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set_mo_source

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dr. M.S. (Matthijs) Berends 2019-01-21 15:53:01 +01:00
parent c6c3088e9f
commit 46dcc7e2e8
36 changed files with 1134 additions and 261 deletions
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1
.Rbuildignore
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@ -15,6 +15,7 @@
^docs$ ^docs$
^git_merge\.sh$ ^git_merge\.sh$
^git_premaster\.sh$ ^git_premaster\.sh$
^git_siteonly\.sh$
^index\.md$ ^index\.md$
^installed_deps$ ^installed_deps$
^Meta$ ^Meta$

1
.gitignore vendored
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@ -20,5 +20,6 @@ vignettes/*.R
^CRAN-RELEASE$ ^CRAN-RELEASE$
git_premaster.sh git_premaster.sh
git_merge.sh git_merge.sh
git_siteonly.sh
packrat/lib*/ packrat/lib*/
packrat/src/ packrat/src/

5
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.5.0.9010 Version: 0.5.0.9011
Date: 2019-01-17 Date: 2019-01-21
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(
@ -58,6 +58,7 @@ Imports:
Suggests: Suggests:
covr (>= 3.0.1), covr (>= 3.0.1),
ggplot2, ggplot2,
readxl,
rmarkdown, rmarkdown,
rstudioapi, rstudioapi,
testthat (>= 1.0.2) testthat (>= 1.0.2)

2
NAMESPACE
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@ -77,6 +77,7 @@ export(full_join_microorganisms)
export(g.test) export(g.test)
export(geom_rsi) export(geom_rsi)
export(get_locale) export(get_locale)
export(get_mo_source)
export(ggplot_rsi) export(ggplot_rsi)
export(ggplot_rsi_predict) export(ggplot_rsi_predict)
export(guess_ab_col) export(guess_ab_col)
@ -136,6 +137,7 @@ export(rsi_predict)
export(scale_rsi_colours) export(scale_rsi_colours)
export(scale_y_percent) export(scale_y_percent)
export(semi_join_microorganisms) export(semi_join_microorganisms)
export(set_mo_source)
export(skewness) export(skewness)
export(theme_rsi) export(theme_rsi)
export(top_freq) export(top_freq)

2
NEWS.md
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@ -6,6 +6,7 @@
* New website: https://msberends.gitlab.io/AMR (built with the great [`pkgdown`](https://pkgdown.r-lib.org/)) * New website: https://msberends.gitlab.io/AMR (built with the great [`pkgdown`](https://pkgdown.r-lib.org/))
* Contains the complete manual of this package and all of its functions with an explanation of their parameters * Contains the complete manual of this package and all of its functions with an explanation of their parameters
* Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis * Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis
* New functions `set_mo_source()` and `get_mo_source()` to use your own predefined MO codes as input for `as.mo()` and consequently all `mo_*` functions
* Support for the upcoming [`dplyr`](https://dplyr.tidyverse.org) version 0.8.0 * Support for the upcoming [`dplyr`](https://dplyr.tidyverse.org) version 0.8.0
* New function `guess_ab_col()` to find an antibiotic column in a table * New function `guess_ab_col()` to find an antibiotic column in a table
* New function `mo_failures()` to review values that could not be coerced to a valid MO code, using `as.mo()`. This latter function will now only show a maximum of 25 uncoerced values. * New function `mo_failures()` to review values that could not be coerced to a valid MO code, using `as.mo()`. This latter function will now only show a maximum of 25 uncoerced values.
@ -55,6 +56,7 @@
* Removed parameter `output_logical`, the function will now always return a logical value * Removed parameter `output_logical`, the function will now always return a logical value
* Renamed parameter `filter_specimen` to `specimen_group`, although using `filter_specimen` will still work * Renamed parameter `filter_specimen` to `specimen_group`, although using `filter_specimen` will still work
* A note to the manual pages of the `portion` functions, that low counts can influence the outcome and that the `portion` functions may camouflage this, since they only return the portion (albeit being dependent on the `minimum` parameter) * A note to the manual pages of the `portion` functions, that low counts can influence the outcome and that the `portion` functions may camouflage this, since they only return the portion (albeit being dependent on the `minimum` parameter)
* Merged data sets `microorganisms.certe` and `microorganisms.umcg` into `microorganisms.codes`
* Function `mo_taxonomy()` now contains the kingdom too * Function `mo_taxonomy()` now contains the kingdom too
* Reduce false positives for `is.rsi.eligible()` * Reduce false positives for `is.rsi.eligible()`
* Summaries of class `mo` will now return the top 3 and the unique count, e.g. using `summary(mo)` * Summaries of class `mo` will now return the top 3 and the unique count, e.g. using `summary(mo)`

