D66;} /* keyword */
|
||||
.co {color: #888888;} /* comment */
|
||||
|
||||
.message { color: black; font-weight: bolder;}
|
||||
.error { color: orange; font-weight: bolder;}
|
||||
.warning { color: #6A0366; font-weight: bolder;}
|
||||
|
||||
/* Clipboard --------------------------*/
|
||||
|
||||
|
||||
@@ -12,7 +12,7 @@ articles:
|
||||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2020-12-21T23:50Z
|
||||
last_built: 2020-12-24T22:24Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR//reference
|
||||
article: https://msberends.github.io/AMR//articles
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Deprecated functions — AMR-deprecated • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -303,7 +272,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>retired</
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>The AMR Package — AMR • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -341,7 +310,7 @@ The Netherlands
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -311,7 +280,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Data set with 500 isolates - WHONET example — WHONET • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -333,7 +302,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Retrieve antimicrobial drug names and doses from clinical text — ab_from_text • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -394,7 +363,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Get properties of an antibiotic — ab_property • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -432,7 +401,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Age in years of individuals — age • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -347,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Split ages into age groups — age_groups • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -372,7 +341,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Antibiotic class selectors — antibiotic_class_selectors • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -373,7 +342,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Data sets with 557 antimicrobials — antibiotics • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -377,7 +346,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Transform input to an antibiotic ID — as.ab • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -394,7 +363,7 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Transform input to disk diffusion diameters — as.disk • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -348,7 +317,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Transform input to minimum inhibitory concentrations (MIC) — as.mic • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -347,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Transform input to a microorganism ID — as.mo • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -506,7 +475,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Interpret MIC and disk values, or clean raw R/SI data — as.rsi • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -547,7 +516,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Get ATC properties from WHOCC website — atc_online_property • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -383,7 +352,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Check availability of columns — availability • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -332,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Determine bug-drug combinations — bug_drug_combinations • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -403,7 +372,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>The Catalogue of Life — catalogue_of_life • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -352,7 +321,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Version info of included Catalogue of Life — catalogue_of_life_version • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -313,7 +282,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Count available isolates — count • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -87,9 +60,6 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -113,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -237,7 +207,6 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -480,7 +449,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
File diff suppressed because one or more lines are too long
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Data set with 2,000 example isolates — example_isolates • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -317,7 +286,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Data set with unclean data — example_isolates_unclean • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -312,7 +281,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Filter isolates on result in antimicrobial class — filter_ab_class • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -395,7 +364,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Determine first (weighted) isolates — first_isolate • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -507,7 +476,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>G-test for Count Data — g.test • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -434,7 +403,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>questioni
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>PCA biplot with ggplot2 — ggplot_pca • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -462,7 +431,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>AMR plots with ggplot2 — ggplot_rsi • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -548,7 +517,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Guess antibiotic column — guess_ab_col • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -355,7 +324,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Function reference • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -85,9 +58,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -111,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -235,7 +205,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -708,7 +677,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Data set with bacterial intrinsic resistance — intrinsic_resistant • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -321,7 +290,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Determine (new) episodes for patients — is_new_episode • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -372,7 +341,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Join microorganisms to a data set — join • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -360,7 +329,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Key antibiotics for first weighted isolates — key_antibiotics • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -471,7 +440,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Kurtosis of the sample — kurtosis • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -332,7 +301,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Lifecycles of functions in the AMR package — lifecycle • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -88,9 +61,6 @@ This page contains a section for every lifecycle (with text borrowed from the af
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -114,7 +84,7 @@ This page contains a section for every lifecycle (with text borrowed from the af
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -238,7 +208,6 @@ This page contains a section for every lifecycle (with text borrowed from the af
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -326,7 +295,7 @@ The lifecycle of this function is <strong>questioning</strong>. This function mi
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Pattern matching with keyboard shortcut — like • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -366,7 +335,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
File diff suppressed because one or more lines are too long
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Data set with 5,583 common microorganism codes — microorganisms.codes • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -319,7 +288,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Data set with 67,151 microorganisms — microorganisms • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -362,7 +331,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Data set with previously accepted taxonomic names — microorganisms.old • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -325,7 +294,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Calculate the matching score for microorganisms — mo_matching_score • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -338,7 +307,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Get properties of a microorganism — mo_property • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -332,7 +301,7 @@
|
||||
<colgroup><col class="name" /><col class="desc" /></colgroup>
|
||||
<tr>
|
||||
<th>x</th>
|
||||
<td><p>any character (vector) that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code>. Can be omitted for auto-guessing in <code>mo_is_*()</code> functions when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>, please see <em>Examples</em>.</p></td>
|
||||
<td><p>any character (vector) that can be coerced to a valid microorganism code with <code><a href='as.mo.html'>as.mo()</a></code>. Can be omitted for auto-guessing the column containing microorganism codes when used inside <code>dplyr</code> verbs, such as <code><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter()</a></code>, <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code> and <code><a href='https://dplyr.tidyverse.org/reference/summarise.html'>summarise()</a></code>, please see <em>Examples</em>.</p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>language</th>
|
||||
@@ -348,7 +317,7 @@
|
||||
</tr>
|
||||
<tr>
|
||||
<th>open</th>
|
||||
<td><p>browse the URL using <code><a href='https://rdrr.io/r/utils/browseURL.html'>utils::browseURL()</a></code></p></td>
|
||||
<td><p>browse the URL using <code><a href='https://rdrr.io/r/utils/browseURL.html'>browseURL()</a></code></p></td>
|
||||
</tr>
|
||||
<tr>
|
||||
<th>property</th>
|
||||
@@ -550,7 +519,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>User-defined reference data set for microorganisms — mo_source • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -76,8 +49,8 @@
|
||||
<script src="../extra.js"></script>
|
||||
|
||||
<meta property="og:title" content="User-defined reference data set for microorganisms — mo_source" />
|
||||
<meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions like mo_genus() and mo_gramstain().
