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AMR
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memory for as.mo()

This commit is contained in:
dr. M.S. (Matthijs) Berends 2019-03-15 13:57:25 +01:00
parent 504a042fba
commit fdffc2791b
84 changed files with 767 additions and 477 deletions
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6
.gitlab-ci.yml
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@ -61,10 +61,7 @@ cache:
R:
stage: build
allow_failure: false
variables:
WARNINGS_ARE_ERRORS: 1
script:
- export WARNINGS_ARE_ERRORS=1
# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
- rm -rf vignettes
- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
@ -86,7 +83,8 @@ coverage:
- master
script:
- apt-get install --yes git
- Rscript -e 'cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = "50ffa0aa-fee0-4f8b-a11d-8c7edc6d32ca"); cat("Code coverage:", covr::percent_coverage(cc))'
# codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd
- Rscript -e 'cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = "${codecov_token}"); cat("Code coverage:", covr::percent_coverage(cc))'
coverage: '/Code coverage: \d+\.\d+/'
pages:

4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.5.0.9022
Date: 2019-03-12
Version: 0.5.0.9023
Date: 2019-03-15
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(

1
NAMESPACE
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@ -71,6 +71,7 @@ export(atc_umcg)
export(availability)
export(brmo)
export(catalogue_of_life_version)
export(clean_mo_history)
export(count_I)
export(count_IR)
export(count_R)

53
NEWS.md
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@ -101,34 +101,35 @@ We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.git
* Function `guess_mo()` is now deprecated in favour of `as.mo()` and will be removed in future versions
* Function `guess_atc()` is now deprecated in favour of `as.atc()` and will be removed in future versions
* Improvements for `as.mo()`:
* Now handles incorrect spelling like `i` instead of `y` and `f` instead of `ph`:
```r
# mo_fullname() uses as.mo() internally
mo_fullname("Sthafilokockus aaureuz")
#> [1] "Staphylococcus aureus"
mo_fullname("S. klossi")
#> [1] "Staphylococcus kloosii"
```
* Now handles incorrect spelling, like `i` instead of `y` and `f` instead of `ph`:
```r
# mo_fullname() uses as.mo() internally
mo_fullname("Sthafilokockus aaureuz")
#> [1] "Staphylococcus aureus"
mo_fullname("S. klossi")
#> [1] "Staphylococcus kloosii"
```
* Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default `allow_uncertain = TRUE` is equal to uncertainty level 2. Run `?as.mo` for more info about these levels.
```r
# equal:
as.mo(..., allow_uncertain = TRUE)
as.mo(..., allow_uncertain = 2)
# also equal:
as.mo(..., allow_uncertain = FALSE)
as.mo(..., allow_uncertain = 0)
```
Using `as.mo(..., allow_uncertain = 3)` could lead to very unreliable results.
```r
# equal:
as.mo(..., allow_uncertain = TRUE)
as.mo(..., allow_uncertain = 2)
# also equal:
as.mo(..., allow_uncertain = FALSE)
as.mo(..., allow_uncertain = 0)
```
Using `as.mo(..., allow_uncertain = 3)` could lead to very unreliable results.
* All microbial IDs that are found with zero uncertainty are now saved to a local file `~/.Rhistory_mo`. Use the new function `clean_mo_history()` to delete this file, which resets the algorithms.
* Incoercible results will now be considered 'unknown', MO code `UNKNOWN`. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:
```r
mo_genus("qwerty", language = "es")
# Warning:
# one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.
#> [1] "(género desconocido)"
```
```r
mo_genus("qwerty", language = "es")
# Warning:
# one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.
#> [1] "(género desconocido)"
```
* Fix for vector containing only empty values
* Finds better results when input is in other languages
* Better handling for subspecies

32
R/misc.R
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@ -75,7 +75,9 @@ check_available_columns <- function(tbl, col.list, info = TRUE) {
col.list.bak <- col.list
# are they available as upper case or lower case then?
for (i in 1:length(col.list)) {
if (toupper(col.list[i]) %in% colnames(tbl)) {
if (is.null(col.list[i]) | isTRUE(is.na(col.list[i]))) {
col.list[i] <- NULL
} else if (toupper(col.list[i]) %in% colnames(tbl)) {
col.list[i] <- toupper(col.list[i])
} else if (tolower(col.list[i]) %in% colnames(tbl)) {
col.list[i] <- tolower(col.list[i])
@ -124,7 +126,7 @@ size_humanreadable <- function(bytes, decimals = 1) {
out
}
#' @importFrom crayon blue bold
#' @importFrom crayon blue bold red
#' @importFrom dplyr %>% pull
search_type_in_df <- function(tbl, type) {
# try to find columns based on type
@ -151,16 +153,22 @@ search_type_in_df <- function(tbl, type) {
}
# -- date
if (type == "date") {
for (i in 1:ncol(tbl)) {
if (any(colnames(tbl) %like% "^(Specimen date)")) {
# WHONET support
found <- colnames(tbl)[colnames(tbl) %like% "^(Specimen date)"][1]
} else if ("Date" %in% class(tbl %>% pull(i)) | "POSIXct" %in% class(tbl %>% pull(i))) {
found <- colnames(tbl)[i]
break
if (any(colnames(tbl) %like% "^(specimen date|specimen_date|spec_date)")) {
# WHONET support
found <- colnames(tbl)[colnames(tbl) %like% "^(specimen date|specimen_date|spec_date)"][1]
if (!any(class(tbl %>% pull(found)) %in% c("Date", "POSIXct"))) {
stop(red(paste0("ERROR: Found column `", bold(found), "` to be used as input for `col_", type,
"`, but this column contains no valid dates. Transform its values to valid dates first.")),
call. = FALSE)
}
} else {
for (i in 1:ncol(tbl)) {
if (any(class(tbl %>% pull(i)) %in% c("Date", "POSIXct"))) {
found <- colnames(tbl)[i]
break
}
}
}
}
# -- patient id
if (type == "patient_id") {
@ -170,8 +178,8 @@ search_type_in_df <- function(tbl, type) {
}
# -- specimen
if (type == "specimen") {
if (any(colnames(tbl) %like% "(specimen type)")) {
found <- colnames(tbl)[colnames(tbl) %like% "(specimen type)"][1]
if (any(colnames(tbl) %like% "(specimen type|spec_type)")) {
found <- colnames(tbl)[colnames(tbl) %like% "(specimen type|spec_type)"][1]
} else if (any(colnames(tbl) %like% "^(specimen)")) {
found <- colnames(tbl)[colnames(tbl) %like% "^(specimen)"][1]
}