24
R/data.R
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@ -148,7 +148,7 @@
#' } #' }
#' @source [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}. #' @source [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}} #' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.codes}}
"microorganisms" "microorganisms"
#' Data set with old taxonomic data from ITIS #' Data set with old taxonomic data from ITIS
@ -167,29 +167,17 @@
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}} #' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}}
"microorganisms.old" "microorganisms.old"
#' Translation table for UMCG #' Translation table for microorganism codes
#' #'
#' A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}. #' A data set containing commonly used codes for microorganisms. Define your own with \code{\link{set_mo_source}}.
#' @format A \code{\link{data.frame}} with 1,095 observations and 2 variables: #' @format A \code{\link{data.frame}} with 3,303 observations and 2 variables:
#' \describe{ #' \describe{
#' \item{\code{umcg}}{Code of microorganism according to UMCG MMB} #' \item{\code{certe}}{Commonly used code of a microorganism}
#' \item{\code{certe}}{Code of microorganism according to Certe MMB}
#' }
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{microorganisms.certe}} \code{\link{microorganisms}}
"microorganisms.umcg"
#' Translation table for Certe
#'
#' A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
#' @format A \code{\link{data.frame}} with 2,665 observations and 2 variables:
#' \describe{
#' \item{\code{certe}}{Code of microorganism according to Certe MMB}
#' \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}} #' \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
#' } #' }
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{microorganisms}} #' @seealso \code{\link{as.mo}} \code{\link{microorganisms}}
"microorganisms.certe" "microorganisms.codes"
#' Data set with 2000 blood culture isolates of septic patients #' Data set with 2000 blood culture isolates of septic patients
#' #'

3
R/globals.R
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@ -54,11 +54,10 @@ globalVariables(c(".",
"median", "median",
"mic", "mic",
"microorganisms", "microorganisms",
"microorganisms.certe", "microorganisms.codes",
"microorganisms.old", "microorganisms.old",
"microorganisms.oldDT", "microorganisms.oldDT",
"microorganisms.prevDT", "microorganisms.prevDT",
"microorganisms.umcg",
"microorganisms.unprevDT", "microorganisms.unprevDT",
"microorganismsDT", "microorganismsDT",
"mo", "mo",