|
||||
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package." />
|
||||
<meta property="og:description" content="These functions can be used to predefine your own reference to be used in as.mo() and consequently all mo_* functions (such as mo_genus() and mo_gramstain()).
|
||||
This is the fastest way to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once." />
|
||||
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png" />
|
||||
|
||||
|
||||
@@ -87,9 +60,6 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -113,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -237,7 +207,6 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -271,8 +240,8 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
<p>These functions can be used to predefine your own reference to be used in <code><a href='as.mo.html'>as.mo()</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus()</a></code> and <code><a href='mo_property.html'>mo_gramstain()</a></code>.</p>
|
||||
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package.</p>
|
||||
<p>These functions can be used to predefine your own reference to be used in <code><a href='as.mo.html'>as.mo()</a></code> and consequently all <code><a href='mo_property.html'>mo_*</a></code> functions (such as <code><a href='mo_property.html'>mo_genus()</a></code> and <code><a href='mo_property.html'>mo_gramstain()</a></code>).</p>
|
||||
<p>This is <strong>the fastest way</strong> to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.</p>
|
||||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>set_mo_source</span><span class='op'>(</span>
|
||||
@@ -348,7 +317,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
|
||||
<p>...any new usage of an MO function in this package will update your data file:</p><pre><span class='fu'><a href='as.mo.html'>as.mo</a></span><span class='op'>(</span><span class='st'>"lab_mo_ecoli"</span><span class='op'>)</span>
|
||||
<span class='co'>#> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from </span>
|
||||
<span class='co'>#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span>
|
||||
<span class='co'>#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns</span>
|
||||
<span class='co'>#> "Organisation XYZ" and "mo"</span>
|
||||
<span class='co'>#> Class <mo></span>
|
||||
<span class='co'>#> [1] B_ESCHR_COLI</span>
|
||||
@@ -361,7 +330,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
||||
<span class='co'>#> Removed mo_source file '/Users/me/mo_source.rds'</span>
|
||||
</pre>
|
||||
|
||||
<p>If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of <code><a href='as.mo.html'>as.mo()</a></code>.</p>
|
||||
<p>If the original file (in the previous case an Excel file) is moved or deleted, the <code>mo_source.rds</code> file will be removed upon the next use of <code><a href='as.mo.html'>as.mo()</a></code> or any <code><a href='mo_property.html'>mo_*</a></code> function.</p>
|
||||
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable lifecycle</h2>
|
||||
|
||||
|
||||
@@ -390,7 +359,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Principal Component Analysis (for AMR) — pca • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -388,7 +357,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Plotting for classes rsi, mic and disk — plot • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -416,7 +385,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Calculate microbial resistance — proportion • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -87,9 +60,6 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -113,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -237,7 +207,6 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -511,7 +480,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Random MIC values/disk zones/RSI generation — random • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -354,7 +323,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Predict antimicrobial resistance — resistance_predict • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -491,7 +460,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Data set for R/SI interpretation — rsi_translation • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9042</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -323,7 +292,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Skewness of the sample — skewness • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -87,9 +60,6 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -113,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -237,7 +207,6 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -330,7 +299,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Translate strings from AMR package — translate • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="../preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="../code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="../code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="../bootstrap-toc.css">
|
||||
<script src="../bootstrap-toc.js"></script>
|
||||
@@ -86,9 +59,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -112,7 +82,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -236,7 +206,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -347,7 +316,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
@@ -6,22 +6,6 @@
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=edge">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1.0">
|
||||
|
||||
<!-- Inform modern browsers that this page supports both dark and light color schemes,
|
||||
and the page author prefers light. -->
|
||||
<meta name="color-scheme" content="dark light">
|
||||
<script>
|
||||
// If `prefers-color-scheme` is not supported, fall back to light mode.