155
R/mo.R
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@ -31,10 +31,12 @@
#' This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.
#' @param allow_uncertain a logical (\code{TRUE} or \code{FALSE}) or a value between 0 and 3 to indicate whether the input should be checked for less possible results, see Details
#' @param reference_df a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. See \code{\link{set_mo_source}} and \code{\link{get_mo_source}} to automate the usage of your own codes (e.g. used in your analysis or organisation).
#' @param ... other parameters passed on to functions
#' @rdname as.mo
#' @aliases mo
#' @keywords mo Becker becker Lancefield lancefield guess
#' @details
#' \strong{General info} \cr
#' A microbial ID from this package (class: \code{mo}) typically looks like these examples:\cr
#' \preformatted{
#' Code Full name
@ -53,7 +55,9 @@
#'
#' Values that cannot be coered will be considered 'unknown' and have an MO code \code{UNKNOWN}.
#'
#' Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
#' Use the \code{\link{mo_property}_*} functions to get properties based on the returned code, see Examples.
#'
#' All IDs that are found with zero uncertainty are saved to a local file (\code{"~/.Rhistory_mo"}) to improve speed for every next time. Use \code{clean_mo_history()} to delete this file, which resets the algorithms. Only previous results will be used from this version of the \code{AMR} package, since the taxonomic tree may change in the future for any organism.
#'
#' \strong{Intelligent rules} \cr
#' This function uses intelligent rules to help getting fast and logical results. It tries to find matches in this order:
@ -174,12 +178,14 @@
#' df <- df %>%
#' mutate(mo = as.mo(paste(genus, species)))
#' }
as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = get_mo_source()) {
as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = get_mo_source(), ...) {
if (!"AMR" %in% base::.packages()) {
library("AMR")
# check onLoad() in R/zzz.R: data tables are created there.
}
mo_hist <- get_mo_history(x, force = isTRUE(list(...)$force_mo_history))
if (mo_source_isvalid(reference_df)
& isFALSE(Becker)
& isFALSE(Lancefield)
@ -211,6 +217,13 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
& isFALSE(Lancefield)) {
y <- x
} else if (sum(is.na(mo_hist)) == 0
& isFALSE(Becker)
& isFALSE(Lancefield)) {
# check previously found results
y <- mo_hist
} else if (all(tolower(x) %in% microorganismsDT$fullname_lower)
& isFALSE(Becker)
& isFALSE(Lancefield)) {
@ -229,13 +242,22 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
on = "fullname_lower",
"mo"][[1]]
}
# save them too
mo_hist <- read_mo_history(force = isTRUE(list(...)$force_mo_history))
if (any(!x %in% mo_hist$x)) {
for (i in 1:length(y)) {
set_mo_history(x[i], y[i], force = isTRUE(list(...)$force_mo_history))
}
}
} else {
# will be checked for mo class in validation and uses exec_as.mo internally if necessary
y <- mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,
allow_uncertain = allow_uncertain, reference_df = reference_df,
force_mo_history = isTRUE(list(...)$force_mo_history))
}
} else {
# will be checked for mo class in validation and uses exec_as.mo internally if necessary
y <- mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,
allow_uncertain = allow_uncertain, reference_df = reference_df)
}
structure(.Data = y, class = "mo")
}
@ -249,9 +271,14 @@ is.mo <- function(x) {
#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated filter distinct
#' @importFrom data.table data.table as.data.table setkey
#' @importFrom crayon magenta red blue silver italic has_color
exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
allow_uncertain = TRUE, reference_df = get_mo_source(),
property = "mo", clear_options = TRUE) {
exec_as.mo <- function(x,
Becker = FALSE,
Lancefield = FALSE,
allow_uncertain = TRUE,
reference_df = get_mo_source(),
property = "mo",
clear_options = TRUE,
force_mo_history = FALSE) {
if (!"AMR" %in% base::.packages()) {
library("AMR")
@ -412,7 +439,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# replace hemolytic by haemolytic
x <- gsub("ha?emoly", "haemoly", x)
# place minus back in streptococci
x <- gsub("(alpha|beta|gamma) ha?emoly", "\\1-haemoly", x)
x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x)
# remove genus as first word
x <- gsub("^Genus ", "", x)
# allow characters that resemble others
@ -458,6 +485,13 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
progress$tick()$print()
found <- microorganismsDT[mo == get_mo_history(x_backup[i], force = force_mo_history), ..property][[1]]
# previously found result
if (length(found) > 0) {
x[i] <- found[1L]
next
}
found <- microorganismsDT[mo == toupper(x_backup[i]), ..property][[1]]
# is a valid MO code
if (length(found) > 0) {
@ -469,6 +503,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# most probable: is exact match in fullname
if (length(found) > 0) {
x[i] <- found[1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
@ -494,6 +531,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# return first genus that begins with x_trimmed, e.g. when "E. spp."
if (length(found) > 0) {
x[i] <- found[1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
}
@ -515,50 +555,80 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
if (!is.na(x_trimmed[i])) {
if (toupper(x_backup_without_spp[i]) %in% c('MRSA', 'MSSA', 'VISA', 'VRSA')) {
x[i] <- microorganismsDT[mo == 'B_STPHY_AUR', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) %in% c('MRSE', 'MSSE')) {
x[i] <- microorganismsDT[mo == 'B_STPHY_EPI', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) == "VRE"
| x_backup_without_spp[i] %like% '(enterococci|enterokok|enterococo)[a-z]*?$') {
x[i] <- microorganismsDT[mo == 'B_ENTRC', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) %in% c("EHEC", "EPEC", "EIEC", "STEC", "ATEC")) {
x[i] <- microorganismsDT[mo == 'B_ESCHR_COL', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) == 'MRPA') {
# multi resistant P. aeruginosa
x[i] <- microorganismsDT[mo == 'B_PSDMN_AER', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) == 'CRS'
| toupper(x_backup_without_spp[i]) == 'CRSM') {
# co-trim resistant S. maltophilia
x[i] <- microorganismsDT[mo == 'B_STNTR_MAL', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
# peni I, peni R, vanco I, vanco R: S. pneumoniae
x[i] <- microorganismsDT[mo == 'B_STRPT_PNE', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (x_backup_without_spp[i] %like% '^G[ABCDFGHK]S$') {
# Streptococci, like GBS = Group B Streptococci (B_STRPT_GRB)
x[i] <- microorganismsDT[mo == gsub("G([ABCDFGHK])S", "B_STRPT_GR\\1", x_backup_without_spp[i], ignore.case = TRUE), ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (x_backup_without_spp[i] %like% '(streptococ|streptokok).* [ABCDFGHK]$') {
# Streptococci in different languages, like "estreptococos grupo B"
x[i] <- microorganismsDT[mo == gsub(".*(streptococ|streptokok|estreptococ).* ([ABCDFGHK])$", "B_STRPT_GR\\2", x_backup_without_spp[i], ignore.case = TRUE), ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (x_backup_without_spp[i] %like% 'group [ABCDFGHK] (streptococ|streptokok|estreptococ)') {
# Streptococci in different languages, like "Group A Streptococci"
x[i] <- microorganismsDT[mo == gsub(".*group ([ABCDFGHK]) (streptococ|streptokok|estreptococ).*", "B_STRPT_GR\\1", x_backup_without_spp[i], ignore.case = TRUE), ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
@ -567,6 +637,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
| x_backup_without_spp[i] %like% '[ck]o?ns[^a-z]?$') {
# coerce S. coagulase negative
x[i] <- microorganismsDT[mo == 'B_STPHY_CNS', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (x_backup_without_spp[i] %like% '[ck]oagulas[ea] positie?[vf]'
@ -574,24 +647,38 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
| x_backup_without_spp[i] %like% '[ck]o?ps[^a-z]?$') {
# coerce S. coagulase positive
x[i] <- microorganismsDT[mo == 'B_STPHY_CPS', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (x_backup_without_spp[i] %like% 'gram[ -]?neg.*'
| x_backup_without_spp[i] %like% 'negatie?[vf]'
| x_trimmed[i] %like% 'gram[ -]?neg.*') {
# coerce Gram negatives
x[i] <- microorganismsDT[mo == 'B_GRAMN', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (x_backup_without_spp[i] %like% 'gram[ -]?pos.*'
| x_backup_without_spp[i] %like% 'positie?[vf]'
| x_trimmed[i] %like% 'gram[ -]?pos.*') {
# coerce Gram positives
x[i] <- microorganismsDT[mo == 'B_GRAMP', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_backup_without_spp[i], ignore.case = FALSE)) {
if (x_backup_without_spp[i] %like% "Salmonella group") {
# Salmonella Group A to Z, just return S. species for now
x[i] <- microorganismsDT[mo == 'B_SLMNL', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
options(mo_renamed = c(getOption("mo_renamed"),
magenta(paste0("Note: ",
italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])),
@ -601,6 +688,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
} else {
# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
x[i] <- microorganismsDT[mo == 'B_SLMNL_ENT', ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
options(mo_renamed = c(getOption("mo_renamed"),
magenta(paste0("Note: ",
italic("Salmonella"), " ", trimws(gsub("Salmonella", "", x_backup_without_spp[i])),
@ -618,12 +708,18 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
found <- microorganismsDT[fullname_lower %in% tolower(c(x_species[i], x_trimmed_species[i])), ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
if (nchar(x_backup_without_spp[i]) >= 6) {
found <- microorganismsDT[fullname_lower %like% paste0("^", x_backup_without_spp[i], "[a-z]+"), ..property][[1]]
found <- microorganismsDT[fullname_lower %like% paste0("^", unregex(x_backup_without_spp[i]), "[a-z]+"), ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
}
@ -636,6 +732,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
mo_found <- AMR::microorganisms.codes[toupper(x_backup[i]) == AMR::microorganisms.codes[, 1], "mo"][1L]
if (length(mo_found) > 0) {
x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
}
@ -737,6 +836,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
f.x_withspaces_end_only = x_withspaces_end_only[i],
g.x_backup_without_spp = x_backup_without_spp[i])
if (!empty_result(x[i])) {
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
# THEN TRY PREVALENT IN HUMAN INFECTIONS ----
@ -749,6 +851,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
f.x_withspaces_end_only = x_withspaces_end_only[i],
g.x_backup_without_spp = x_backup_without_spp[i])
if (!empty_result(x[i])) {
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
# THEN UNPREVALENT IN HUMAN INFECTIONS ----
@ -761,6 +866,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
f.x_withspaces_end_only = x_withspaces_end_only[i],
g.x_backup_without_spp = x_backup_without_spp[i])
if (!empty_result(x[i])) {
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
@ -784,16 +892,19 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
ref_old = found[1, ref],
ref_new = microorganismsDT[col_id == found[1, col_id_new], ref],
mo = microorganismsDT[col_id == found[1, col_id_new], mo])
if (property == "mo") {
set_mo_history(x_backup[i], x[i], force = force_mo_history)
}
next
}
# check for uncertain results ----
uncertain_fn <- function(a.x_backup,
b.x_trimmed,
c.x_withspaces_start_end,
d.x_withspaces_start_only,
f.x_withspaces_end_only,
g.x_backup_without_spp) {
b.x_trimmed,
c.x_withspaces_start_end,
d.x_withspaces_start_only,
f.x_withspaces_end_only,
g.x_backup_without_spp) {
if (allow_uncertain == 0) {
# do not allow uncertainties
@ -936,15 +1047,15 @@ g.x_backup_without_spp) {
}
x[i] <- uncertain_fn(x_backup[i],
x_trimmed[i],
x_withspaces_start_end[i],
x_withspaces_start_end[i],
x_withspaces_start_only[i],
x_withspaces_end_only[i],
x_backup_without_spp[i])
if (!empty_result(x[i])) {
# no set_mo_history here; these are uncertain
next
}
# not found ----
x[i] <- microorganismsDT[mo == "UNKNOWN", ..property][[1]]
failures <- c(failures, x_backup[i])
@ -1232,3 +1343,7 @@ nr2char <- function(x) {
x
}
}
unregex <- function(x) {
gsub("[^a-zA-Z0-9 -]", "", x)
}

