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(v0.7.0.9008) T. vaginalis, rsi_df

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dr. M.S. (Matthijs) Berends
2019-06-13 14:28:46 +02:00
parent 699e87ab4a
commit 254745061c
32 changed files with 382 additions and 259 deletions
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DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.7.0.9007 Version: 0.7.0.9008
Date: 2019-06-12 Date: 2019-06-13
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(
NAMESPACE
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@@ -172,6 +172,7 @@ export(ratio)
export(read.4D) export(read.4D)
export(resistance_predict) export(resistance_predict)
export(right_join_microorganisms) export(right_join_microorganisms)
export(rsi_df)
export(rsi_predict) export(rsi_predict)
export(scale_rsi_colours) export(scale_rsi_colours)
export(scale_type.ab) export(scale_type.ab)
NEWS.md
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@@ -1,6 +1,17 @@
# AMR 0.7.0.9007 # AMR 0.7.0.9008
#### New #### New
* Function `rsi_df()` to transform a `data.frame` to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combinations of existing functions `count_df()` and `portion_df()` to immediately show resistance percentages and number of available isolates:
```r
septic_patients %>%
select(AMX, CIP) %>%
rsi_df()
# antibiotic interpretation value isolates
# 1 Amoxicillin SI 0.4442636 546
# 2 Amoxicillin R 0.5557364 683
# 3 Ciprofloxacin SI 0.8381831 1181
# 4 Ciprofloxacin R 0.1618169 228
```
* Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*: * Support for all scientifically published pathotypes of *E. coli* to date. Supported are: AIEC (Adherent-Invasive *E. coli*), ATEC (Atypical Entero-pathogenic *E. coli*), DAEC (Diffusely Adhering *E. coli*), EAEC (Entero-Aggresive *E. coli*), EHEC (Entero-Haemorrhagic *E. coli*), EIEC (Entero-Invasive *E. coli*), EPEC (Entero-Pathogenic *E. coli*), ETEC (Entero-Toxigenic *E. coli*), NMEC (Neonatal Meningitis‐causing *E. coli*), STEC (Shiga-toxin producing *E. coli*) and UPEC (Uropathogenic *E. coli*). All these lead to the microbial ID of *E. coli*:
```r ```r
as.mo("UPEC") as.mo("UPEC")
@@ -11,6 +22,7 @@
* Function `mo_info()` as an analogy to `ab_info()`. The `mo_info()` prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism * Function `mo_info()` as an analogy to `ab_info()`. The `mo_info()` prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism
#### Changed #### Changed
* Column names of output `count_df()` and `portion_df()` are now lowercase
* Fixed bug in translation of microorganism names * Fixed bug in translation of microorganism names
* Fixed bug in determining taxonomic kingdoms * Fixed bug in determining taxonomic kingdoms
* Algorithm improvements for `as.ab()` and `as.mo()` to understand even more severely misspelled input * Algorithm improvements for `as.ab()` and `as.mo()` to understand even more severely misspelled input
@@ -23,6 +35,7 @@
* Removed `latest_annual_release` from the `catalogue_of_life_version()` function * Removed `latest_annual_release` from the `catalogue_of_life_version()` function
* Removed antibiotic code `PVM1` from the `antibiotics` data set as this was a duplicate of `PME` * Removed antibiotic code `PVM1` from the `antibiotics` data set as this was a duplicate of `PME`
* Fixed bug where not all old taxonomic named would not be printed when using a vector as input for `as.mo()` * Fixed bug where not all old taxonomic named would not be printed when using a vector as input for `as.mo()`
* Manually added *Trichomonas vaginalis* from the kingdom of Protozoa, which is missing from the Catalogue of Life
#### Other #### Other
* Fixed a note thrown by CRAN tests * Fixed a note thrown by CRAN tests
R/ab.R
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@@ -203,7 +203,6 @@ as.ab <- function(x) {
# try by removing all spaces # try by removing all spaces
if (x[i] %like% " ") { if (x[i] %like% " ") {
found <- suppressWarnings(as.ab(gsub(" +", "", x[i]))) found <- suppressWarnings(as.ab(gsub(" +", "", x[i])))
print(found)
if (length(found) > 0 & !is.na(found)) { if (length(found) > 0 & !is.na(found)) {
x_new[i] <- found[1L] x_new[i] <- found[1L]
next next
R/age.R
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@@ -136,6 +136,9 @@ age <- function(x, reference = Sys.Date(), exact = FALSE) {
#' select(age_group, CIP) %>% #' select(age_group, CIP) %>%
#' ggplot_rsi(x = "age_group") #' ggplot_rsi(x = "age_group")
age_groups <- function(x, split_at = c(12, 25, 55, 75)) { age_groups <- function(x, split_at = c(12, 25, 55, 75)) {
if (!is.numeric(x)) {
stop("`x` and must be numeric, not a ", paste0(class(x), collapse = "/"), ".")
}
if (is.character(split_at)) { if (is.character(split_at)) {
split_at <- split_at[1L] split_at <- split_at[1L]
if (split_at %like% "^(child|kid|junior)") { if (split_at %like% "^(child|kid|junior)") {
@@ -148,11 +151,7 @@ age_groups <- function(x, split_at = c(12, 25, 55, 75)) {
split_at <- 1:10 * 10 split_at <- 1:10 * 10
} }
} }
split_at <- as.integer(split_at) split_at <- sort(unique(as.integer(split_at)))
if (!is.numeric(x) | !is.numeric(split_at)) {
stop("`x` and `split_at` must both be numeric.")
}
split_at <- sort(unique(split_at))
if (!split_at[1] == 0) { if (!split_at[1] == 0) {
# add base number 0 # add base number 0
split_at <- c(0, split_at) split_at <- c(0, split_at)
R/count.R
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@@ -29,9 +29,11 @@
#' @inheritSection as.rsi Interpretation of S, I and R #' @inheritSection as.rsi Interpretation of S, I and R
#' @details These functions are meant to count isolates. Use the \code{\link{portion}_*} functions to calculate microbial resistance. #' @details These functions are meant to count isolates. Use the \code{\link{portion}_*} functions to calculate microbial resistance.
#' #'
#' \code{n_rsi} is an alias of \code{count_all}. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to \code{\link{n_distinct}}. Their function is equal to \code{count_S(...) + count_IR(...)}. #' The function \code{n_rsi} is an alias of \code{count_all}. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to \code{\link{n_distinct}}. Their function is equal to \code{count_S(...) + count_IR(...)}.
#' #'
#' \code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}. #' The function \code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of S, I and R. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
#'
#' The function \code{rsi_df} works exactly like \code{count_df}, but add the percentage of S, I and R.
#' @source Wickham H. \strong{Tidy Data.} The Journal of Statistical Software, vol. 59, 2014. \url{http://vita.had.co.nz/papers/tidy-data.html} #' @source Wickham H. \strong{Tidy Data.} The Journal of Statistical Software, vol. 59, 2014. \url{http://vita.had.co.nz/papers/tidy-data.html}
#' @seealso \code{\link{portion}_*} to calculate microbial resistance and susceptibility. #' @seealso \code{\link{portion}_*} to calculate microbial resistance and susceptibility.
#' @keywords resistance susceptibility rsi antibiotics isolate isolates #' @keywords resistance susceptibility rsi antibiotics isolate isolates
R/data.R
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@@ -55,7 +55,7 @@
#' #'
#' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}. #' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}.
#' @inheritSection catalogue_of_life Catalogue of Life #' @inheritSection catalogue_of_life Catalogue of Life
#' @format A \code{\link{data.frame}} with 67,903 observations and 16 variables: #' @format A \code{\link{data.frame}} with 67,906 observations and 16 variables:
#' \describe{ #' \describe{
#' \item{\code{mo}}{ID of microorganism as used by this package} #' \item{\code{mo}}{ID of microorganism as used by this package}
#' \item{\code{col_id}}{Catalogue of Life ID} #' \item{\code{col_id}}{Catalogue of Life ID}
@@ -69,9 +69,10 @@
#' } #' }
#' @details Manually added were: #' @details Manually added were:
#' \itemize{ #' \itemize{
#' \item{9 species of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)} #' \item{9 entries of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
#' \item{2 species of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])} #' \item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
#' \item{3 other undefined (unknown, unknown Gram negatives and unknown Gram positives)} #' \item{3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)}
#' \item{3 other 'undefined' entries (unknown, unknown Gram negatives and unknown Gram positives)}
#' \item{8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life} #' \item{8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life}
#' } #' }
#' @section About the records from DSMZ (see source): #' @section About the records from DSMZ (see source):
R/ggplot_rsi.R
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@@ -24,11 +24,11 @@
#' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}2} functions. #' Use these functions to create bar plots for antimicrobial resistance analysis. All functions rely on internal \code{\link[ggplot2]{ggplot}2} functions.
#' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}}) #' @param data a \code{data.frame} with column(s) of class \code{"rsi"} (see \code{\link{as.rsi}})
#' @param position position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"} #' @param position position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"}
#' @param x variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable #' @param x variable to show on x axis, either \code{"antibiotic"} (default) or \code{"interpretation"} or a grouping variable
#' @param fill variable to categorise using the plots legend, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable #' @param fill variable to categorise using the plots legend, either \code{"antibiotic"} (default) or \code{"interpretation"} or a grouping variable
#' @param breaks numeric vector of positions #' @param breaks numeric vector of positions
#' @param limits numeric vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum #' @param limits numeric vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum
#' @param facet variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable #' @param facet variable to split plots by, either \code{"interpretation"} (default) or \code{"antibiotic"} or a grouping variable
#' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}} #' @param fun function to transform \code{data}, either \code{\link{count_df}} (default) or \code{\link{portion_df}}
#' @inheritParams portion #' @inheritParams portion
#' @param nrow (when using \code{facet}) number of rows #' @param nrow (when using \code{facet}) number of rows
@@ -129,7 +129,7 @@
#' select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>% #' select(hospital_id, AMX, NIT, FOS, TMP, CIP) %>%
#' group_by(hospital_id) %>% #' group_by(hospital_id) %>%
#' ggplot_rsi(x = "hospital_id", #' ggplot_rsi(x = "hospital_id",
#' facet = "Antibiotic", #' facet = "antibiotic",
#' nrow = 1, #' nrow = 1,
#' title = "AMR of Anti-UTI Drugs Per Hospital", #' title = "AMR of Anti-UTI Drugs Per Hospital",
#' x.title = "Hospital", #' x.title = "Hospital",
@@ -150,7 +150,7 @@
#' # group by MO #' # group by MO
#' group_by(bug) %>% #' group_by(bug) %>%
#' # plot the thing, putting MOs on the facet #' # plot the thing, putting MOs on the facet
#' ggplot_rsi(x = "Antibiotic", #' ggplot_rsi(x = "antibiotic",
#' facet = "bug", #' facet = "bug",
#' translate_ab = FALSE, #' translate_ab = FALSE,
#' nrow = 1, #' nrow = 1,
@@ -161,8 +161,8 @@
#' } #' }
ggplot_rsi <- function(data, ggplot_rsi <- function(data,
position = NULL, position = NULL,
x = "Antibiotic", x = "antibiotic",
fill = "Interpretation", fill = "interpretation",
# params = list(), # params = list(),
facet = NULL, facet = NULL,
breaks = seq(0, 1, 0.1), breaks = seq(0, 1, 0.1),
@@ -226,7 +226,7 @@ ggplot_rsi <- function(data,
fun = fun, combine_SI = combine_SI, combine_IR = combine_IR, ...) + fun = fun, combine_SI = combine_SI, combine_IR = combine_IR, ...) +
theme_rsi() theme_rsi()
if (fill == "Interpretation") { if (fill == "interpretation") {
# set RSI colours # set RSI colours
if (isFALSE(colours) & missing(datalabels.colour)) { if (isFALSE(colours) & missing(datalabels.colour)) {
# set datalabel colour to middle gray # set datalabel colour to middle gray
@@ -267,8 +267,8 @@ ggplot_rsi <- function(data,
#' @rdname ggplot_rsi #' @rdname ggplot_rsi
#' @export #' @export
geom_rsi <- function(position = NULL, geom_rsi <- function(position = NULL,
x = c("Antibiotic", "Interpretation"), x = c("antibiotic", "interpretation"),
fill = "Interpretation", fill = "interpretation",
translate_ab = "name", translate_ab = "name",
language = get_locale(), language = get_locale(),
combine_SI = TRUE, combine_SI = TRUE,
@@ -286,7 +286,7 @@ geom_rsi <- function(position = NULL,
if (!fun_name %in% c("portion_df", "count_df", "fun")) { if (!fun_name %in% c("portion_df", "count_df", "fun")) {
stop("`fun` must be portion_df or count_df") stop("`fun` must be portion_df or count_df")
} }
y <- "Value" y <- "value"
if (identical(fun, count_df)) { if (identical(fun, count_df)) {
if (missing(position) | is.null(position)) { if (missing(position) | is.null(position)) {
position <- "fill" position <- "fill"
@@ -312,10 +312,10 @@ geom_rsi <- function(position = NULL,
x <- substr(x, 2, nchar(x) - 1) x <- substr(x, 2, nchar(x) - 1)
} }
if (tolower(x) %in% tolower(c('ab', 'antibiotic', 'abx', 'antibiotics'))) { if (tolower(x) %in% tolower(c('ab', 'abx', 'antibiotics'))) {
x <- "Antibiotic" x <- "antibiotic"
} else if (tolower(x) %in% tolower(c('SIR', 'RSI', 'interpretation', 'interpretations', 'result'))) { } else if (tolower(x) %in% tolower(c('SIR', 'RSI', 'interpretations', 'result'))) {
x <- "Interpretation" x <- "interpretation"
} }
ggplot2::layer(geom = "bar", stat = "identity", position = position, ggplot2::layer(geom = "bar", stat = "identity", position = position,
@@ -332,7 +332,7 @@ geom_rsi <- function(position = NULL,
#' @rdname ggplot_rsi #' @rdname ggplot_rsi
#' @export #' @export
facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) { facet_rsi <- function(facet = c("interpretation", "antibiotic"), nrow = NULL) {
stopifnot_installed_package("ggplot2") stopifnot_installed_package("ggplot2")
@@ -347,10 +347,10 @@ facet_rsi <- function(facet = c("Interpretation", "Antibiotic"), nrow = NULL) {
facet <- substr(facet, 2, nchar(facet) - 1) facet <- substr(facet, 2, nchar(facet) - 1)
} }
if (tolower(facet) %in% tolower(c('SIR', 'RSI', 'interpretation', 'interpretations', 'result'))) { if (tolower(facet) %in% tolower(c('SIR', 'RSI', 'interpretations', 'result'))) {
facet <- "Interpretation" facet <- "interpretation"
} else if (tolower(facet) %in% tolower(c('ab', 'antibiotic', 'abx', 'antibiotics'))) { } else if (tolower(facet) %in% tolower(c('ab', 'abx', 'antibiotics'))) {
facet <- "Antibiotic" facet <- "antibiotic"
} }
ggplot2::facet_wrap(facets = facet, scales = "free_x", nrow = nrow) ggplot2::facet_wrap(facets = facet, scales = "free_x", nrow = nrow)
@@ -408,7 +408,7 @@ theme_rsi <- function() {
#' @importFrom dplyr mutate %>% group_by_at #' @importFrom dplyr mutate %>% group_by_at
#' @export #' @export
labels_rsi_count <- function(position = NULL, labels_rsi_count <- function(position = NULL,
x = "Antibiotic", x = "antibiotic",
translate_ab = "name", translate_ab = "name",
combine_SI = TRUE, combine_SI = TRUE,
combine_IR = FALSE, combine_IR = FALSE,
@@ -424,7 +424,7 @@ labels_rsi_count <- function(position = NULL,
x_name <- x x_name <- x
ggplot2::geom_text(mapping = ggplot2::aes_string(label = "lbl", ggplot2::geom_text(mapping = ggplot2::aes_string(label = "lbl",
x = x, x = x,
y = "Value"), y = "value"),
position = position, position = position,
inherit.aes = FALSE, inherit.aes = FALSE,
size = datalabels.size, size = datalabels.size,
@@ -438,7 +438,7 @@ labels_rsi_count <- function(position = NULL,
combine_SI = combine_SI, combine_SI = combine_SI,
combine_IR = combine_IR) %>% combine_IR = combine_IR) %>%
group_by_at(x_name) %>% group_by_at(x_name) %>%
mutate(lbl = paste0(percent(Value / sum(Value, na.rm = TRUE), force_zero = TRUE), mutate(lbl = paste0(percent(value / sum(value, na.rm = TRUE), force_zero = TRUE),
"\n(n=", Value, ")")) "\n(n=", value, ")"))
}) })
} }
R/portion.R
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@@ -38,7 +38,9 @@
#' #'
#' These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the \code{\link[AMR]{count}} functions to count isolates. \emph{Low counts can infuence the outcome - these \code{portion} functions may camouflage this, since they only return the portion albeit being dependent on the \code{minimum} parameter.} #' These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the \code{\link[AMR]{count}} functions to count isolates. \emph{Low counts can infuence the outcome - these \code{portion} functions may camouflage this, since they only return the portion albeit being dependent on the \code{minimum} parameter.}
#' #'
#' \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}. #' The function \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each group and each variable with class \code{"rsi"}.
#'
#' The function \code{rsi_df} works exactly like \code{portion_df}, but add the number of isolates.
#' \if{html}{ #' \if{html}{
# (created with https://www.latex4technics.com/) # (created with https://www.latex4technics.com/)
#' \cr\cr #' \cr\cr
R/rsi_calc.R
+9 -7
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@@ -151,6 +151,7 @@ rsi_calc <- function(...,
} }
} }
#' @importFrom dplyr %>% summarise_if mutate select everything bind_rows
rsi_calc_df <- function(type, # "portion" or "count" rsi_calc_df <- function(type, # "portion" or "count"
data, data,
translate_ab = "name", translate_ab = "name",
@@ -196,8 +197,8 @@ rsi_calc_df <- function(type, # "portion" or "count"
.funs = int_fn) .funs = int_fn)
} }
summ %>% summ %>%
mutate(Interpretation = int) %>% mutate(interpretation = int) %>%
select(Interpretation, everything()) select(interpretation, everything())
} }
resS <- get_summaryfunction("S") resS <- get_summaryfunction("S")
@@ -209,28 +210,29 @@ rsi_calc_df <- function(type, # "portion" or "count"
if (isFALSE(combine_SI) & isFALSE(combine_IR)) { if (isFALSE(combine_SI) & isFALSE(combine_IR)) {
res <- bind_rows(resS, resI, resR) %>% res <- bind_rows(resS, resI, resR) %>%
mutate(Interpretation = factor(Interpretation, mutate(interpretation = factor(interpretation,
levels = c("S", "I", "R"), levels = c("S", "I", "R"),
ordered = TRUE)) ordered = TRUE))
} else if (isTRUE(combine_IR)) { } else if (isTRUE(combine_IR)) {
res <- bind_rows(resS, resIR) %>% res <- bind_rows(resS, resIR) %>%
mutate(Interpretation = factor(Interpretation, mutate(interpretation = factor(interpretation,
levels = c("S", "IR"), levels = c("S", "IR"),
ordered = TRUE)) ordered = TRUE))
} else if (isTRUE(combine_SI)) { } else if (isTRUE(combine_SI)) {
res <- bind_rows(resSI, resR) %>% res <- bind_rows(resSI, resR) %>%
mutate(Interpretation = factor(Interpretation, mutate(interpretation = factor(interpretation,
levels = c("SI", "R"), levels = c("SI", "R"),
ordered = TRUE)) ordered = TRUE))
} }
res <- res %>% res <- res %>%
tidyr::gather(Antibiotic, Value, -Interpretation, -data.groups) tidyr::gather(antibiotic, value, -interpretation, -data.groups) %>%
select(antibiotic, everything())
if (!translate_ab == FALSE) { if (!translate_ab == FALSE) {
res <- res %>% mutate(Antibiotic = ab_property(Antibiotic, property = translate_ab, language = language)) res <- res %>% mutate(antibiotic = ab_property(antibiotic, property = translate_ab, language = language))
} }
res res
R/rsi_df.R
+58
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@@ -0,0 +1,58 @@
# ==================================================================== #
# 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.gitlab.io/AMR. #
# ==================================================================== #
#' @rdname portion
#' @rdname count
#' @importFrom dplyr %>% select_if bind_rows summarise_if mutate group_vars select everything
#' @export
rsi_df <- function(data,
translate_ab = "name",
language = get_locale(),
minimum = 30,
as_percent = FALSE,
combine_SI = TRUE,
combine_IR = FALSE) {
portions <- rsi_calc_df(type = "portion",
data = data,
translate_ab = translate_ab,
language = language,
minimum = minimum,
as_percent = as_percent,
combine_SI = combine_SI,
combine_IR = combine_IR,
combine_SI_missing = missing(combine_SI))
counts <- rsi_calc_df(type = "count",
data = data,
translate_ab = FALSE,
language = "en",
minimum = minimum,
as_percent = as_percent,
combine_SI = combine_SI,
combine_IR = combine_IR,
combine_SI_missing = missing(combine_SI))
data.frame(portions,
isolates = counts$value,
stringsAsFactors = FALSE)
}
R/sysdata.rda
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data-raw/reproduction_of_microorganisms.R
+42 -2
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@@ -444,7 +444,43 @@ MOs <- MOs %>%
fullname = "Beta-haemolytic Streptococcus", fullname = "Beta-haemolytic Streptococcus",
ref = NA_character_, ref = NA_character_,
species_id = "", species_id = "",
source = "manually added") source = "manually added"),
# Trichomonas vaginalis is missing, same order as Dientamoeba
MOs %>%