56
R/mo.R
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@ -30,7 +30,7 @@
#' #'
#' This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D. #' This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.
#' @param allow_uncertain a logical to indicate whether the input should be checked for less possible results, see Details #' @param allow_uncertain a logical to indicate whether the input should be checked for less possible results, see Details
#' @param reference_df a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. The first column can be any microbial name, code or ID (used in your analysis or organisation), the second column must be a valid \code{mo} as found in the \code{\link{microorganisms}} data set. #' @param reference_df a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. See \code{\link{set_mo_source}} and \code{\link{get_mo_source}} to automate the usage of your own codes (e.g. used in your analysis or organisation).
#' @rdname as.mo #' @rdname as.mo
#' @aliases mo #' @aliases mo
#' @keywords mo Becker becker Lancefield lancefield guess #' @keywords mo Becker becker Lancefield lancefield guess
@ -139,7 +139,7 @@
#' df <- df %>% #' df <- df %>%
#' mutate(mo = as.mo(paste(genus, species))) #' mutate(mo = as.mo(paste(genus, species)))
#' } #' }
as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = NULL) { as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = get_mo_source()) {
mo <- mo_validate(x = x, property = "mo", mo <- mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield, Becker = Becker, Lancefield = Lancefield,
allow_uncertain = allow_uncertain, reference_df = reference_df) allow_uncertain = allow_uncertain, reference_df = reference_df)
@ -152,11 +152,11 @@ is.mo <- function(x) {
identical(class(x), "mo") identical(class(x), "mo")
} }
#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated #' @importFrom dplyr %>% pull left_join n_distinct progress_estimated filter
#' @importFrom data.table data.table as.data.table setkey #' @importFrom data.table data.table as.data.table setkey
#' @importFrom crayon magenta red italic #' @importFrom crayon magenta red italic
exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
allow_uncertain = TRUE, reference_df = NULL, allow_uncertain = TRUE, reference_df = get_mo_source(),
property = "mo", clear_options = TRUE) { property = "mo", clear_options = TRUE) {
if (!"AMR" %in% base::.packages()) { if (!"AMR" %in% base::.packages()) {
@ -206,11 +206,16 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
if (!is.data.frame(reference_df) | NCOL(reference_df) < 2) { if (!is.data.frame(reference_df) | NCOL(reference_df) < 2) {
stop('`reference_df` must be a data.frame with at least two columns.', call. = FALSE) stop('`reference_df` must be a data.frame with at least two columns.', call. = FALSE)
} }
# remove factors, just keep characters if (!"mo" %in% colnames(reference_df)) {
stop("`reference_df` must contain a column `mo` with values from the 'microorganisms' data set.", call. = FALSE)
}
reference_df <- reference_df %>% filter(!is.na(mo))
# # remove factors, just keep characters
suppressWarnings( suppressWarnings(
reference_df[] <- lapply(reference_df, as.character) reference_df[] <- lapply(reference_df, as.character)
) )
} }
if (all(identical(trimws(x_input), "") | is.na(x_input))) { if (all(identical(trimws(x_input), "") | is.na(x_input))) {
# all empty # all empty
if (property == "mo") { if (property == "mo") {
@ -220,24 +225,25 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
} else { } else {
return(rep(NA_character_, length(x_input))) return(rep(NA_character_, length(x_input)))
} }
} else if (all(x %in% microorganismsDT[["mo"]])) {
# existing mo codes when not looking for property "mo", like mo_genus("B_ESCHR_COL") } else if (all(x %in% reference_df[, 1])
x <- microorganismsDT[data.table(mo = x), on = "mo", ..property][[1]] & all(reference_df[, "mo"] %in% microorganismsDT[["mo"]])) {
} else if (!is.null(reference_df) # all in reference df
& all(x %in% reference_df[, 1])
& all(reference_df[, 2] %in% microorganismsDT[["mo"]])) {
# manually defined reference
colnames(reference_df)[1] <- "x" colnames(reference_df)[1] <- "x"
colnames(reference_df)[2] <- "mo"
suppressWarnings( suppressWarnings(
x <- data.frame(x = x, stringsAsFactors = FALSE) %>% x <- data.frame(x = x, stringsAsFactors = FALSE) %>%
left_join(reference_df, by = "x") %>% left_join(reference_df, by = "x") %>%
left_join(microorganisms, by = "mo") %>% left_join(microorganisms, by = "mo") %>%
pull(property) pull(property)
) )
} else if (all(toupper(x) %in% microorganisms.certe[, "certe"])) {
# old Certe codes } else if (all(x %in% microorganismsDT[["mo"]])) {
y <- as.data.table(microorganisms.certe)[data.table(certe = toupper(x)), on = "certe", ] # existing mo codes when not looking for property "mo", like mo_genus("B_ESCHR_COL")
x <- microorganismsDT[data.table(mo = x), on = "mo", ..property][[1]]
} else if (all(toupper(x) %in% microorganisms.codes[, "code"])) {
# commonly used MO codes
y <- as.data.table(microorganisms.codes)[data.table(code = toupper(x)), on = "code", ]
x <- microorganismsDT[data.table(mo = y[["mo"]]), on = "mo", ..property][[1]] x <- microorganismsDT[data.table(mo = y[["mo"]]), on = "mo", ..property][[1]]
} else if (!all(x %in% microorganismsDT[[property]])) { } else if (!all(x %in% microorganismsDT[[property]])) {
@ -419,28 +425,16 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
} }
# TRY OTHER SOURCES ---- # TRY OTHER SOURCES ----
if (toupper(x_backup[i]) %in% microorganisms.certe[, 1]) { if (toupper(x_backup[i]) %in% microorganisms.codes[, 1]) {
mo_found <- microorganisms.certe[toupper(x_backup[i]) == microorganisms.certe[, 1], 2][1L] mo_found <- microorganisms.codes[toupper(x_backup[i]) == microorganisms.codes[, 1], "mo"][1L]
if (length(mo_found) > 0) { if (length(mo_found) > 0) {
x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L] x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
next next
} }
} }
if (x_backup[i] %in% microorganisms.umcg[, 1]) {
mo_umcg <- microorganisms.umcg[microorganisms.umcg[, 1] == x_backup[i], 2]
mo_found <- microorganisms.certe[microorganisms.certe[, 1] == mo_umcg, 2][1L]
if (length(mo_found) == 0) {
# not found
x[i] <- NA_character_
failures <- c(failures, x_backup[i])
} else {
x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
}
next
}
if (!is.null(reference_df)) { if (!is.null(reference_df)) {
if (x_backup[i] %in% reference_df[, 1]) { if (x_backup[i] %in% reference_df[, 1]) {
ref_mo <- reference_df[reference_df[, 1] == x_backup[i], 2] ref_mo <- reference_df[reference_df[, 1] == x_backup[i], "mo"]
if (ref_mo %in% microorganismsDT[, mo]) { if (ref_mo %in% microorganismsDT[, mo]) {
x[i] <- microorganismsDT[mo == ref_mo, ..property][[1]][1L] x[i] <- microorganismsDT[mo == ref_mo, ..property][[1]][1L]
next next