74
R/mo_history.R Normal file
View File

@ -0,0 +1,74 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
# print successful as.mo coercions to file, not uncertain ones
#' @importFrom dplyr %>% filter
set_mo_history <- function(x, mo, force = FALSE) {
file_location <- base::path.expand('~/.Rhistory_mo')
if ((base::interactive() & mo != "UNKNOWN") | force == TRUE) {
mo_hist <- read_mo_history(force = force)
if (NROW(mo_hist[base::which(mo_hist$x == x & mo_hist$package_version == utils::packageVersion("AMR")),]) == 0) {
base::write(x = c(x, mo, base::as.character(utils::packageVersion("AMR"))),
file = file_location,
ncolumns = 3,
append = TRUE,
sep = "\t")
}
}
return(base::invisible())
}
get_mo_history <- function(x, force = FALSE) {
file_read <- read_mo_history(force = force)
if (base::is.null(file_read)) {
NA
} else {
data.frame(x, stringsAsFactors = FALSE) %>%
left_join(file_read, by = "x") %>%
pull(mo)
}
}
read_mo_history <- function(force = FALSE) {
file_location <- base::path.expand('~/.Rhistory_mo')
if (!base::file.exists(file_location) | (!base::interactive() & force == FALSE)) {
return(NULL)
}
file_read <- utils::read.table(file = file_location,
header = FALSE,
sep = "\t",
col.names = c("x", "mo", "package_version"),
stringsAsFactors = FALSE)
# Below: filter on current package version.
# Future fullnames may even be replaced by new taxonomic names, so new versions of
# the Catalogue of Life must not lead to data corruption.
file_read[base::which(file_read$package_version == utils::packageVersion("AMR")), c("x", "mo")]
}
#' @rdname as.mo
#' @export
clean_mo_history <- function() {
file_location <- base::path.expand('~/.Rhistory_mo')
if (base::file.exists(file_location)) {
base::unlink(file_location)
}
}

21
R/mo_source.R
View File

@ -99,6 +99,8 @@
#' @inheritSection AMR Read more on our website!
set_mo_source <- function(path) {
file_location <- path.expand('~/mo_source.rds')
if (!is.character(path) | length(path) > 1) {
stop("`path` must be a character of length 1.")
}
@ -106,9 +108,9 @@ set_mo_source <- function(path) {
if (path %in% c(NULL, "")) {
options(mo_source = NULL)
options(mo_source_timestamp = NULL)
if (file.exists("~/.mo_source.rds")) {
unlink("~/.mo_source.rds")
message("Removed mo_source file '~/.mo_source.rds'.")
if (file.exists(file_location)) {
unlink(file_location)
message("Removed mo_source file '", file_location, "'.")
}
return(invisible())
}
@ -165,23 +167,22 @@ set_mo_source <- function(path) {
df <- as.data.frame(df, stringAsFactors = FALSE)
# success
if (file.exists("~/.mo_source.rds")) {
if (file.exists(file_location)) {
action <- "Updated"
} else {
action <- "Created"
}
saveRDS(df, "~/.mo_source.rds")
saveRDS(df, file_location)
options(mo_source = path)
options(mo_source_timestamp = as.character(file.info(path)$mtime))
message(action, " mo_source file '~/.mo_source.rds' from '", path, "'.")
message(action, " mo_source file '", file_location, "' from '", path, "'.")
}
#' @rdname mo_source
#' @export
get_mo_source <- function() {
if (is.null(getOption("mo_source", NULL))) {
return(NULL)
NULL
} else {
old_time <- as.POSIXct(getOption("mo_source_timestamp"))
new_time <- as.POSIXct(as.character(file.info(getOption("mo_source", ""))$mtime))
@ -195,9 +196,9 @@ get_mo_source <- function() {
# set updated source
set_mo_source(getOption("mo_source"))
}
file_location <- path.expand('~/mo_source.rds')
readRDS(file_location)
}
readRDS("~/.mo_source.rds")
}
mo_source_isvalid <- function(x) {

10
README.md
View File

@ -25,11 +25,11 @@ Bhanu N.M. Sinha <a href="https://orcid.org/0000-0003-1634-0010"><img src="https
<sup>a</sup> Thesis dissertant<br>
<sup>b</sup> Thesis advisor
<a href="https://www.rug.nl"><img src="pkgdown/logos/logo_rug.png" height="60px"></a>
<a href="https://www.umcg.nl"><img src="pkgdown/logos/logo_umcg.png" height="60px"></a>
<a href="https://www.certe.nl"><img src="pkgdown/logos/logo_certe.png" height="60px"></a>
<a href="http://www.eurhealth-1health.eu"><img src="pkgdown/logos/logo_eh1h.png" height="60px"></a>
<a href="http://www.eurhealth-1health.eu"><img src="pkgdown/logos/logo_interreg.png" height="60px"></a>
<a href="https://www.rug.nl"><img src="man/figures/logo_rug.png" height="60px"></a>
<a href="https://www.umcg.nl"><img src="man/figures/logo_umcg.png" height="60px"></a>
<a href="https://www.certe.nl"><img src="man/figures/logo_certe.png" height="60px"></a>
<a href="http://www.eurhealth-1health.eu"><img src="man/figures/logo_eh1h.png" height="60px"></a>
<a href="http://www.eurhealth-1health.eu"><img src="man/figures/logo_interreg.png" height="60px"></a>
## How to get this package
All stable versions of this package [are published on CRAN](https://CRAN.R-project.org/package=AMR), the official R network with a peer-reviewed submission process.