filter(fullname == "Dientamoeba") %>%
mutate(mo = gsub("DNTMB", "THMNS", mo),
col_id = NA,
fullname = "Trichomonas",
family = "Trichomonadidae",
genus = "Trichomonas",
source = "manually added",
ref = "Donne, 1836",
species_id = ""),
MOs %>%
filter(fullname == "Dientamoeba fragilis") %>%
mutate(mo = gsub("DNTMB", "THMNS", mo),
mo = gsub("FRA", "VAG", mo),
col_id = NA,
fullname = "Trichomonas vaginalis",
family = "Trichomonadidae",
genus = "Trichomonas",
species = "vaginalis",
source = "manually added",
ref = "Donne, 1836",
species_id = ""),
MOs %>% # add family as such too
filter(fullname == "Monocercomonadidae") %>%
mutate(mo = gsub("MNCRCMND", "TRCHMNDD", mo),
col_id = NA,
fullname = "Trichomonadidae",
family = "Trichomonadidae",
rank = "family",
genus = "",
species = "",
source = "manually added",
ref = "",
species_id = ""),
) )
@@ -485,8 +521,12 @@ MOs <- MOs %>%
TRUE ~ 3 TRUE ~ 3
)) ))
# arrange
MOs <- MOs %>% arrange(fullname)
MOs.old <- MOs.old %>% arrange(fullname)
# save it # save it
MOs <- as.data.frame(MOs %>% arrange(fullname), stringsAsFactors = FALSE) MOs <- as.data.frame(MOs, stringsAsFactors = FALSE)
MOs.old <- as.data.frame(MOs.old, stringsAsFactors = FALSE) MOs.old <- as.data.frame(MOs.old, stringsAsFactors = FALSE)
class(MOs$mo) <- "mo" class(MOs$mo) <- "mo"
data-raw/translations.tsv
+4
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@@ -154,6 +154,8 @@ pt vegetative vegetativo FALSE FALSE
pt ([([ ]*?)group \\1grupo FALSE FALSE pt ([([ ]*?)group \\1grupo FALSE FALSE
pt ([([ ]*?)Group \\1Grupo FALSE FALSE pt ([([ ]*?)Group \\1Grupo FALSE FALSE
de clavulanic acid Clavulansäure FALSE TRUE
nl 4-aminosalicylic acid 4-aminosalicylzuur nl 4-aminosalicylic acid 4-aminosalicylzuur
nl Adefovir dipivoxil Adefovir nl Adefovir dipivoxil Adefovir
nl Aldesulfone sodium Aldesulfon nl Aldesulfone sodium Aldesulfon
@@ -348,8 +350,10 @@ nl Thiamphenicol Thiamfenicol
nl Thioacetazone/isoniazid Thioacetazon/isoniazide nl Thioacetazone/isoniazid Thioacetazon/isoniazide
nl Ticarcillin Ticarcilline nl Ticarcillin Ticarcilline
nl Ticarcillin/beta-lactamase inhibitor Ticarcilline/enzymremmer nl Ticarcillin/beta-lactamase inhibitor Ticarcilline/enzymremmer
nl Ticarcillin/clavulanic acid Ticarcilline/clavulaanzuur
nl Tinidazole Tinidazol nl Tinidazole Tinidazol
nl Tobramycin Tobramycine nl Tobramycin Tobramycine
nl Trimethoprim/sulfamethoxazole Trimethoprim/sulfamethoxazol
nl Troleandomycin Troleandomycine nl Troleandomycin Troleandomycine
nl Trovafloxacin Trovafloxacine nl Trovafloxacin Trovafloxacine
nl Vancomycin Vancomycine nl Vancomycin Vancomycine
1 lang pattern replacement fixed ignore.case
154 pt ([([ ]*?)group \\1grupo FALSE FALSE
155 pt ([([ ]*?)Group \\1Grupo FALSE FALSE
156 nl de 4-aminosalicylic acid clavulanic acid 4-aminosalicylzuur Clavulansäure FALSE TRUE
157 nl 4-aminosalicylic acid 4-aminosalicylzuur
158 nl Adefovir dipivoxil Adefovir
159 nl Adefovir dipivoxil Aldesulfone sodium Adefovir Aldesulfon
160 nl Aldesulfone sodium Amikacin Aldesulfon Amikacine
161 nl Amikacin Amoxicillin Amikacine Amoxicilline
350 nl Ticarcillin Ticarcillin/beta-lactamase inhibitor Ticarcilline Ticarcilline/enzymremmer
351 nl Ticarcillin/beta-lactamase inhibitor Ticarcillin/clavulanic acid Ticarcilline/enzymremmer Ticarcilline/clavulaanzuur
352 nl Tinidazole Tinidazol
353 nl Tobramycin Tobramycine
354 nl Tobramycin Trimethoprim/sulfamethoxazole Tobramycine Trimethoprim/sulfamethoxazol
355 nl Troleandomycin Troleandomycine
356 nl Trovafloxacin Trovafloxacine
357 nl Trovafloxacin Vancomycin Trovafloxacine Vancomycine
358 nl Vancomycin Voriconazole Vancomycine Voriconazol
359 nl Voriconazole Aminoglycosides Voriconazol Aminoglycosiden TRUE FALSE
data/microorganisms.codes.rda
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docs/LICENSE-text.html
+1 -1
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@@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
</span> </span>
</div> </div>
docs/articles/index.html
+1 -1
View File
@@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
</span> </span>
</div> </div>
docs/authors.html
+1 -1
View File
@@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
</span> </span>
</div> </div>
docs/index.html
+1 -1
View File
@@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
</span> </span>
</div> </div>
docs/news/index.html
+142 -129
View File
@@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
</span> </span>
</div> </div>
@@ -232,20 +232,31 @@
</div> </div>
<div id="amr-0709007" class="section level1"> <div id="amr-0709008" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0709007" class="anchor"></a>AMR 0.7.0.9007<small> Unreleased </small> <a href="#amr-0709008" class="anchor"></a>AMR 0.7.0.9008<small> Unreleased </small>
</h1> </h1>
<div id="new" class="section level4"> <div id="new" class="section level4">
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h4> <a href="#new" class="anchor"></a>New</h4>
<ul> <ul>
<li> <li>
<p>Function <code><a href="../reference/portion.html">rsi_df()</a></code> to transform a <code>data.frame</code> to a data set containing only the microbial interpretation (S, I, R), the antibiotic, the percentage of S/I/R and the number of available isolates. This is a convenient combinations of existing functions <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> to immediately show resistance percentages and number of available isolates:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb1-2" title="2"><span class="st"> </span><span class="kw">select</span>(AMX, CIP) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb1-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/portion.html">rsi_df</a></span>()</a>
<a class="sourceLine" id="cb1-4" title="4"><span class="co"># antibiotic interpretation value isolates</span></a>
<a class="sourceLine" id="cb1-5" title="5"><span class="co"># 1 Amoxicillin SI 0.4442636 546</span></a>
<a class="sourceLine" id="cb1-6" title="6"><span class="co"># 2 Amoxicillin R 0.5557364 683</span></a>
<a class="sourceLine" id="cb1-7" title="7"><span class="co"># 3 Ciprofloxacin SI 0.8381831 1181</span></a>
<a class="sourceLine" id="cb1-8" title="8"><span class="co"># 4 Ciprofloxacin R 0.1618169 228</span></a></code></pre></div>
</li>
<li>
<p>Support for all scientifically published pathotypes of <em>E. coli</em> to date. Supported are: AIEC (Adherent-Invasive <em>E. coli</em>), ATEC (Atypical Entero-pathogenic <em>E. coli</em>), DAEC (Diffusely Adhering <em>E. coli</em>), EAEC (Entero-Aggresive <em>E. coli</em>), EHEC (Entero-Haemorrhagic <em>E. coli</em>), EIEC (Entero-Invasive <em>E. coli</em>), EPEC (Entero-Pathogenic <em>E. coli</em>), ETEC (Entero-Toxigenic <em>E. coli</em>), NMEC (Neonatal Meningitis‐causing <em>E. coli</em>), STEC (Shiga-toxin producing <em>E. coli</em>) and UPEC (Uropathogenic <em>E. coli</em>). All these lead to the microbial ID of <em>E. coli</em>:</p> <p>Support for all scientifically published pathotypes of <em>E. coli</em> to date. Supported are: AIEC (Adherent-Invasive <em>E. coli</em>), ATEC (Atypical Entero-pathogenic <em>E. coli</em>), DAEC (Diffusely Adhering <em>E. coli</em>), EAEC (Entero-Aggresive <em>E. coli</em>), EHEC (Entero-Haemorrhagic <em>E. coli</em>), EIEC (Entero-Invasive <em>E. coli</em>), EPEC (Entero-Pathogenic <em>E. coli</em>), ETEC (Entero-Toxigenic <em>E. coli</em>), NMEC (Neonatal Meningitis‐causing <em>E. coli</em>), STEC (Shiga-toxin producing <em>E. coli</em>) and UPEC (Uropathogenic <em>E. coli</em>). All these lead to the microbial ID of <em>E. coli</em>:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a> <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"UPEC"</span>)</a>
<a class="sourceLine" id="cb1-2" title="2"><span class="co"># B_ESCHR_COL</span></a> <a class="sourceLine" id="cb2-2" title="2"><span class="co"># B_ESCHR_COL</span></a>
<a class="sourceLine" id="cb1-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"UPEC"</span>)</a> <a class="sourceLine" id="cb2-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"UPEC"</span>)</a>
<a class="sourceLine" id="cb1-4" title="4"><span class="co"># "Escherichia coli"</span></a></code></pre></div> <a class="sourceLine" id="cb2-4" title="4"><span class="co"># "Escherichia coli"</span></a></code></pre></div>
</li> </li>
<li><p>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</p></li> <li><p>Function <code><a href="../reference/mo_property.html">mo_info()</a></code> as an analogy to <code><a href="../reference/ab_property.html">ab_info()</a></code>. The <code><a href="../reference/mo_property.html">mo_info()</a></code> prints a list with the full taxonomy, authors, and the URL to the online database of a microorganism</p></li>
</ul> </ul>
@@ -254,6 +265,7 @@
<h4 class="hasAnchor"> <h4 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h4> <a href="#changed" class="anchor"></a>Changed</h4>
<ul> <ul>
<li>Column names of output <code><a href="../reference/count.html">count_df()</a></code> and <code><a href="../reference/portion.html">portion_df()</a></code> are now lowercase</li>
<li>Fixed bug in translation of microorganism names</li> <li>Fixed bug in translation of microorganism names</li>
<li>Fixed bug in determining taxonomic kingdoms</li> <li>Fixed bug in determining taxonomic kingdoms</li>
<li>Algorithm improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code> and <code><a href="../reference/as.mo.html">as.mo()</a></code> to understand even more severely misspelled input</li> <li>Algorithm improvements for <code><a href="../reference/as.ab.html">as.ab()</a></code> and <code><a href="../reference/as.mo.html">as.mo()</a></code> to understand even more severely misspelled input</li>
@@ -270,6 +282,7 @@
</li> </li>
<li>Fixed bug where not all old taxonomic named would not be printed when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> <li>Fixed bug where not all old taxonomic named would not be printed when using a vector as input for <code><a href="../reference/as.mo.html">as.mo()</a></code>
</li> </li>
<li>Manually added <em>Trichomonas vaginalis</em> from the kingdom of Protozoa, which is missing from the Catalogue of Life</li>
</ul> </ul>
</div> </div>
<div id="other" class="section level4"> <div id="other" class="section level4">
@@ -338,14 +351,14 @@ Please <a href="https://gitlab.com/msberends/AMR/issues/new?issue%5Btitle%5D=Tra
<li>when all values are unique it now shows a message instead of a warning</li> <li>when all values are unique it now shows a message instead of a warning</li>
<li> <li>
<p>support for boxplots:</p> <p>support for boxplots:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb3-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a> <a class="sourceLine" id="cb3-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a>
<a class="sourceLine" id="cb2-4" title="4"><span class="co"># grouped boxplots:</span></a> <a class="sourceLine" id="cb3-4" title="4"><span class="co"># grouped boxplots:</span></a>
<a class="sourceLine" id="cb2-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb3-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-6" title="6"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb3-6" title="6"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb2-7" title="7"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb3-7" title="7"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb2-8" title="8"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a></code></pre></div> <a class="sourceLine" id="cb3-8" title="8"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/boxplot">boxplot</a></span>()</a></code></pre></div>
</li> </li>
</ul> </ul>
</li> </li>
@@ -430,32 +443,32 @@ This data is updated annually - check the included version with the new function
</li> </li>
<li> <li>
<p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p> <p>New filters for antimicrobial classes. Use these functions to filter isolates on results in one of more antibiotics from a specific class:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a> <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="../reference/filter_ab_class.html">filter_aminoglycosides</a></span>()</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a> <a class="sourceLine" id="cb4-2" title="2"><span class="kw"><a href="../reference/filter_ab_class.html">filter_carbapenems</a></span>()</a>