|
||||
// i.e. In this case, inject the `light` CSS before the others, with
|
||||
// no media filter so that it will be downloaded with highest priority.
|
||||
if (window.matchMedia("(prefers-color-scheme: dark)").media === "not all") {
|
||||
document.documentElement.style.display = "none";
|
||||
document.head.insertAdjacentHTML(
|
||||
"beforeend",
|
||||
"<link id=\"css\" rel=\"stylesheet\" href=\"bootstrap.css\" onload=\"document.documentElement.style.display = ''\">"
|
||||
);
|
||||
}
|
||||
</script>
|
||||
|
||||
<title>Survey • AMR (for R)</title>
|
||||
|
||||
<!-- favicons -->
|
||||
@@ -36,21 +20,10 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
|
||||
<!-- Bootstrap -->
|
||||
|
||||
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- Flatly Theme - Light -->
|
||||
<link id="css-light" rel="stylesheet" href="https://bootswatch.com/3/flatly/bootstrap.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
|
||||
<!-- Darkly Theme - Dark -->
|
||||
<link id="css-dark" rel="stylesheet" href="https://bootswatch.com/3/darkly/bootstrap.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
<!-- preferably CSS -->
|
||||
<link rel="stylesheet" href="preferably.css">
|
||||
<link id="css-code-light" rel="stylesheet" href="code-color-scheme-light.css" media="(prefers-color-scheme: light), (prefers-color-scheme: no-preference)">
|
||||
<link id="css-code-dark" rel="stylesheet" href="code-color-scheme-dark.css" media="(prefers-color-scheme: dark)">
|
||||
|
||||
|
||||
|
||||
<!-- bootstrap-toc -->
|
||||
<link rel="stylesheet" href="bootstrap-toc.css">
|
||||
<script src="bootstrap-toc.js"></script>
|
||||
@@ -85,9 +58,6 @@
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
|
||||
|
||||
|
||||
|
||||
|
||||
<!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
|
||||
@@ -111,7 +81,7 @@
|
||||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9043</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9044</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
@@ -235,7 +205,6 @@
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
|
||||
<li>
|
||||
<a href="https://github.com/msberends/AMR">
|
||||
<span class="fab fa-github"></span>
|
||||
@@ -286,7 +255,7 @@
|
||||
</div>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Made with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1, using <a href="https://preferably.amirmasoudabdol.name/?source=footer">preferably</a> template.</p>
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
|
||||
</div>
|
||||
|
||||
</footer>
|
||||
|
||||
File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@@ -85,7 +85,7 @@ mo_url(x, open = FALSE, language = get_locale(), ...)
|
||||
mo_property(x, property = "fullname", language = get_locale(), ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{any character (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be omitted for auto-guessing in \verb{mo_is_*()} functions when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}, please see \emph{Examples}.}
|
||||
\item{x}{any character (vector) that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be omitted for auto-guessing the column containing microorganism codes when used inside \code{dplyr} verbs, such as \code{\link[dplyr:filter]{filter()}}, \code{\link[dplyr:mutate]{mutate()}} and \code{\link[dplyr:summarise]{summarise()}}, please see \emph{Examples}.}
|
||||
|
||||
\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_locale]{get_locale()}}) and can be overwritten by setting the option \code{AMR_locale}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Also used to translate text like "no growth". Use \code{language = NULL} or \code{language = ""} to prevent translation.}
|
||||
|
||||
@@ -93,7 +93,7 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
|
||||
|
||||
\item{ab}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}}
|
||||
|
||||
\item{open}{browse the URL using \code{\link[utils:browseURL]{utils::browseURL()}}}
|
||||
\item{open}{browse the URL using \code{\link[utils:browseURL]{browseURL()}}}
|
||||
|
||||
\item{property}{one of the column names of the \link{microorganisms} data set: "\code{mo}", "\code{fullname}", "\code{kingdom}", "\code{phylum}", "\code{class}", "\code{order}", "\code{family}", "\code{genus}", "\code{species}", "\code{subspecies}", "\code{rank}", "\code{ref}", "\code{species_id}", "\code{source}", "\code{prevalence}", "\code{snomed}", or must be \code{"shortname"}}
|
||||
}
|
||||
|
||||
@@ -19,9 +19,9 @@ get_mo_source(destination = getOption("AMR_mo_source", "~/mo_source.rds"))
|
||||
\item{destination}{destination of the compressed data file, default to the user's home directory.}
|
||||
}
|
||||
\description{
|
||||
These functions can be used to predefine your own reference to be used in \code{\link[=as.mo]{as.mo()}} and consequently all \verb{mo_*} functions like \code{\link[=mo_genus]{mo_genus()}} and \code{\link[=mo_gramstain]{mo_gramstain()}}.