10
_pkgdown.yml
View File

@ -147,7 +147,7 @@ reference:
- '`WHONET`'
- '`microorganisms.codes`'
- '`microorganisms.old`'
- title: Other
- title: Other functions
desc: >
These functions are mostly for internal use, but some of
them may also be suitable for your analysis. Especially the
@ -155,7 +155,13 @@ reference:
contents:
- '`get_locale`'
- '`like`'
- '`ab_property`'
- title: Deprecated functions
desc: >
These functions are deprecated, meaning that they still
work but show a warning with every use and will be removed
in a future version.
contents:
- '`AMR-deprecated`'
authors:
Matthijs S. Berends:

3
appveyor.yml
View File

@ -55,9 +55,6 @@ on_failure:
- 7z a failure.zip *.Rcheck\*
- appveyor PushArtifact failure.zip
#on_success:
# - Rscript -e "library(covr); cc <- package_coverage(); codecov(coverage = cc, token = '50ffa0aa-fee0-4f8b-a11d-8c7edc6d32ca'); cat('Code coverage:', percent_coverage(cc))"
artifacts:
- path: '*.Rcheck\**\*.log'
name: Logs

2
docs/LICENSE-text.html
View File

@ -78,7 +78,7 @@
</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="Released version">0.5.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

467
docs/articles/AMR.html
View File

@ -40,7 +40,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -201,7 +201,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 05 March 2019.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 15 March 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -217,21 +217,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-03-05</td>
<td align="center">2019-03-15</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2019-03-05</td>
<td align="center">2019-03-15</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2019-03-05</td>
<td align="center">2019-03-15</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -327,21 +327,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-01-23</td>
<td align="center">E2</td>
<td align="center">2011-03-23</td>
<td align="center">H4</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-12-07</td>
<td align="center">L8</td>
<td align="center">2016-02-07</td>
<td align="center">A10</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -349,49 +349,49 @@
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-07-19</td>
<td align="center">W5</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2017-05-30</td>
<td align="center">Q9</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-11-26</td>
<td align="center">L7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-01-24</td>
<td align="center">M7</td>
<td align="center">2016-09-19</td>
<td align="center">U5</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-11-13</td>
<td align="center">V10</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<tr class="odd">
<td align="center">2016-03-20</td>
<td align="center">X10</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-07-29</td>
<td align="center">D10</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -411,15 +411,15 @@
#&gt;
#&gt; Item Count Percent Cum. Count Cum. Percent
#&gt; --- ----- ------- -------- ----------- -------------
#&gt; 1 M 10,562 52.8% 10,562 52.8%
#&gt; 2 F 9,438 47.2% 20,000 100.0%</code></pre>
#&gt; 1 M 10,422 52.1% 10,422 52.1%
#&gt; 2 F 9,578 47.9% 20,000 100.0%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researcher perspective: there are slightly more men. Nothing we didn’t already know.</p>
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb12-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">bacteria =</span> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(bacteria))</a></code></pre></div>
<p>We also want to transform the antibiotics, because in real life data we don’t know if they are really clean. The <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function ensures reliability and reproducibility in these kind of variables. The <code><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">mutate_at()</a></code> will run the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function on defined variables:</p>
<p>We also want to transform the antibiotics, because in real life data we don’t know if they are really clean. The <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function ensures reliability and reproducibility in these kind of variables. The <code><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at()</a></code> will run the <code><a href="../reference/as.rsi.html">as.rsi()</a></code> function on defined variables:</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb13-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(amox<span class="op">:</span>gent), as.rsi)</a></code></pre></div>
<a class="sourceLine" id="cb13-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(amox<span class="op">:</span>gent), as.rsi)</a></code></pre></div>
<p>Finally, we will apply <a href="http://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a> on our antimicrobial results. In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
<p>Because the amoxicillin (column <code>amox</code>) and amoxicillin/clavulanic acid (column <code>amcl</code>) in our data were generated randomly, some rows will undoubtedly contain amox = S and amcl = R, which is technically impossible. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> fixes this:</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">data &lt;-<span class="st"> </span><span class="kw"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(data, <span class="dt">col_mo =</span> <span class="st">"bacteria"</span>)</a>
@ -443,10 +443,10 @@
<a class="sourceLine" id="cb14-19" title="19"><span class="co">#&gt; Kingella kingae (no changes)</span></a>
<a class="sourceLine" id="cb14-20" title="20"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co">#&gt; EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#&gt; Table 1: Intrinsic resistance in Enterobacteriaceae (1344 changes)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#&gt; Table 1: Intrinsic resistance in Enterobacteriaceae (1315 changes)</span></a>
<a class="sourceLine" id="cb14-23" title="23"><span class="co">#&gt; Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-24" title="24"><span class="co">#&gt; Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 4: Intrinsic resistance in Gram-positive bacteria (2767 changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 4: Intrinsic resistance in Gram-positive bacteria (2799 changes)</span></a>
<a class="sourceLine" id="cb14-26" title="26"><span class="co">#&gt; Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb14-27" title="27"><span class="co">#&gt; Table 9: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co">#&gt; Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)</span></a>
@ -462,9 +462,9 @@
<a class="sourceLine" id="cb14-38" title="38"><span class="co">#&gt; Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb14-39" title="39"><span class="co">#&gt; Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<a class="sourceLine" id="cb14-40" title="40"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#&gt; =&gt; EUCAST rules affected 7,383 out of 20,000 rows</span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#&gt; =&gt; EUCAST rules affected 7,488 out of 20,000 rows</span></a>
<a class="sourceLine" id="cb14-42" title="42"><span class="co">#&gt; -&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#&gt; -&gt; changed 4,111 test results (0 to S; 0 to I; 4,111 to R)</span></a></code></pre></div>
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#&gt; -&gt; changed 4,114 test results (0 to S; 0 to I; 4,114 to R)</span></a></code></pre></div>
</div>
<div id="adding-new-variables" class="section level1">
<h1 class="hasAnchor">
@ -489,7 +489,7 @@
<a class="sourceLine" id="cb16-3" title="3"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb16-4" title="4"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
<a class="sourceLine" id="cb16-5" title="5"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#&gt; =&gt; Found 5,676 first isolates (28.4% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#&gt; =&gt; Found 5,688 first isolates (28.4% of total)</span></a></code></pre></div>
<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb17-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
@ -516,19 +516,19 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-20</td>
<td align="center">L10</td>
<td align="center">2010-04-01</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-26</td>
<td align="center">L10</td>
<td align="center">2010-04-30</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -538,10 +538,10 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-05-05</td>
<td align="center">L10</td>
<td align="center">2010-10-12</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -549,19 +549,19 @@
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-20</td>
<td align="center">L10</td>
<td align="center">2010-12-05</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-10</td>
<td align="center">L10</td>
<td align="center">2011-01-19</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -571,21 +571,21 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-08-01</td>
<td align="center">L10</td>
<td align="center">2011-04-07</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-08-27</td>
<td align="center">L10</td>
<td align="center">2011-06-16</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -593,19 +593,19 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-09-09</td>
<td align="center">L10</td>
<td align="center">2011-07-16</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-09-26</td>
<td align="center">L10</td>
<td align="center">2011-08-25</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -615,18 +615,18 @@
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-10-11</td>
<td align="center">L10</td>
<td align="center">2011-09-11</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb19-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">keyab =</span> <span class="kw"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(.)) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -637,7 +637,7 @@
<a class="sourceLine" id="cb19-7" title="7"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb19-8" title="8"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
<a class="sourceLine" id="cb19-9" title="9"><span class="co">#&gt; [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#&gt; =&gt; Found 15,767 first weighted isolates (78.8% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#&gt; =&gt; Found 15,948 first weighted isolates (79.7% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -654,56 +654,80 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-20</td>
<td align="center">L10</td>
<td align="center">2010-04-01</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-03-26</td>
<td align="center">L10</td>
<td align="center">2010-04-30</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-05-05</td>
<td align="center">L10</td>
<td align="center">2010-10-12</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-20</td>
<td align="center">L10</td>
<td align="center">2010-12-05</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2011-01-19</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2011-04-07</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-10</td>
<td align="center">L10</td>
<td align="center">7</td>
<td align="center">2011-06-16</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -713,21 +737,21 @@
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-08-01</td>
<td align="center">L10</td>
<td align="center">8</td>
<td align="center">2011-07-16</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-08-27</td>
<td align="center">L10</td>
<td align="center">9</td>
<td align="center">2011-08-25</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
@ -737,48 +761,24 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-09-09</td>
<td align="center">L10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-09-26</td>
<td align="center">L10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-10-11</td>
<td align="center">L10</td>
<td align="center">2011-09-11</td>
<td align="center">K1</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Instead of 1, now 4 isolates are flagged. In total, 78.8% of all isolates are marked ‘first weighted’ - 50.5% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 2, now 7 isolates are flagged. In total, 79.7% of all isolates are marked ‘first weighted’ - 51.3% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb20-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
<p>So we end up with 15,767 isolates for analysis.</p>
<p>So we end up with 15,948 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
@ -786,6 +786,7 @@
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(data_1st)</a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -802,90 +803,96 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-01-23</td>
<td align="center">E2</td>
<td>1</td>
<td align="center">2011-03-23</td>
<td align="center">H4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>2</td>
<td align="center">2016-02-07</td>
<td align="center">A10</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>5</td>
<td align="center">2016-03-20</td>
<td align="center">X10</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>7</td>
<td align="center">2015-08-01</td>
<td align="center">Q4</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-12-07</td>
<td align="center">L8</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-07-19</td>
<td align="center">W5</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-11-26</td>
<td align="center">L7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-01-24</td>
<td align="center">M7</td>
<td align="center">Hospital B</td>
<td>8</td>
<td align="center">2012-03-10</td>
<td align="center">Z10</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-11-13</td>
<td align="center">V10</td>
<td align="center">Hospital A</td>
<td>11</td>
<td align="center">2014-10-21</td>
<td align="center">G8</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -908,9 +915,9 @@
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(data_1st<span class="op">$</span>genus, data_1st<span class="op">$</span>species))</a></code></pre></div>
<p>Or can be used like the <code>dplyr</code> way, which is easier readable:</p>
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,767 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,948 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,767 (of which NA: 0 = 0.00%)<br>
Length: 15,948 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -927,33 +934,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,762</td>
<td align="right">49.2%</td>
<td align="right">7,762</td>
<td align="right">49.2%</td>
<td align="right">7,952</td>
<td align="right">49.9%</td>
<td align="right">7,952</td>
<td align="right">49.9%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">4,014</td>
<td align="right">25.5%</td>
<td align="right">11,776</td>
<td align="right">74.7%</td>
<td align="right">3,886</td>
<td align="right">24.4%</td>
<td align="right">11,838</td>
<td align="right">74.2%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,450</td>
<td align="right">15.5%</td>
<td align="right">14,226</td>
<td align="right">90.2%</td>
<td align="right">2,509</td>
<td align="right">15.7%</td>
<td align="right">14,347</td>
<td align="right">90.0%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,541</td>
<td align="right">9.8%</td>
<td align="right">15,767</td>
<td align="right">1,601</td>
<td align="right">10.0%</td>
<td align="right">15,948</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -964,7 +971,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code><a href="../reference/portion.html">portion_R()</a></code>, <code>portion_RI()</code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code>portion_IS()</code> and <code><a href="../reference/portion.html">portion_S()</a></code> can be used to determine the portion of a specific antimicrobial outcome. They can be used on their own:</p>
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_IR</a></span>(amox)</a>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4762479</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4812516</span></a></code></pre></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb26-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -977,19 +984,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4717496</td>
<td align="center">0.4801481</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4754662</td>
<td align="center">0.4811895</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4748170</td>
<td align="center">0.4707087</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4854430</td>
<td align="center">0.4915144</td>
</tr>
</tbody>
</table>
@ -1007,23 +1014,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4717496</td>
<td align="center">4761</td>
<td align="center">0.4801481</td>
<td align="center">4861</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4754662</td>
<td align="center">5523</td>
<td align="center">0.4811895</td>
<td align="center">5582</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4748170</td>
<td align="center">2323</td>
<td align="center">0.4707087</td>
<td align="center">2441</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4854430</td>
<td align="center">3160</td>
<td align="center">0.4915144</td>
<td align="center">3064</td>
</tr>
</tbody>
</table>
@ -1043,27 +1050,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7333162</td>
<td align="center">0.9035043</td>
<td align="center">0.9748776</td>
<td align="center">0.7282445</td>
<td align="center">0.9031690</td>
<td align="center">0.9756036</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.7352369</td>
<td align="center">0.9104478</td>
<td align="center">0.9733939</td>
<td align="center">0.7270456</td>
<td align="center">0.9000625</td>
<td align="center">0.9787633</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7416542</td>
<td align="center">0.9160438</td>
<td align="center">0.9763328</td>
<td align="center">0.7220793</td>
<td align="center">0.9184251</td>
<td align="center">0.9796706</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.7473469</td>
<td align="center">0.7182144</td>
<td align="center">0.0000000</td>
<td align="center">0.7473469</td>
<td align="center">0.7182144</td>
</tr>
</tbody>
</table>