<a class="sourceLine" id="cb3-3" title="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a> <a class="sourceLine" id="cb4-3" title="3"><span class="kw"><a href="../reference/filter_ab_class.html">filter_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb3-4" title="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a> <a class="sourceLine" id="cb4-4" title="4"><span class="kw"><a href="../reference/filter_ab_class.html">filter_1st_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb3-5" title="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a> <a class="sourceLine" id="cb4-5" title="5"><span class="kw"><a href="../reference/filter_ab_class.html">filter_2nd_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb3-6" title="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a> <a class="sourceLine" id="cb4-6" title="6"><span class="kw"><a href="../reference/filter_ab_class.html">filter_3rd_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb3-7" title="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a> <a class="sourceLine" id="cb4-7" title="7"><span class="kw"><a href="../reference/filter_ab_class.html">filter_4th_cephalosporins</a></span>()</a>
<a class="sourceLine" id="cb3-8" title="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a> <a class="sourceLine" id="cb4-8" title="8"><span class="kw"><a href="../reference/filter_ab_class.html">filter_fluoroquinolones</a></span>()</a>
<a class="sourceLine" id="cb3-9" title="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a> <a class="sourceLine" id="cb4-9" title="9"><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>()</a>
<a class="sourceLine" id="cb3-10" title="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a> <a class="sourceLine" id="cb4-10" title="10"><span class="kw"><a href="../reference/filter_ab_class.html">filter_macrolides</a></span>()</a>
<a class="sourceLine" id="cb3-11" title="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div> <a class="sourceLine" id="cb4-11" title="11"><span class="kw"><a href="../reference/filter_ab_class.html">filter_tetracyclines</a></span>()</a></code></pre></div>
<p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p> <p>The <code>antibiotics</code> data set will be searched, after which the input data will be checked for column names with a value in any abbreviations, codes or official names found in the <code>antibiotics</code> data set. For example:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a> <div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>)</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a> <a class="sourceLine" id="cb5-2" title="2"><span class="co"># Filtering on glycopeptide antibacterials: any of `vanc` or `teic` is R</span></a>
<a class="sourceLine" id="cb4-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a> <a class="sourceLine" id="cb5-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/filter_ab_class.html">filter_glycopeptides</a></span>(<span class="dt">result =</span> <span class="st">"R"</span>, <span class="dt">scope =</span> <span class="st">"all"</span>)</a>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div> <a class="sourceLine" id="cb5-4" title="4"><span class="co"># Filtering on glycopeptide antibacterials: all of `vanc` and `teic` is R</span></a></code></pre></div>
</li> </li>
<li> <li>
<p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p> <p>All <code>ab_*</code> functions are deprecated and replaced by <code>atc_*</code> functions:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">ab_property -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_property</a></span>()</a> <div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">ab_property -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_property</a></span>()</a>
<a class="sourceLine" id="cb5-2" title="2">ab_name -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_name</a></span>()</a> <a class="sourceLine" id="cb6-2" title="2">ab_name -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_name</a></span>()</a>
<a class="sourceLine" id="cb5-3" title="3">ab_official -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_official</a></span>()</a> <a class="sourceLine" id="cb6-3" title="3">ab_official -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_official</a></span>()</a>
<a class="sourceLine" id="cb5-4" title="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_trivial_nl</a></span>()</a> <a class="sourceLine" id="cb6-4" title="4">ab_trivial_nl -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_trivial_nl</a></span>()</a>
<a class="sourceLine" id="cb5-5" title="5">ab_certe -&gt;<span class="st"> </span><span class="kw">atc_certe</span>()</a> <a class="sourceLine" id="cb6-5" title="5">ab_certe -&gt;<span class="st"> </span><span class="kw">atc_certe</span>()</a>
<a class="sourceLine" id="cb5-6" title="6">ab_umcg -&gt;<span class="st"> </span><span class="kw">atc_umcg</span>()</a> <a class="sourceLine" id="cb6-6" title="6">ab_umcg -&gt;<span class="st"> </span><span class="kw">atc_umcg</span>()</a>
<a class="sourceLine" id="cb5-7" title="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_tradenames</a></span>()</a></code></pre></div> <a class="sourceLine" id="cb6-7" title="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw"><a href="../reference/AMR-deprecated.html">atc_tradenames</a></span>()</a></code></pre></div>
These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li> These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li> <li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li> <li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
@@ -467,20 +480,20 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li> <li>New function <code><a href="../reference/age_groups.html">age_groups()</a></code> to split ages into custom or predefined groups (like children or elderly). This allows for easier demographic antimicrobial resistance analysis per age group.</li>
<li> <li>
<p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p> <p>New function <code><a href="../reference/resistance_predict.html">ggplot_rsi_predict()</a></code> as well as the base R <code><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot()</a></code> function can now be used for resistance prediction calculated with <code><a href="../reference/resistance_predict.html">resistance_predict()</a></code>:</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a> <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">x &lt;-<span class="st"> </span><span class="kw"><a href="../reference/resistance_predict.html">resistance_predict</a></span>(septic_patients, <span class="dt">col_ab =</span> <span class="st">"amox"</span>)</a>
<a class="sourceLine" id="cb6-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a> <a class="sourceLine" id="cb7-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(x)</a>
<a class="sourceLine" id="cb6-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div> <a class="sourceLine" id="cb7-3" title="3"><span class="kw"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span>(x)</a></code></pre></div>
</li> </li>
<li> <li>
<p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p> <p>Functions <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code> and <code><a href="../reference/first_isolate.html">filter_first_weighted_isolate()</a></code> to shorten and fasten filtering on data sets with antimicrobial results, e.g.:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a> <div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(...)</a>
<a class="sourceLine" id="cb7-2" title="2"><span class="co"># or</span></a> <a class="sourceLine" id="cb8-2" title="2"><span class="co"># or</span></a>
<a class="sourceLine" id="cb7-3" title="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div> <a class="sourceLine" id="cb8-3" title="3"><span class="kw"><a href="../reference/first_isolate.html">filter_first_isolate</a></span>(septic_patients, ...)</a></code></pre></div>
<p>is equal to:</p> <p>is equal to:</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">septic_patients <span class="op">%&gt;%</span></a> <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-2" title="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb9-2" title="2"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">only_firsts =</span> <span class="kw"><a href="../reference/first_isolate.html">first_isolate</a></span>(septic_patients, ...)) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb9-3" title="3"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/stats/topics/filter">filter</a></span>(only_firsts <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb8-4" title="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div> <a class="sourceLine" id="cb9-4" title="4"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>only_firsts)</a></code></pre></div>
</li> </li>
<li>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code> <li>New function <code><a href="../reference/availability.html">availability()</a></code> to check the number of available (non-empty) results in a <code>data.frame</code>
</li> </li>
@@ -509,33 +522,33 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<ul> <ul>
<li> <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> <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="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a> <div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="co"># mo_fullname() uses as.mo() internally</span></a>
<a class="sourceLine" id="cb9-2" title="2"></a> <a class="sourceLine" id="cb10-2" title="2"></a>
<a class="sourceLine" id="cb9-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a> <a class="sourceLine" id="cb10-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"Sthafilokockus aaureuz"</span>)</a>
<a class="sourceLine" id="cb9-4" title="4"><span class="co">#&gt; [1] "Staphylococcus aureus"</span></a> <a class="sourceLine" id="cb10-4" title="4"><span class="co">#&gt; [1] "Staphylococcus aureus"</span></a>
<a class="sourceLine" id="cb9-5" title="5"></a> <a class="sourceLine" id="cb10-5" title="5"></a>
<a class="sourceLine" id="cb9-6" 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="cb10-6" 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="cb9-7" title="7"><span class="co">#&gt; [1] "Staphylococcus kloosii"</span></a></code></pre></div> <a class="sourceLine" id="cb10-7" title="7"><span class="co">#&gt; [1] "Staphylococcus kloosii"</span></a></code></pre></div>
</li> </li>
<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> <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="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="co"># equal:</span></a> <div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="co"># equal:</span></a>
<a class="sourceLine" id="cb10-2" 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="cb11-2" 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="cb10-3" 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> <a class="sourceLine" id="cb11-3" 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>
<a class="sourceLine" id="cb10-4" title="4"></a> <a class="sourceLine" id="cb11-4" title="4"></a>
<a class="sourceLine" id="cb10-5" title="5"><span class="co"># also equal:</span></a> <a class="sourceLine" id="cb11-5" title="5"><span class="co"># also equal:</span></a>
<a class="sourceLine" id="cb10-6" 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="cb11-6" 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="cb10-7" 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> <a class="sourceLine" id="cb11-7" 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.</li> Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a></code> could lead to very unreliable results.</li>
<li>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em> <li>Implemented the latest publication of Becker <em>et al.</em> (2019), for categorising coagulase-negative <em>Staphylococci</em>
</li> </li>