|
||||
These functions can be used to predefine your own reference to be used in \code{\link[=as.mo]{as.mo()}} and consequently all \code{\link[=mo_property]{mo_*}} functions (such as \code{\link[=mo_genus]{mo_genus()}} and \code{\link[=mo_gramstain]{mo_gramstain()}}).
|
||||
|
||||
This is \strong{the fastest way} to have your organisation (or analysis) specific codes picked up and translated by this package.
|
||||
This is \strong{the fastest way} to have your organisation (or analysis) specific codes picked up and translated by this package, since you don't have to bother about it again after setting it up once.
|
||||
}
|
||||
\details{
|
||||
The reference file can be a text file separated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an \R object file (extension '.rds'). To use an Excel file, you will need to have the \code{readxl} package installed.
|
||||
@@ -79,7 +79,7 @@ If we edit the Excel file by, let's say, adding row 4 like this:\preformatted{
|
||||
|
||||
...any new usage of an MO function in this package will update your data file:\preformatted{as.mo("lab_mo_ecoli")
|
||||
#> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from
|
||||
#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
|
||||
#> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns
|
||||
#> "Organisation XYZ" and "mo"
|
||||
#> Class <mo>
|
||||
#> [1] B_ESCHR_COLI
|
||||
@@ -92,7 +92,7 @@ To delete the reference data file, just use \code{""}, \code{NULL} or \code{FALS
|
||||
#> Removed mo_source file '/Users/me/mo_source.rds'
|
||||
}
|
||||
|
||||
If the original Excel file is moved or deleted, the mo_source file will be removed upon the next use of \code{\link[=as.mo]{as.mo()}}.
|
||||
If the original file (in the previous case an Excel file) is moved or deleted, the \code{mo_source.rds} file will be removed upon the next use of \code{\link[=as.mo]{as.mo()}} or any \code{\link[=mo_property]{mo_*}} function.
|
||||
}
|
||||
|
||||
\section{Stable lifecycle}{
|
||||
|
||||
@@ -81,34 +81,27 @@ example_isolates %>%
|
||||
For another example, I will create a data set to determine multi-drug resistant TB:
|
||||
|
||||
```{r}
|
||||
# a helper function to get a random vector with values S, I and R
|
||||
# with the probabilities 50% - 10% - 40%
|
||||
sample_rsi <- function() {
|
||||
sample(c("S", "I", "R"),
|
||||
size = 5000,
|
||||
prob = c(0.5, 0.1, 0.4),
|
||||
replace = TRUE)
|
||||
}
|
||||
|
||||
my_TB_data <- data.frame(rifampicin = sample_rsi(),
|
||||
isoniazid = sample_rsi(),
|
||||
gatifloxacin = sample_rsi(),
|
||||
ethambutol = sample_rsi(),
|
||||
pyrazinamide = sample_rsi(),
|
||||
moxifloxacin = sample_rsi(),
|
||||
kanamycin = sample_rsi())
|
||||
# random_rsi() is a helper function to generate
|
||||
# a random vector with values S, I and R
|
||||
my_TB_data <- data.frame(rifampicin = random_rsi(5000),
|
||||
isoniazid = random_rsi(5000),
|
||||
gatifloxacin = random_rsi(5000),
|
||||
ethambutol = random_rsi(5000),
|
||||
pyrazinamide = random_rsi(5000),
|
||||
moxifloxacin = random_rsi(5000),
|
||||
kanamycin = random_rsi(5000))
|
||||
```
|
||||
|
||||
Because all column names are automatically verified for valid drug names or codes, this would have worked exactly the same:
|
||||
|
||||
```{r, eval = FALSE}
|
||||
my_TB_data <- data.frame(RIF = sample_rsi(),
|
||||
INH = sample_rsi(),
|
||||
GAT = sample_rsi(),
|
||||
ETH = sample_rsi(),
|
||||
PZA = sample_rsi(),
|
||||
MFX = sample_rsi(),
|
||||
KAN = sample_rsi())
|
||||
my_TB_data <- data.frame(RIF = random_rsi(5000),
|
||||
INH = random_rsi(5000),
|
||||
GAT = random_rsi(5000),
|
||||
ETH = random_rsi(5000),
|
||||
PZA = random_rsi(5000),
|
||||
MFX = random_rsi(5000),
|
||||
KAN = random_rsi(5000))
|
||||
```
|
||||
|
||||
The data set now looks like this:
|
||||
|
||||
Reference in New Issue
Block a user