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@ -40,7 +40,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

4
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@ -40,7 +40,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to use the <em>G</em>-test</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>G_test.Rmd</code></div>

4
docs/articles/SPSS.html
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@ -40,7 +40,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">09 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>SPSS.Rmd</code></div>

38
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@ -40,7 +40,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@ -227,17 +227,17 @@
<a class="sourceLine" id="cb3-3" title="3"><span class="st"> </span><span class="co"># get microbial ID based on given organism</span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">mo =</span> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(Organism)) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb3-5" title="5"><span class="st"> </span><span class="co"># transform everything from "AMP_ND10" to "CIP_EE" to the new `rsi` class</span></a>
<a class="sourceLine" id="cb3-6" title="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(AMP_ND10<span class="op">:</span>CIP_EE), as.rsi)</a></code></pre></div>
<a class="sourceLine" id="cb3-6" title="6"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html">mutate_at</a></span>(<span class="kw"><a href="https://dplyr.tidyverse.org/reference/vars.html">vars</a></span>(AMP_ND10<span class="op">:</span>CIP_EE), as.rsi)</a></code></pre></div>
<p>No errors or warnings, so all values are transformed succesfully. Let’s check it though, with a couple of frequency tables:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co"># our newly created `mo` variable</span></a>
<a class="sourceLine" id="cb4-2" title="2">data <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(mo, <span class="dt">nmax =</span> <span class="dv">10</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>mo</code> from a <code>data.frame</code> (500 x 54)</strong></p>
<p>Class: <code>mo</code> (<code>character</code>)<br>
Length: 500 (of which NA: 0 = 0.00%)<br>
Unique: 39</p>
<p>Families: 9<br>
Genera: 16<br>
Species: 36</p>
Unique: 37</p>
<p>Families: 10<br>
Genera: 17<br>
Species: 35</p>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
@ -258,7 +258,7 @@ Species: 36</p>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">B_STPHY_CNS</td>
<td align="left">B_STPHY</td>
<td align="right">74</td>
<td align="right">14.8%</td>
<td align="right">319</td>
@ -314,23 +314,23 @@ Species: 36</p>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="left">B_ENTRB_CLO</td>
<td align="right">5</td>
<td align="right">1.0%</td>
<td align="right">439</td>
<td align="right">87.8%</td>
<td align="left">B_STRPT</td>
<td align="right">8</td>
<td align="right">1.6%</td>
<td align="right">442</td>
<td align="right">88.4%</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="left">B_ENTRC</td>
<td align="right">4</td>
<td align="right">0.8%</td>
<td align="right">443</td>
<td align="right">88.6%</td>
<td align="left">B_ENTRB_CLO</td>
<td align="right">5</td>
<td align="right">1.0%</td>
<td align="right">447</td>
<td align="right">89.4%</td>
</tr>
</tbody>
</table>
<p>(omitted 29 entries, n = 57 [11.4%])</p>
<p>(omitted 27 entries, n = 53 [10.6%])</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"></a>
<a class="sourceLine" id="cb5-2" title="2"><span class="co"># our transformed antibiotic columns</span></a>
<a class="sourceLine" id="cb5-3" title="3"><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></a>

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@ -40,7 +40,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to get properties of an antibiotic</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>atc_property.Rmd</code></div>