<li>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</li> <li>All microbial IDs that found are now saved to a local file <code>~/.Rhistory_mo</code>. Use the new function <code>clean_mo_history()</code> to delete this file, which resets the algorithms.</li>
<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> <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="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" 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> <div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" 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="cb11-2" title="2"><span class="co"># Warning: </span></a> <a class="sourceLine" id="cb12-2" title="2"><span class="co"># Warning: </span></a>
<a class="sourceLine" id="cb11-3" 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="cb12-3" 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="cb11-4" title="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div> <a class="sourceLine" id="cb12-4" title="4"><span class="co">#&gt; [1] "(género desconocido)"</span></a></code></pre></div>
</li> </li>
<li>Fix for vector containing only empty values</li> <li>Fix for vector containing only empty values</li>
<li>Finds better results when input is in other languages</li> <li>Finds better results when input is in other languages</li>
@@ -581,19 +594,19 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<ul> <ul>
<li> <li>
<p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p> <p>Support for tidyverse quasiquotation! Now you can create frequency tables of function outcomes:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a> <div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="co"># Determine genus of microorganisms (mo) in `septic_patients` data set:</span></a>
<a class="sourceLine" id="cb12-2" title="2"><span class="co"># OLD WAY</span></a> <a class="sourceLine" id="cb13-2" title="2"><span class="co"># OLD WAY</span></a>
<a class="sourceLine" id="cb12-3" title="3">septic_patients <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb13-3" title="3">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb12-4" title="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb13-4" title="4"><span class="st"> </span><span class="kw">mutate</span>(<span class="dt">genus =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo)) <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb12-5" title="5"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a> <a class="sourceLine" id="cb13-5" title="5"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus)</a>
<a class="sourceLine" id="cb12-6" title="6"><span class="co"># NEW WAY</span></a> <a class="sourceLine" id="cb13-6" title="6"><span class="co"># NEW WAY</span></a>
<a class="sourceLine" id="cb12-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb13-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb12-8" title="8"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a> <a class="sourceLine" id="cb13-8" title="8"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a>
<a class="sourceLine" id="cb12-9" title="9"></a> <a class="sourceLine" id="cb13-9" title="9"></a>
<a class="sourceLine" id="cb12-10" title="10"><span class="co"># Even supports grouping variables:</span></a> <a class="sourceLine" id="cb13-10" title="10"><span class="co"># Even supports grouping variables:</span></a>
<a class="sourceLine" id="cb12-11" title="11">septic_patients <span class="op">%&gt;%</span></a> <a class="sourceLine" id="cb13-11" title="11">septic_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb12-12" title="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb13-12" title="12"><span class="st"> </span><span class="kw">group_by</span>(gender) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb12-13" title="13"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div> <a class="sourceLine" id="cb13-13" title="13"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(mo))</a></code></pre></div>
</li> </li>
<li>Header info is now available as a list, with the <code>header</code> function</li> <li>Header info is now available as a list, with the <code>header</code> function</li>
<li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li> <li>The parameter <code>header</code> is now set to <code>TRUE</code> at default, even for markdown</li>
@@ -668,10 +681,10 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li> <li>Fewer than 3 characters as input for <code>as.mo</code> will return NA</li>
<li> <li>
<p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p> <p>Function <code>as.mo</code> (and all <code>mo_*</code> wrappers) now supports genus abbreviations with “species” attached</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a> <div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. species"</span>) <span class="co"># B_ESCHR</span></a>
<a class="sourceLine" id="cb13-2" title="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a> <a class="sourceLine" id="cb14-2" title="2"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"E. spp."</span>) <span class="co"># "Escherichia species"</span></a>
<a class="sourceLine" id="cb13-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a> <a class="sourceLine" id="cb14-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S. spp"</span>) <span class="co"># B_STPHY</span></a>
<a class="sourceLine" id="cb13-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div> <a class="sourceLine" id="cb14-4" title="4"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. species"</span>) <span class="co"># "Staphylococcus species"</span></a></code></pre></div>
</li> </li>
<li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li> <li>Added parameter <code>combine_IR</code> (TRUE/FALSE) to functions <code>portion_df</code> and <code>count_df</code>, to indicate that all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)</li>
<li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li> <li>Fix for <code>portion_*(..., as_percent = TRUE)</code> when minimal number of isolates would not be met</li>
@@ -684,15 +697,15 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<ul> <ul>
<li> <li>
<p>Support for grouping variables, test with:</p> <p>Support for grouping variables, test with:</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb14-2" title="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb15-2" title="2"><span class="st"> </span><span class="kw">group_by</span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb14-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div> <a class="sourceLine" id="cb15-3" title="3"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li> </li>
<li> <li>
<p>Support for (un)selecting columns:</p> <p>Support for (un)selecting columns:</p>
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a> <div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb15-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a> <a class="sourceLine" id="cb16-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(hospital_id) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb15-3" title="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div> <a class="sourceLine" id="cb16-3" title="3"><span class="st"> </span><span class="kw">select</span>(<span class="op">-</span>count, <span class="op">-</span>cum_count) <span class="co"># only get item, percent, cum_percent</span></a></code></pre></div>
</li> </li>
<li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code> <li>Check for <code><a href="https://www.rdocumentation.org/packages/hms/topics/hms">hms::is.hms</a></code>
</li> </li>
@@ -772,18 +785,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li> </li>
</ul> </ul>
<p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p> <p>They also come with support for German, Dutch, French, Italian, Spanish and Portuguese:</p>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a> <div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb16-2" title="2"><span class="co"># [1] "Gram negative"</span></a> <a class="sourceLine" id="cb17-2" title="2"><span class="co"># [1] "Gram negative"</span></a>
<a class="sourceLine" id="cb16-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a> <a class="sourceLine" id="cb17-3" title="3"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"de"</span>) <span class="co"># German</span></a>
<a class="sourceLine" id="cb16-4" title="4"><span class="co"># [1] "Gramnegativ"</span></a> <a class="sourceLine" id="cb17-4" title="4"><span class="co"># [1] "Gramnegativ"</span></a>
<a class="sourceLine" id="cb16-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a> <a class="sourceLine" id="cb17-5" title="5"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"E. coli"</span>, <span class="dt">language =</span> <span class="st">"es"</span>) <span class="co"># Spanish</span></a>
<a class="sourceLine" id="cb16-6" title="6"><span class="co"># [1] "Gram negativo"</span></a> <a class="sourceLine" id="cb17-6" title="6"><span class="co"># [1] "Gram negativo"</span></a>
<a class="sourceLine" id="cb16-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a> <a class="sourceLine" id="cb17-7" title="7"><span class="kw"><a href="../reference/mo_property.html">mo_fullname</a></span>(<span class="st">"S. group A"</span>, <span class="dt">language =</span> <span class="st">"pt"</span>) <span class="co"># Portuguese</span></a>
<a class="sourceLine" id="cb16-8" title="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div> <a class="sourceLine" id="cb17-8" title="8"><span class="co"># [1] "Streptococcus grupo A"</span></a></code></pre></div>
<p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p> <p>Furthermore, former taxonomic names will give a note about the current taxonomic name:</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a> <div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1"><span class="kw"><a href="../reference/mo_property.html">mo_gramstain</a></span>(<span class="st">"Esc blattae"</span>)</a>
<a class="sourceLine" id="cb17-2" title="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a> <a class="sourceLine" id="cb18-2" title="2"><span class="co"># Note: 'Escherichia blattae' (Burgess et al., 1973) was renamed 'Shimwellia blattae' (Priest and Barker, 2010)</span></a>
<a class="sourceLine" id="cb17-3" title="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div> <a class="sourceLine" id="cb18-3" title="3"><span class="co"># [1] "Gram negative"</span></a></code></pre></div>
</li> </li>
<li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates <li>Functions <code>count_R</code>, <code>count_IR</code>, <code>count_I</code>, <code>count_SI</code> and <code>count_S</code> to selectively count resistant or susceptible isolates
<ul> <ul>
@@ -794,18 +807,18 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li> </li>
<li> <li>
<p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p> <p>Functions <code>as.mo</code> and <code>is.mo</code> as replacements for <code>as.bactid</code> and <code>is.bactid</code> (since the <code>microoganisms</code> data set not only contains bacteria). These last two functions are deprecated and will be removed in a future release. The <code>as.mo</code> function determines microbial IDs using intelligent rules:</p>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a> <div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"E. coli"</span>)</a>
<a class="sourceLine" id="cb18-2" title="2"><span class="co"># [1] B_ESCHR_COL</span></a> <a class="sourceLine" id="cb19-2" title="2"><span class="co"># [1] B_ESCHR_COL</span></a>
<a class="sourceLine" id="cb18-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a> <a class="sourceLine" id="cb19-3" title="3"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"MRSA"</span>)</a>
<a class="sourceLine" id="cb18-4" title="4"><span class="co"># [1] B_STPHY_AUR</span></a> <a class="sourceLine" id="cb19-4" title="4"><span class="co"># [1] B_STPHY_AUR</span></a>
<a class="sourceLine" id="cb18-5" title="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a> <a class="sourceLine" id="cb19-5" title="5"><span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"S group A"</span>)</a>
<a class="sourceLine" id="cb18-6" title="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div> <a class="sourceLine" id="cb19-6" title="6"><span class="co"># [1] B_STRPTC_GRA</span></a></code></pre></div>