99
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@ -40,7 +40,7 @@
</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="Released version">0.5.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">12 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -215,33 +215,33 @@
<a class="sourceLine" id="cb2-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. aureus"</span>),</a>
<a class="sourceLine" id="cb2-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Staphylococcus aureus"</span>),</a>
<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb2-9" title="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-10" title="10"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-11" title="11"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; as.mo("sau") 16.70 16.8 25.70 17.00 19.60 59.7 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 39.10 39.2 43.70 39.30 40.60 80.4 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 16.70 16.8 24.60 17.00 18.20 58.9 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("STAAUR") 16.70 16.7 22.70 16.80 17.20 74.5 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 29.70 29.7 46.70 29.80 71.30 110.0 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 29.60 29.7 36.10 29.70 33.10 83.7 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 7.03 7.1 7.14 7.14 7.17 7.3 10</span></a></code></pre></div>
<a class="sourceLine" id="cb2-11" title="11"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" title="12"><span class="co">#&gt; as.mo("sau") 17.0 17.0 22.0 17.0 19.0 59.0 10</span></a>
<a class="sourceLine" id="cb2-13" title="13"><span class="co">#&gt; as.mo("stau") 41.0 41.0 46.0 41.0 44.0 83.0 10</span></a>
<a class="sourceLine" id="cb2-14" title="14"><span class="co">#&gt; as.mo("staaur") 17.0 17.0 26.0 17.0 18.0 74.0 10</span></a>
<a class="sourceLine" id="cb2-15" title="15"><span class="co">#&gt; as.mo("STAAUR") 17.0 17.0 29.0 17.0 52.0 62.0 10</span></a>
<a class="sourceLine" id="cb2-16" title="16"><span class="co">#&gt; as.mo("S. aureus") 31.0 31.0 32.0 31.0 32.0 32.0 10</span></a>
<a class="sourceLine" id="cb2-17" title="17"><span class="co">#&gt; as.mo("S. aureus") 31.0 31.0 48.0 32.0 73.0 110.0 10</span></a>
<a class="sourceLine" id="cb2-18" title="18"><span class="co">#&gt; as.mo("Staphylococcus aureus") 7.4 7.4 7.7 7.4 8.2 8.6 10</span></a></code></pre></div>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
<a class="sourceLine" id="cb3-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"THEISL"</span>),</a>
<a class="sourceLine" id="cb3-3" title="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Thermus islandicus"</span>),</a>
<a class="sourceLine" id="cb3-6" title="6"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb3-2" title="2"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"THEISL"</span>),</a>
<a class="sourceLine" id="cb3-3" title="3"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-4" title="4"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb3-5" title="5"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"Thermus islandicus"</span>),</a>
<a class="sourceLine" id="cb3-6" title="6"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb3-8" title="8"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" title="9"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#&gt; as.mo("theisl") 417.0 419.0 450.0 460.0 464.0 474 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("THEISL") 415.0 416.0 443.0 458.0 460.0 468 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("T. islandicus") 281.0 281.0 299.0 285.0 325.0 352 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("T. islandicus") 292.0 298.0 341.0 336.0 340.0 495 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("Thermus islandicus") 66.2 66.5 75.5 66.9 68.2 112 10</span></a></code></pre></div>
<p>That takes 10.9 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<a class="sourceLine" id="cb3-9" title="9"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" title="10"><span class="co">#&gt; as.mo("theisl") 420 430 450 470 470 470 10</span></a>
<a class="sourceLine" id="cb3-11" title="11"><span class="co">#&gt; as.mo("THEISL") 420 440 480 470 480 680 10</span></a>
<a class="sourceLine" id="cb3-12" title="12"><span class="co">#&gt; as.mo("T. islandicus") 290 290 310 300 330 350 10</span></a>
<a class="sourceLine" id="cb3-13" title="13"><span class="co">#&gt; as.mo("T. islandicus") 300 300 330 330 350 350 10</span></a>
<a class="sourceLine" id="cb3-14" title="14"><span class="co">#&gt; as.mo("Thermus islandicus") 67 67 86 68 110 120 10</span></a></code></pre></div>
<p>That takes 11 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is very uncommon):</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
<a class="sourceLine" id="cb4-2" title="2"></a>
@ -251,12 +251,15 @@
<a class="sourceLine" id="cb4-6" title="6"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"T. islandicus"</span>),</a>
<a class="sourceLine" id="cb4-7" title="7"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"P. brevis"</span>),</a>
<a class="sourceLine" id="cb4-8" title="8"> <span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>),</a>
<a class="sourceLine" id="cb4-9" title="9"> <span class="dt">times =</span> <span class="dv">50</span>),</a>
<a class="sourceLine" id="cb4-9" title="9"> <span class="dt">times =</span> <span class="dv">10</span>),</a>
<a class="sourceLine" id="cb4-10" title="10"> <span class="dt">horizontal =</span> <span class="ot">TRUE</span>, <span class="dt">las =</span> <span class="dv">1</span>, <span class="dt">unit =</span> <span class="st">"s"</span>, <span class="dt">log =</span> <span class="ot">FALSE</span>,</a>
<a class="sourceLine" id="cb4-11" title="11"> <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylab =</span> <span class="st">"Time in seconds"</span>,</a>
<a class="sourceLine" id="cb4-11" title="11"> <span class="dt">xlab =</span> <span class="st">""</span>, <span class="dt">ylab =</span> <span class="st">"Time in seconds"</span>, <span class="dt">ylim =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="fl">0.5</span>),</a>
<a class="sourceLine" id="cb4-12" title="12"> <span class="dt">main =</span> <span class="st">"Benchmarks per prevalence"</span>)</a></code></pre></div>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-5-1.png" width="720"></p>
<p>Uncommon microorganisms take a lot more time than common microorganisms. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
<p>In reality, the <code><a href="../reference/as.mo.html">as.mo()</a></code> functions <strong>learns from its own output to speed up determinations for next times</strong>. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use <code><a href="../reference/as.mo.html">as.mo()</a></code> yourself:</p>
<p><img src="benchmarks_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
<p>The highest outliers are the first times. All next determinations were done in only thousands of seconds.</p>
<p>Still, uncommon microorganisms take a lot more time than common microorganisms, especially the first time. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: <strong>repetitive results</strong> and <strong>already precalculated results</strong>.</p>
<div id="repetitive-results" class="section level3">
<h3 class="hasAnchor">
<a href="#repetitive-results" class="anchor"></a>Repetitive results</h3>
@ -286,9 +289,9 @@
<a class="sourceLine" id="cb5-23" title="23"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb5-24" title="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-25" title="25"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-26" title="26"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" title="27"><span class="co">#&gt; mo_fullname(x) 794 834 863 844 876 1050 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.84 seconds (844 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb5-26" title="26"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" title="27"><span class="co">#&gt; mo_fullname(x) 738 813 847 819 921 975 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.82 seconds (818 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -301,9 +304,9 @@
<a class="sourceLine" id="cb6-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-6" title="6"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-7" title="7"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#&gt; A 10.900 11.100 11.200 11.200 11.300 11.400 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 27.300 27.900 28.300 28.000 28.100 31.500 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.319 0.326 0.472 0.563 0.568 0.579 10</span></a></code></pre></div>
<a class="sourceLine" id="cb6-8" title="8"><span class="co">#&gt; A 11.000 11.100 15.700 11.300 11.400 52.900 10</span></a>
<a class="sourceLine" id="cb6-9" title="9"><span class="co">#&gt; B 28.700 28.900 29.400 29.200 29.500 30.500 10</span></a>
<a class="sourceLine" id="cb6-10" title="10"><span class="co">#&gt; C 0.322 0.556 0.523 0.568 0.581 0.586 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0006 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="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb7-2" title="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
@ -317,14 +320,14 @@
<a class="sourceLine" id="cb7-10" title="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-11" title="11"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-12" title="12"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#&gt; A 0.308 0.332 0.396 0.393 0.457 0.498 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.349 0.376 0.419 0.444 0.462 0.467 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.351 0.398 0.529 0.555 0.628 0.702 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.302 0.330 0.378 0.381 0.424 0.465 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.282 0.329 0.371 0.374 0.384 0.539 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.281 0.354 0.364 0.366 0.402 0.444 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.275 0.309 0.347 0.351 0.380 0.420 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.279 0.306 0.356 0.363 0.404 0.411 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-13" title="13"><span class="co">#&gt; A 0.314 0.339 0.399 0.380 0.460 0.507 10</span></a>
<a class="sourceLine" id="cb7-14" title="14"><span class="co">#&gt; B 0.347 0.387 0.455 0.402 0.493 0.684 10</span></a>
<a class="sourceLine" id="cb7-15" title="15"><span class="co">#&gt; C 0.429 0.505 0.566 0.588 0.656 0.660 10</span></a>
<a class="sourceLine" id="cb7-16" title="16"><span class="co">#&gt; D 0.321 0.340 0.383 0.367 0.412 0.490 10</span></a>
<a class="sourceLine" id="cb7-17" title="17"><span class="co">#&gt; E 0.303 0.328 0.369 0.379 0.403 0.449 10</span></a>
<a class="sourceLine" id="cb7-18" title="18"><span class="co">#&gt; F 0.251 0.323 0.346 0.348 0.391 0.400 10</span></a>
<a class="sourceLine" id="cb7-19" title="19"><span class="co">#&gt; G 0.286 0.305 0.345 0.338 0.389 0.398 10</span></a>
<a class="sourceLine" id="cb7-20" title="20"><span class="co">#&gt; H 0.272 0.297 0.355 0.338 0.427 0.450 10</span></a></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> too, 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">
@ -351,13 +354,13 @@
<a class="sourceLine" id="cb8-18" title="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb8-19" title="19"><span class="co">#&gt; Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-20" title="20"><span class="co">#&gt; expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#&gt; en 16.61 17.17 17.23 17.28 17.38 17.56 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 28.83 28.85 29.31 29.50 29.63 29.67 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 29.08 29.44 33.71 29.65 29.72 71.15 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 28.86 29.52 38.07 29.70 30.60 72.14 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 28.71 29.48 34.04 29.63 31.28 71.09 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 29.32 29.47 41.44 29.53 62.86 73.16 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 29.05 29.43 33.93 29.62 30.93 71.00 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-21" title="21"><span class="co">#&gt; en 18.05 18.11 19.33 18.25 18.65 25.12 10</span></a>
<a class="sourceLine" id="cb8-22" title="22"><span class="co">#&gt; de 30.15 30.84 43.57 31.08 72.47 73.96 10</span></a>
<a class="sourceLine" id="cb8-23" title="23"><span class="co">#&gt; nl 30.30 30.63 34.96 30.71 30.73 73.40 10</span></a>
<a class="sourceLine" id="cb8-24" title="24"><span class="co">#&gt; es 30.24 30.49 31.39 30.97 32.20 33.68 10</span></a>
<a class="sourceLine" id="cb8-25" title="25"><span class="co">#&gt; it 30.53 30.71 31.18 30.83 31.71 32.38 10</span></a>
<a class="sourceLine" id="cb8-26" title="26"><span class="co">#&gt; fr 29.64 30.49 35.32 30.84 32.25 73.00 10</span></a>
<a class="sourceLine" id="cb8-27" title="27"><span class="co">#&gt; pt 30.73 30.81 39.47 31.09 32.29 73.25 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
</div>