<p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p> <p>And with great speed too - on a quite regular Linux server from 2007 it takes us less than 0.02 seconds to transform 25,000 items:</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a> <div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">thousands_of_E_colis &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="st">"E. coli"</span>, <span class="dv">25000</span>)</a>
<a class="sourceLine" id="cb19-2" title="2">microbenchmark<span class="op">::</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>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a> <a class="sourceLine" id="cb20-2" title="2">microbenchmark<span class="op">::</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>(thousands_of_E_colis), <span class="dt">unit =</span> <span class="st">"s"</span>)</a>
<a class="sourceLine" id="cb19-3" title="3"><span class="co"># Unit: seconds</span></a> <a class="sourceLine" id="cb20-3" title="3"><span class="co"># Unit: seconds</span></a>
<a class="sourceLine" id="cb19-4" title="4"><span class="co"># min median max neval</span></a> <a class="sourceLine" id="cb20-4" title="4"><span class="co"># min median max neval</span></a>
<a class="sourceLine" id="cb19-5" title="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div> <a class="sourceLine" id="cb20-5" title="5"><span class="co"># 0.01817717 0.01843957 0.03878077 100</span></a></code></pre></div>
</li> </li>
<li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li> <li>Added parameter <code>reference_df</code> for <code>as.mo</code>, so users can supply their own microbial IDs, name or codes as a reference table</li>
<li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like: <li>Renamed all previous references to <code>bactid</code> to <code>mo</code>, like:
@@ -833,12 +846,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li> <li>Added three antimicrobial agents to the <code>antibiotics</code> data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)</li>
<li> <li>
<p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p> <p>Added 163 trade names to the <code>antibiotics</code> data set, it now contains 298 different trade names in total, e.g.:</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a> <div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1"><span class="kw"><a href="../reference/AMR-deprecated.html">ab_official</a></span>(<span class="st">"Bactroban"</span>)</a>
<a class="sourceLine" id="cb20-2" title="2"><span class="co"># [1] "Mupirocin"</span></a> <a class="sourceLine" id="cb21-2" title="2"><span class="co"># [1] "Mupirocin"</span></a>
<a class="sourceLine" id="cb20-3" title="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a> <a class="sourceLine" id="cb21-3" title="3"><span class="kw"><a href="../reference/ab_property.html">ab_name</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb20-4" title="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a> <a class="sourceLine" id="cb21-4" title="4"><span class="co"># [1] "Mupirocin" "Amoxicillin" "Azithromycin" "Flucloxacillin"</span></a>
<a class="sourceLine" id="cb20-5" title="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a> <a class="sourceLine" id="cb21-5" title="5"><span class="kw"><a href="../reference/ab_property.html">ab_atc</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Bactroban"</span>, <span class="st">"Amoxil"</span>, <span class="st">"Zithromax"</span>, <span class="st">"Floxapen"</span>))</a>
<a class="sourceLine" id="cb20-6" title="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div> <a class="sourceLine" id="cb21-6" title="6"><span class="co"># [1] "R01AX06" "J01CA04" "J01FA10" "J01CF05"</span></a></code></pre></div>
</li> </li>
<li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li> <li>For <code>first_isolate</code>, rows will be ignored when there’s no species available</li>
<li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li> <li>Function <code>ratio</code> is now deprecated and will be removed in a future release, as it is not really the scope of this package</li>
@@ -849,13 +862,13 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li> </li>
<li> <li>
<p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p> <p>Support for quasiquotation in the functions series <code>count_*</code> and <code>portions_*</code>, and <code>n_rsi</code>. This allows to check for more than 2 vectors or columns.</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a> <div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw">select</span>(amox, cipr) <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>()</a>
<a class="sourceLine" id="cb21-2" title="2"><span class="co"># which is the same as:</span></a> <a class="sourceLine" id="cb22-2" title="2"><span class="co"># which is the same as:</span></a>
<a class="sourceLine" id="cb21-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a> <a class="sourceLine" id="cb22-3" title="3">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/count.html">count_IR</a></span>(amox, cipr)</a>
<a class="sourceLine" id="cb21-4" title="4"></a> <a class="sourceLine" id="cb22-4" title="4"></a>
<a class="sourceLine" id="cb21-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a> <a class="sourceLine" id="cb22-5" title="5">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl)</a>
<a class="sourceLine" id="cb21-6" title="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a> <a class="sourceLine" id="cb22-6" title="6">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent)</a>
<a class="sourceLine" id="cb21-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div> <a class="sourceLine" id="cb22-7" title="7">septic_patients <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_S</a></span>(amcl, gent, pita)</a></code></pre></div>
</li> </li>
<li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li> <li>Edited <code>ggplot_rsi</code> and <code>geom_rsi</code> so they can cope with <code>count_df</code>. The new <code>fun</code> parameter has value <code>portion_df</code> at default, but can be set to <code>count_df</code>.</li>
<li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li> <li>Fix for <code>ggplot_rsi</code> when the <code>ggplot2</code> package was not loaded</li>
@@ -869,12 +882,12 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
</li> </li>
<li> <li>
<p>Support for types (classes) list and matrix for <code>freq</code></p> <p>Support for types (classes) list and matrix for <code>freq</code></p>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a> <div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1">my_matrix =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/with">with</a></span>(septic_patients, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/matrix">matrix</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(age, gender), <span class="dt">ncol =</span> <span class="dv">2</span>))</a>
<a class="sourceLine" id="cb22-2" title="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div> <a class="sourceLine" id="cb23-2" title="2"><span class="kw"><a href="../reference/freq.html">freq</a></span>(my_matrix)</a></code></pre></div>
<p>For lists, subsetting is possible:</p> <p>For lists, subsetting is possible:</p>
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a> <div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1">my_list =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="dt">age =</span> septic_patients<span class="op">$</span>age, <span class="dt">gender =</span> septic_patients<span class="op">$</span>gender)</a>
<a class="sourceLine" id="cb23-2" title="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a> <a class="sourceLine" id="cb24-2" title="2">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(age)</a>
<a class="sourceLine" id="cb23-3" title="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div> <a class="sourceLine" id="cb24-3" title="3">my_list <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(gender)</a></code></pre></div>
</li> </li>
</ul> </ul>
</div> </div>
@@ -1108,7 +1121,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0709007">0.7.0.9007</a></li> <li><a href="#amr-0709008">0.7.0.9008</a></li>
<li><a href="#amr-070">0.7.0</a></li> <li><a href="#amr-070">0.7.0</a></li>
<li><a href="#amr-061">0.6.1</a></li> <li><a href="#amr-061">0.6.1</a></li>
<li><a href="#amr-060">0.6.0</a></li> <li><a href="#amr-060">0.6.0</a></li>
docs/reference/count.html
+4 -10
View File
@@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">0.7.0.9000</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
</span> </span>
</div> </div>
@@ -166,13 +166,6 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
Create frequency tables Create frequency tables
</a> </a>
</li> </li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li> <li>
<a href="../articles/benchmarks.html"> <a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span> <span class="fa fa-shipping-fast"></span>
@@ -311,8 +304,9 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p> <p>These functions are meant to count isolates. Use the <code><a href='portion.html'>portion</a>_*</code> functions to calculate microbial resistance.</p>
<p><code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p> <p>The function <code>n_rsi</code> is an alias of <code>count_all</code>. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to <code><a href='https://dplyr.tidyverse.org/reference/n_distinct.html'>n_distinct</a></code>. Their function is equal to <code>count_S(...) + count_IR(...)</code>.</p>
<p><code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p> <p>The function <code>count_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and counts the amounts of S, I and R. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>.</p>
<p>The function <code>rsi_df</code> works exactly like <code>count_df</code>, but add the percentage of S, I and R.</p>
<h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2> <h2 class="hasAnchor" id="interpretation-of-s-i-and-r"><a class="anchor" href="#interpretation-of-s-i-and-r"></a>Interpretation of S, I and R</h2>
docs/reference/ggplot_rsi.html
+12 -19
View File
@@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">0.7.0.9000</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
</span> </span>
</div> </div>
@@ -165,13 +165,6 @@
Create frequency tables Create frequency tables
</a> </a>
</li> </li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li> <li>
<a href="../articles/benchmarks.html"> <a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span> <span class="fa fa-shipping-fast"></span>
@@ -248,8 +241,8 @@
</div> </div>
<pre class="usage"><span class='fu'>ggplot_rsi</span>(<span class='no'>data</span>, <span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>, <pre class="usage"><span class='fu'>ggplot_rsi</span>(<span class='no'>data</span>, <span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), <span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"interpretation"</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>),
<span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>S</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>I</span> <span class='kw'>=</span> <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>colours</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>S</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>SI</span> <span class='kw'>=</span> <span class='st'>"#61a8ff"</span>, <span class='kw'>I</span> <span class='kw'>=</span>
@@ -258,12 +251,12 @@
<span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>caption</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>y.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>subtitle</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>caption</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>y.title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='no'>...</span>) <span class='no'>...</span>)
<span class='fu'>geom_rsi</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Antibiotic"</span>, <span class='st'>"Interpretation"</span>), <span class='fu'>geom_rsi</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"antibiotic"</span>, <span class='st'>"interpretation"</span>),
<span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"Interpretation"</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>fill</span> <span class='kw'>=</span> <span class='st'>"interpretation"</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>,
<span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>, <span class='no'>...</span>) <span class='kw'>fun</span> <span class='kw'>=</span> <span class='no'>count_df</span>, <span class='no'>...</span>)
<span class='fu'>facet_rsi</span>(<span class='kw'>facet</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"Interpretation"</span>, <span class='st'>"Antibiotic"</span>), <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>) <span class='fu'>facet_rsi</span>(<span class='kw'>facet</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"interpretation"</span>, <span class='st'>"antibiotic"</span>), <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
<span class='fu'>scale_y_percent</span>(<span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>) <span class='fu'>scale_y_percent</span>(<span class='kw'>breaks</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>), <span class='kw'>limits</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)
@@ -272,7 +265,7 @@
<span class='fu'>theme_rsi</span>() <span class='fu'>theme_rsi</span>()
<span class='fu'>labels_rsi_count</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>, <span class='fu'>labels_rsi_count</span>(<span class='kw'>position</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"gray15"</span>)</pre> <span class='kw'>datalabels.size</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>datalabels.colour</span> <span class='kw'>=</span> <span class='st'>"gray15"</span>)</pre>
@@ -289,15 +282,15 @@
</tr> </tr>
<tr> <tr>
<th>x</th> <th>x</th>
<td><p>variable to show on x axis, either <code>"Antibiotic"</code> (default) or <code>"Interpretation"</code> or a grouping variable</p></td> <td><p>variable to show on x axis, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable</p></td>
</tr> </tr>
<tr> <tr>
<th>fill</th> <th>fill</th>
<td><p>variable to categorise using the plots legend, either <code>"Antibiotic"</code> (default) or <code>"Interpretation"</code> or a grouping variable</p></td> <td><p>variable to categorise using the plots legend, either <code>"antibiotic"</code> (default) or <code>"interpretation"</code> or a grouping variable</p></td>
</tr> </tr>
<tr> <tr>
<th>facet</th> <th>facet</th>
<td><p>variable to split plots by, either <code>"Interpretation"</code> (default) or <code>"Antibiotic"</code> or a grouping variable</p></td> <td><p>variable to split plots by, either <code>"interpretation"</code> (default) or <code>"antibiotic"</code> or a grouping variable</p></td>
</tr> </tr>
<tr> <tr>
<th>breaks</th> <th>breaks</th>
@@ -458,7 +451,7 @@
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/select.html'>select</a></span>(<span class='no'>hospital_id</span>, <span class='no'>AMX</span>, <span class='no'>NIT</span>, <span class='no'>FOS</span>, <span class='no'>TMP</span>, <span class='no'>CIP</span>) <span class='kw'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%&gt;%</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"hospital_id"</span>, <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"hospital_id"</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,
<span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='st'>"AMR of Anti-UTI Drugs Per Hospital"</span>,
<span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Hospital"</span>, <span class='kw'>x.title</span> <span class='kw'>=</span> <span class='st'>"Hospital"</span>,
@@ -479,7 +472,7 @@
<span class='co'># group by MO</span> <span class='co'># group by MO</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>bug</span>) <span class='kw'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>bug</span>) <span class='kw'>%&gt;%</span>
<span class='co'># plot the thing, putting MOs on the facet</span> <span class='co'># plot the thing, putting MOs on the facet</span>
<span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"Antibiotic"</span>, <span class='fu'>ggplot_rsi</span>(<span class='kw'>x</span> <span class='kw'>=</span> <span class='st'>"antibiotic"</span>,
<span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"bug"</span>, <span class='kw'>facet</span> <span class='kw'>=</span> <span class='st'>"bug"</span>,
<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>nrow</span> <span class='kw'>=</span> <span class='fl'>1</span>,
docs/reference/index.html
+2 -2
View File
@@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9007</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
</span> </span>
</div> </div>
@@ -435,7 +435,7 @@
</tr><tr> </tr><tr>
<td> <td>
<p><code><a href="portion.html">portion_R()</a></code> <code><a href="portion.html">portion_IR()</a></code> <code><a href="portion.html">portion_I()</a></code> <code><a href="portion.html">portion_SI()</a></code> <code><a href="portion.html">portion_S()</a></code> <code><a href="portion.html">portion_df()</a></code> </p> <p><code><a href="portion.html">portion_R()</a></code> <code><a href="portion.html">portion_IR()</a></code> <code><a href="portion.html">portion_I()</a></code> <code><a href="portion.html">portion_SI()</a></code> <code><a href="portion.html">portion_S()</a></code> <code><a href="portion.html">portion_df()</a></code> <code><a href="portion.html">rsi_df()</a></code> </p>
</td> </td>
<td><p>Calculate resistance of isolates</p></td> <td><p>Calculate resistance of isolates</p></td>
</tr><tr> </tr><tr>
docs/reference/microorganisms.html
+6 -12
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@@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">0.7.0.9000</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
</span> </span>
</div> </div>
@@ -165,13 +165,6 @@
Create frequency tables Create frequency tables
</a> </a>
</li> </li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li> <li>
<a href="../articles/benchmarks.html"> <a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span> <span class="fa fa-shipping-fast"></span>
@@ -252,7 +245,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 67,903 observations and 16 variables:</p><dl class='dl-horizontal'> <p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 67,906 observations and 16 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd> <dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd> <dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd> <dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd>
@@ -272,9 +265,10 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Manually added were:</p><ul> <p>Manually added were:</p><ul>
<li><p>9 species of <em>Streptococcus</em> (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li> <li><p>9 entries of <em>Streptococcus</em> (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
<li><p>2 species of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li> <li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
<li><p>3 other undefined (unknown, unknown Gram negatives and unknown Gram positives)</p></li> <li><p>3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)</p></li>
<li><p>3 other 'undefined' entries (unknown, unknown Gram negatives and unknown Gram positives)</p></li>
<li><p>8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life</p></li> <li><p>8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life</p></li>
</ul> </ul>
docs/reference/portion.html
+7 -9
View File
@@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <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">0.7.0.9000</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.0.9008</span>
</span> </span>
</div> </div>
@@ -166,13 +166,6 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
Create frequency tables Create frequency tables
</a> </a>
</li> </li>
<li>
<a href="../reference/g.test.html">
<span class="fa fa-clipboard-check"></span>
Use the G-test
</a>
</li>
<li> <li>
<a href="../articles/benchmarks.html"> <a href="../articles/benchmarks.html">
<span class="fa fa-shipping-fast"></span> <span class="fa fa-shipping-fast"></span>
@@ -266,6 +259,10 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>portion_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(), <span class='fu'>portion_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)
<span class='fu'>rsi_df</span>(<span class='no'>data</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span>(),
<span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>as_percent</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>combine_SI</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> <span class='kw'>combine_IR</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
@@ -323,7 +320,8 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
<p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> Use <code><a href='first_isolate.html'>first_isolate</a></code> to determine them in your data set.</p> <p><strong>Remember that you should filter your table to let it contain only first isolates!</strong> Use <code><a href='first_isolate.html'>first_isolate</a></code> to determine them in your data set.</p>
<p>These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the <code><a href='count.html'>count</a></code> functions to count isolates. <em>Low counts can infuence the outcome - these <code>portion</code> functions may camouflage this, since they only return the portion albeit being dependent on the <code>minimum</code> parameter.</em></p> <p>These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the <code><a href='count.html'>count</a></code> functions to count isolates. <em>Low counts can infuence the outcome - these <code>portion</code> functions may camouflage this, since they only return the portion albeit being dependent on the <code>minimum</code> parameter.</em></p>
<p><code>portion_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and calculates the portions R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each variable with class <code>"rsi"</code>. <p>The function <code>portion_df</code> takes any variable from <code>data</code> that has an <code>"rsi"</code> class (created with <code><a href='as.rsi.html'>as.rsi</a></code>) and calculates the portions R, I and S. The resulting <em>tidy data</em> (see Source) <code>data.frame</code> will have three rows (S/I/R) and a column for each group and each variable with class <code>"rsi"</code>.</p>
<p>The function <code>rsi_df</code> works exactly like <code>portion_df</code>, but add the number of isolates.
<br /><br /> <br /><br />
To calculate the probability (<em>p</em>) of susceptibility of one antibiotic, we use this formula: To calculate the probability (<em>p</em>) of susceptibility of one antibiotic, we use this formula:
<div style="text-align: center;"><img src='figures/combi_therapy_2.png' alt='' /></div> <div style="text-align: center;"><img src='figures/combi_therapy_2.png' alt='' /></div>
man/count.Rd
+4 -2
View File
@@ -58,9 +58,11 @@ These functions can be used to count resistant/susceptible microbial isolates. A
\details{ \details{
These functions are meant to count isolates. Use the \code{\link{portion}_*} functions to calculate microbial resistance. These functions are meant to count isolates. Use the \code{\link{portion}_*} functions to calculate microbial resistance.
\code{n_rsi} is an alias of \code{count_all}. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to \code{\link{n_distinct}}. Their function is equal to \code{count_S(...) + count_IR(...)}. The function \code{n_rsi} is an alias of \code{count_all}. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to \code{\link{n_distinct}}. Their function is equal to \code{count_S(...) + count_IR(...)}.
\code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}. The function \code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of S, I and R. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
The function \code{rsi_df} works exactly like \code{count_df}, but add the percentage of S, I and R.