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</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>freq.Rmd</code></div>

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</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="Released version">0.5.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
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</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to get properties of a microorganism</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>mo_property.Rmd</code></div>

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</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">05 March 2019</h4>
<h4 class="date">15 March 2019</h4>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>

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</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="Released version">0.5.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
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2
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@ -42,7 +42,7 @@
</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="Released version">0.5.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
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</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="Released version">0.5.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -349,8 +349,8 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li>Function <code><a href="../reference/AMR-deprecated.html">guess_atc()</a></code> is now deprecated in favour of <code><a href="../reference/as.atc.html">as.atc()</a></code> and will be removed in future versions</li>
<li>Improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:
<ul>
<li>Now handles incorrect spelling like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</li>
</ul>
<li>
<p>Now handles incorrect spelling, like <code>i</code> instead of <code>y</code> and <code>f</code> instead of <code>ph</code>:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
<a class="sourceLine" id="cb7-2" title="2"></a>
<a class="sourceLine" id="cb7-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
@ -358,9 +358,9 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<a class="sourceLine" id="cb7-5" title="5"></a>
<a class="sourceLine" id="cb7-6" title="6"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. klossi"</span>)</a>
<a class="sourceLine" id="cb7-7" title="7"><span class="co">#&gt; [1] "Staphylococcus kloosii"</span></a></code></pre></div>
<ul>
<li>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</li>
</ul>
</li>
<li>
<p>Uncertainty of the algorithm is now divided into four levels, 0 to 3, where the default <code>allow_uncertain = TRUE</code> is equal to uncertainty level 2. Run <code><a href="../reference/as.mo.html">?as.mo</a></code> for more info about these levels.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="co"># equal:</span></a>
<a class="sourceLine" id="cb8-2" title="2"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">TRUE</span>)</a>
<a class="sourceLine" id="cb8-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">2</span>)</a>
@ -368,15 +368,15 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<a class="sourceLine" id="cb8-5" title="5"><span class="co"># also equal:</span></a>
<a class="sourceLine" id="cb8-6" title="6"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="ot">FALSE</span>)</a>
<a class="sourceLine" id="cb8-7" title="7"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(..., <span class="dt">allow_uncertain =</span> <span class="dv">0</span>)</a></code></pre></div>
Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.
<ul>
<li>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</li>
</ul>
Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</li>
<li>All microbial IDs that are found with zero uncertainty are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code><a href="../reference/as.mo.html">clean_mo_history()</a></code> to delete this file, which resets the algorithms.</li>
<li>
<p>Incoercible results will now be considered ‘unknown’, MO code <code>UNKNOWN</code>. On foreign systems, properties of these will be translated to all languages already previously supported: German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"qwerty"</span>, <span class="dt">language =</span> <span class="st">"es"</span>)</a>
<a class="sourceLine" id="cb9-2" title="2"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb9-3" title="3"><span class="co"># one unique value (^= 100.0%) could not be coerced and is considered 'unknown': "qwerty". Use mo_failures() to review it.</span></a>
<a class="sourceLine" id="cb9-4" title="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div>
<ul>
</li>
<li>Fix for vector containing only empty values</li>
<li>Finds better results when input is in other languages</li>
<li>Better handling for subspecies</li>

2
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/AMR.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/WHOCC.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/WHONET.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/abname.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/age.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/age_groups.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/antibiotics.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/as.atc.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/as.mic.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

18
docs/reference/as.mo.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -242,7 +242,7 @@
</div>
<pre class="usage"><span class='fu'>as.mo</span>(<span class='no'>x</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>())
<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>(), <span class='no'>...</span>)
<span class='fu'>is.mo</span>(<span class='no'>x</span>)
@ -250,7 +250,9 @@
<span class='fu'>mo_uncertainties</span>()
<span class='fu'>mo_renamed</span>()</pre>
<span class='fu'>mo_renamed</span>()
<span class='fu'>clean_mo_history</span>()</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -277,6 +279,10 @@
<th>reference_df</th>
<td><p>a <code>data.frame</code> to use for extra reference when translating <code>x</code> to a valid <code>mo</code>. See <code><a href='mo_source.html'>set_mo_source</a></code> and <code><a href='mo_source.html'>get_mo_source</a></code> to automate the usage of your own codes (e.g. used in your analysis or organisation).</p></td>
</tr>
<tr>
<th>...</th>
<td><p>other parameters passed on to functions</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@ -285,7 +291,8 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>A microbial ID from this package (class: <code>mo</code>) typically looks like these examples:<br /></p><pre>
<p><strong>General info</strong> <br />
A microbial ID from this package (class: <code>mo</code>) typically looks like these examples:<br /></p><pre>
Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
@ -300,7 +307,8 @@
F (Fungi), P (Protozoa), PL (Plantae) or V (Viruses)
</pre>
<p>Values that cannot be coered will be considered 'unknown' and have an MO code <code>UNKNOWN</code>.</p>
<p>Use the <code><a href='mo_property.html'>mo_property</a></code> functions to get properties based on the returned code, see Examples.</p>
<p>Use the <code><a href='mo_property.html'>mo_property</a>_*</code> functions to get properties based on the returned code, see Examples.</p>
<p>All IDs that are found with zero uncertainty are saved to a local file (<code>"~/.Rhistory_mo"</code>) to improve speed for every next time. Use <code>clean_mo_history()</code> to delete this file, which resets the algorithms. Only previous results will be used from this version of the <code>AMR</code> package, since the taxonomic tree may change in the future for any organism.</p>
<p><strong>Intelligent rules</strong> <br />
This function uses intelligent rules to help getting fast and logical results. It tries to find matches in this order:</p><ul>
<li><p>Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations</p></li>

6
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -294,12 +294,12 @@
<span class='co'># using dplyr's mutate</span>
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_at</a></span>(<span class='fu'><a href='https://dplyr.tidyverse.org/reference/vars.html'>vars</a></span>(<span class='no'>peni</span>:<span class='no'>rifa</span>), <span class='no'>as.rsi</span>)
<span class='co'># fastest way to transform all columns with already valid AB results to class `rsi`:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/summarise_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span>(<span class='no'>is.rsi.eligible</span>,
<span class='no'>as.rsi</span>)
<span class='co'># default threshold of `is.rsi.eligible` is 5%.</span>

2
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/atc_property.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/availability.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/catalogue_of_life.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/count.html
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/eucast_rules.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/filter_ab_class.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/first_isolate.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/freq.html
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@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/g.test.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/get_locale.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/ggplot_rsi.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

2
docs/reference/guess_ab_col.html
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@ -80,7 +80,7 @@
</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="Released version">0.5.0.9021</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>