} }
\section{Interpretation of S, I and R}{ \section{Interpretation of S, I and R}{
man/ggplot_rsi.Rd
+11 -11
View File
@@ -10,8 +10,8 @@
\alias{labels_rsi_count} \alias{labels_rsi_count}
\title{AMR plots with \code{ggplot2}} \title{AMR plots with \code{ggplot2}}
\usage{ \usage{
ggplot_rsi(data, position = NULL, x = "Antibiotic", ggplot_rsi(data, position = NULL, x = "antibiotic",
fill = "Interpretation", facet = NULL, breaks = seq(0, 1, 0.1), fill = "interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
limits = NULL, translate_ab = "name", combine_SI = TRUE, limits = NULL, translate_ab = "name", combine_SI = TRUE,
combine_IR = FALSE, language = get_locale(), fun = count_df, combine_IR = FALSE, language = get_locale(), fun = count_df,
nrow = NULL, colours = c(S = "#61a8ff", SI = "#61a8ff", I = nrow = NULL, colours = c(S = "#61a8ff", SI = "#61a8ff", I =
@@ -20,12 +20,12 @@ ggplot_rsi(data, position = NULL, x = "Antibiotic",
subtitle = NULL, caption = NULL, x.title = NULL, y.title = NULL, subtitle = NULL, caption = NULL, x.title = NULL, y.title = NULL,
...) ...)
geom_rsi(position = NULL, x = c("Antibiotic", "Interpretation"), geom_rsi(position = NULL, x = c("antibiotic", "interpretation"),
fill = "Interpretation", translate_ab = "name", fill = "interpretation", translate_ab = "name",
language = get_locale(), combine_SI = TRUE, combine_IR = FALSE, language = get_locale(), combine_SI = TRUE, combine_IR = FALSE,
fun = count_df, ...) fun = count_df, ...)
facet_rsi(facet = c("Interpretation", "Antibiotic"), nrow = NULL) facet_rsi(facet = c("interpretation", "antibiotic"), nrow = NULL)
scale_y_percent(breaks = seq(0, 1, 0.1), limits = NULL) scale_y_percent(breaks = seq(0, 1, 0.1), limits = NULL)
@@ -34,7 +34,7 @@ scale_rsi_colours(colours = c(S = "#61a8ff", SI = "#61a8ff", I =
theme_rsi() theme_rsi()
labels_rsi_count(position = NULL, x = "Antibiotic", labels_rsi_count(position = NULL, x = "antibiotic",
translate_ab = "name", combine_SI = TRUE, combine_IR = FALSE, translate_ab = "name", combine_SI = TRUE, combine_IR = FALSE,
datalabels.size = 3, datalabels.colour = "gray15") datalabels.size = 3, datalabels.colour = "gray15")
} }
@@ -43,11 +43,11 @@ labels_rsi_count(position = NULL, x = "Antibiotic",
\item{position}{position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"}} \item{position}{position adjustment of bars, either \code{"fill"} (default when \code{fun} is \code{\link{count_df}}), \code{"stack"} (default when \code{fun} is \code{\link{portion_df}}) or \code{"dodge"}}
\item{x}{variable to show on x axis, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable} \item{x}{variable to show on x axis, either \code{"antibiotic"} (default) or \code{"interpretation"} or a grouping variable}
\item{fill}{variable to categorise using the plots legend, either \code{"Antibiotic"} (default) or \code{"Interpretation"} or a grouping variable} \item{fill}{variable to categorise using the plots legend, either \code{"antibiotic"} (default) or \code{"interpretation"} or a grouping variable}
\item{facet}{variable to split plots by, either \code{"Interpretation"} (default) or \code{"Antibiotic"} or a grouping variable} \item{facet}{variable to split plots by, either \code{"interpretation"} (default) or \code{"antibiotic"} or a grouping variable}
\item{breaks}{numeric vector of positions} \item{breaks}{numeric vector of positions}
@@ -178,7 +178,7 @@ septic_patients \%>\%
select(hospital_id, AMX, NIT, FOS, TMP, CIP) \%>\% select(hospital_id, AMX, NIT, FOS, TMP, CIP) \%>\%
group_by(hospital_id) \%>\% group_by(hospital_id) \%>\%
ggplot_rsi(x = "hospital_id", ggplot_rsi(x = "hospital_id",
facet = "Antibiotic", facet = "antibiotic",
nrow = 1, nrow = 1,
title = "AMR of Anti-UTI Drugs Per Hospital", title = "AMR of Anti-UTI Drugs Per Hospital",
x.title = "Hospital", x.title = "Hospital",
@@ -199,7 +199,7 @@ septic_patients \%>\%
# group by MO # group by MO
group_by(bug) \%>\% group_by(bug) \%>\%
# plot the thing, putting MOs on the facet # plot the thing, putting MOs on the facet
ggplot_rsi(x = "Antibiotic", ggplot_rsi(x = "antibiotic",
facet = "bug", facet = "bug",
translate_ab = FALSE, translate_ab = FALSE,
nrow = 1, nrow = 1,
man/microorganisms.Rd
+5 -4
View File
@@ -4,7 +4,7 @@
\name{microorganisms} \name{microorganisms}
\alias{microorganisms} \alias{microorganisms}
\title{Data set with ~65,000 microorganisms} \title{Data set with ~65,000 microorganisms}
\format{A \code{\link{data.frame}} with 67,903 observations and 16 variables: \format{A \code{\link{data.frame}} with 67,906 observations and 16 variables:
\describe{ \describe{
\item{\code{mo}}{ID of microorganism as used by this package} \item{\code{mo}}{ID of microorganism as used by this package}
\item{\code{col_id}}{Catalogue of Life ID} \item{\code{col_id}}{Catalogue of Life ID}
@@ -30,9 +30,10 @@ A data set containing the microbial taxonomy of six kingdoms from the Catalogue
\details{ \details{
Manually added were: Manually added were:
\itemize{ \itemize{
\item{9 species of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)} \item{9 entries of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
\item{2 species of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])} \item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{3 other undefined (unknown, unknown Gram negatives and unknown Gram positives)} \item{3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)}
\item{3 other 'undefined' entries (unknown, unknown Gram negatives and unknown Gram positives)}
\item{8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life} \item{8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life}
} }
} }
man/portion.Rd
+9 -2
View File
@@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/portion.R % Please edit documentation in R/portion.R, R/rsi_df.R
\name{portion} \name{portion}
\alias{portion} \alias{portion}
\alias{portion_R} \alias{portion_R}
@@ -8,6 +8,7 @@
\alias{portion_SI} \alias{portion_SI}
\alias{portion_S} \alias{portion_S}
\alias{portion_df} \alias{portion_df}
\alias{rsi_df}
\title{Calculate resistance of isolates} \title{Calculate resistance of isolates}
\source{ \source{
\strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}. \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
@@ -33,6 +34,10 @@ portion_S(..., minimum = 30, as_percent = FALSE,
portion_df(data, translate_ab = "name", language = get_locale(), portion_df(data, translate_ab = "name", language = get_locale(),
minimum = 30, as_percent = FALSE, combine_SI = TRUE, minimum = 30, as_percent = FALSE, combine_SI = TRUE,
combine_IR = FALSE) combine_IR = FALSE)
rsi_df(data, translate_ab = "name", language = get_locale(),
minimum = 30, as_percent = FALSE, combine_SI = TRUE,
combine_IR = FALSE)
} }
\arguments{ \arguments{
\item{...}{one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.} \item{...}{one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.}
@@ -66,7 +71,9 @@ These functions can be used to calculate the (co-)resistance of microbial isolat
These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the \code{\link[AMR]{count}} functions to count isolates. \emph{Low counts can infuence the outcome - these \code{portion} functions may camouflage this, since they only return the portion albeit being dependent on the \code{minimum} parameter.} These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the \code{\link[AMR]{count}} functions to count isolates. \emph{Low counts can infuence the outcome - these \code{portion} functions may camouflage this, since they only return the portion albeit being dependent on the \code{minimum} parameter.}
\code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}. The function \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each group and each variable with class \code{"rsi"}.
The function \code{rsi_df} works exactly like \code{portion_df}, but add the number of isolates.
\if{html}{ \if{html}{
\cr\cr \cr\cr
To calculate the probability (\emph{p}) of susceptibility of one antibiotic, we use this formula: To calculate the probability (\emph{p}) of susceptibility of one antibiotic, we use this formula:
tests/testthat/test-count.R
+3 -3
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@@ -50,17 +50,17 @@ test_that("counts work", {
# count_df # count_df
expect_equal( expect_equal(
septic_patients %>% select(AMX) %>% count_df() %>% pull(Value), septic_patients %>% select(AMX) %>% count_df() %>% pull(value),
c(septic_patients$AMX %>% count_SI(), c(septic_patients$AMX %>% count_SI(),
septic_patients$AMX %>% count_R()) septic_patients$AMX %>% count_R())
) )
expect_equal( expect_equal(
septic_patients %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(Value), septic_patients %>% select(AMX) %>% count_df(combine_IR = TRUE) %>% pull(value),
c(septic_patients$AMX %>% count_S(), c(septic_patients$AMX %>% count_S(),
septic_patients$AMX %>% count_IR()) septic_patients$AMX %>% count_IR())
) )
expect_equal( expect_equal(
septic_patients %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(Value), septic_patients %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
c(septic_patients$AMX %>% count_S(), c(septic_patients$AMX %>% count_S(),
septic_patients$AMX %>% count_I(), septic_patients$AMX %>% count_I(),
septic_patients$AMX %>% count_R()) septic_patients$AMX %>% count_R())
tests/testthat/test-portion.R
+3 -3
View File
@@ -100,17 +100,17 @@ test_that("portions works", {
# portion_df # portion_df
expect_equal( expect_equal(
septic_patients %>% select(AMX) %>% portion_df() %>% pull(Value), septic_patients %>% select(AMX) %>% portion_df() %>% pull(value),
c(septic_patients$AMX %>% portion_SI(), c(septic_patients$AMX %>% portion_SI(),
septic_patients$AMX %>% portion_R()) septic_patients$AMX %>% portion_R())
) )
expect_equal( expect_equal(
septic_patients %>% select(AMX) %>% portion_df(combine_IR = TRUE) %>% pull(Value), septic_patients %>% select(AMX) %>% portion_df(combine_IR = TRUE) %>% pull(value),
c(septic_patients$AMX %>% portion_S(), c(septic_patients$AMX %>% portion_S(),
septic_patients$AMX %>% portion_IR()) septic_patients$AMX %>% portion_IR())
) )
expect_equal( expect_equal(
septic_patients %>% select(AMX) %>% portion_df(combine_SI = FALSE) %>% pull(Value), septic_patients %>% select(AMX) %>% portion_df(combine_SI = FALSE) %>% pull(value),
c(septic_patients$AMX %>% portion_S(), c(septic_patients$AMX %>% portion_S(),
septic_patients$AMX %>% portion_I(), septic_patients$AMX %>% portion_I(),
septic_patients$AMX %>% portion_R()) septic_patients$AMX %>% portion_R())