19
docs/reference/index.html
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@ -78,7 +78,7 @@
</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="Released version">0.5.0.9022</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9023</span>
</span>
</div>
@ -293,7 +293,7 @@
</tr><tr>
<td>
<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> </p>
<p><code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> <code><a href="as.mo.html">clean_mo_history()</a></code> </p>
</td>
<td><p>Transform to microorganism ID</p></td>
</tr><tr>
@ -522,7 +522,7 @@
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-other" class="hasAnchor"><a href="#section-other" class="anchor"></a>Other</h2>
<h2 id="section-other-functions" class="hasAnchor"><a href="#section-other-functions" class="anchor"></a>Other functions</h2>
<p class="section-desc"><p>These functions are mostly for internal use, but some of them may also be suitable for your analysis. Especially the ‘like’ function can be useful: <code>if (x %like% y) {...}</code>.</p></p>
</th>
</tr>
@ -538,7 +538,15 @@
<p><code><a href="like.html">like()</a></code> <code><a href="like.html">`%like%`</a></code> </p>
</td>
<td><p>Pattern Matching</p></td>
</tr><tr>
</tr>
</tbody><tbody>
<tr>
<th colspan="2">
<h2 id="section-deprecated-functions" class="hasAnchor"><a href="#section-deprecated-functions" class="anchor"></a>Deprecated functions</h2>
<p class="section-desc"><p>These functions are deprecated, meaning that they still work but show a warning with every use and will be removed in a future version.</p></p>
</th>
</tr>
<tr>
<td>
<p><code><a href="AMR-deprecated.html">ratio()</a></code> <code><a href="AMR-deprecated.html">guess_mo()</a></code> <code><a href="AMR-deprecated.html">guess_atc()</a></code> <code><a href="AMR-deprecated.html">ab_property()</a></code> <code><a href="AMR-deprecated.html">ab_atc()</a></code> <code><a href="AMR-deprecated.html">ab_official()</a></code> <code><a href="AMR-deprecated.html">ab_name()</a></code> <code><a href="AMR-deprecated.html">ab_trivial_nl()</a></code> <code><a href="AMR-deprecated.html">ab_certe()</a></code> <code><a href="AMR-deprecated.html">ab_umcg()</a></code> <code><a href="AMR-deprecated.html">ab_tradenames()</a></code> <code><a href="AMR-deprecated.html">atc_ddd()</a></code> <code><a href="AMR-deprecated.html">atc_groups()</a></code> </p>
@ -557,7 +565,8 @@
<li><a href="#section-adding-variables-to-your-data">Adding variables to your data</a></li>
<li><a href="#section-analysing-your-data">Analysing your data</a></li>
<li><a href="#section-included-data-sets">Included data sets</a></li>
<li><a href="#section-other">Other</a></li>
<li><a href="#section-other-functions">Other functions</a></li>
<li><a href="#section-deprecated-functions">Deprecated functions</a></li>
</ul>
</div>
</div>

2
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@ -80,7 +80,7 @@
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</span>
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@ -80,7 +80,7 @@
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@ -80,7 +80,7 @@
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@ -80,7 +80,7 @@
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2
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@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
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@ -80,7 +80,7 @@
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@ -80,7 +80,7 @@
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@ -80,7 +80,7 @@
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@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
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14
man/as.mo.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mo.R
% Please edit documentation in R/mo.R, R/mo_history.R
\name{as.mo}
\alias{as.mo}
\alias{mo}
@ -7,10 +7,11 @@
\alias{mo_failures}
\alias{mo_uncertainties}
\alias{mo_renamed}
\alias{clean_mo_history}
\title{Transform to microorganism ID}
\usage{
as.mo(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
reference_df = get_mo_source())
reference_df = get_mo_source(), ...)
is.mo(x)
@ -19,6 +20,8 @@ mo_failures()
mo_uncertainties()
mo_renamed()
clean_mo_history()
}
\arguments{
\item{x}{a character vector or a \code{data.frame} with one or two columns}
@ -34,6 +37,8 @@ mo_renamed()
\item{allow_uncertain}{a logical (\code{TRUE} or \code{FALSE}) or a value between 0 and 3 to indicate whether the input should be checked for less possible results, see Details}
\item{reference_df}{a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. See \code{\link{set_mo_source}} and \code{\link{get_mo_source}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
\item{...}{other parameters passed on to functions}
}
\value{
Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
@ -42,6 +47,7 @@ Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
Use this function to determine a valid microorganism ID (\code{mo}). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea, Viruses, and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), an abbreviation known in the field (like \code{"MRSA"}), or just a genus. Please see Examples.
}
\details{
\strong{General info} \cr
A microbial ID from this package (class: \code{mo}) typically looks like these examples:\cr
\preformatted{
Code Full name
@ -60,7 +66,9 @@ A microbial ID from this package (class: \code{mo}) typically looks like these e
Values that cannot be coered will be considered 'unknown' and have an MO code \code{UNKNOWN}.
Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
Use the \code{\link{mo_property}_*} functions to get properties based on the returned code, see Examples.
All IDs that are found with zero uncertainty are saved to a local file (\code{"~/.Rhistory_mo"}) to improve speed for every next time. Use \code{clean_mo_history()} to delete this file, which resets the algorithms. Only previous results will be used from this version of the \code{AMR} package, since the taxonomic tree may change in the future for any organism.
\strong{Intelligent rules} \cr
This function uses intelligent rules to help getting fast and logical results. It tries to find matches in this order:

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34
tests/testthat/test-mo_history.R Normal file
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@ -0,0 +1,34 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
context("mo_history.R")
test_that("mo_history works", {
clean_mo_history()
expect_equal(read_mo_history(force = TRUE),
NULL)
set_mo_history("testsubject", "B_ESCHR_COL", force = TRUE)
expect_equal(get_mo_history("testsubject", force = TRUE),
"B_ESCHR_COL")
expect_equal(colnames(read_mo_history(force = TRUE)),
c("x", "mo"))
})

40
vignettes/benchmarks.Rmd
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@ -49,7 +49,7 @@ S.aureus <- microbenchmark(as.mo("sau"),
as.mo("S. aureus"),
as.mo("Staphylococcus aureus"),
times = 10)
print(S.aureus, unit = "ms", signif = 3)
print(S.aureus, unit = "ms", signif = 2)
```
In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.
@ -58,12 +58,12 @@ To achieve this speed, the `as.mo` function also takes into account the prevalen
```{r}
T.islandicus <- microbenchmark(as.mo("theisl"),
as.mo("THEISL"),
as.mo("T. islandicus"),
as.mo("T. islandicus"),
as.mo("Thermus islandicus"),
times = 10)
print(T.islandicus, unit = "ms", signif = 3)
as.mo("THEISL"),
as.mo("T. islandicus"),
as.mo("T. islandicus"),
as.mo("Thermus islandicus"),
times = 10)
print(T.islandicus, unit = "ms", signif = 2)
```
That takes `r round(mean(T.islandicus$time, na.rm = TRUE) / mean(S.aureus$time, na.rm = TRUE), 1)` times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like *Thermus islandicus*) are almost fast - these are the most probable input from most data sets.
@ -79,13 +79,33 @@ boxplot(microbenchmark(as.mo("Thermus islandicus"),
as.mo("T. islandicus"),
as.mo("P. brevis"),
as.mo("E. coli"),
times = 50),
times = 10),
horizontal = TRUE, las = 1, unit = "s", log = FALSE,
xlab = "", ylab = "Time in seconds",
xlab = "", ylab = "Time in seconds", ylim = c(0, 0.5),
main = "Benchmarks per prevalence")
```
Uncommon microorganisms take a lot more time than common microorganisms. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: **repetitive results** and **already precalculated results**.
In reality, the `as.mo()` functions **learns from its own output to speed up determinations for next times**. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use `as.mo()` yourself:
```{r, echo = FALSE}
clean_mo_history()
par(mar = c(5, 16, 4, 2))
boxplot(microbenchmark(
'as.mo("Thermus islandicus")' = as.mo("Thermus islandicus", force_mo_history = TRUE),
'as.mo("Prevotella brevis")' = as.mo("Prevotella brevis", force_mo_history = TRUE),
'as.mo("Escherichia coli")' = as.mo("Escherichia coli", force_mo_history = TRUE),
'as.mo("T. islandicus")' = as.mo("T. islandicus", force_mo_history = TRUE),
'as.mo("P. brevis")' = as.mo("P. brevis", force_mo_history = TRUE),
'as.mo("E. coli")' = as.mo("E. coli", force_mo_history = TRUE),
times = 10),
horizontal = TRUE, las = 1, unit = "s", log = FALSE,
xlab = "", ylab = "Time in seconds", ylim = c(0, 0.5),
main = "Benchmarks per prevalence")
```
The highest outliers are the first times. All next determinations were done in only thousands of seconds.
Still, uncommon microorganisms take a lot more time than common microorganisms, especially the first time. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: **repetitive results** and **already precalculated results**.
### Repetitive results