174
R/mo_source.R Normal file
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@ -0,0 +1,174 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== #
#' Use predefined reference data set
#'
#' These functions can be used to predefine your own reference to be used in \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}.
#' @param path location of your reference file, see Details
#' @rdname mo_source
#' @name mo_source
#' @aliases set_mo_source get_mo_source
#' @details The reference file can be a text file seperated with commas (CSV) or pipes, an Excel file (old 'xls' format or new 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the \code{readxl} package installed.
#'
#' \code{set_mo_source} will check the file for validity: it must be a \code{data.frame}, must have a column named \code{"mo"} which contains values from \code{microorganisms$mo} and must have a reference column with your own defined values. If all tests pass, \code{set_mo_source} will read the file into R and export it to \code{"~/.mo_source.rds"}. This compressed data file will then be used at default for MO determination (function \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}). The location of the original file will be saved as option with \code{\link{options}(mo_source = path)}. Its timestamp will be saved with \code{\link{options}(mo_source_datetime = ...)}.
#'
#' \code{get_mo_source} will return the data set by reading \code{"~/.mo_source.rds"} with \code{\link{readRDS}}. If the original file has changed (the file defined with \code{path}), it will call \code{set_mo_source} to update the data file automatically.
#'
#' Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file will have a size of 0.1 kB and can be read by \code{get_mo_source} in only a couple of microseconds (a millionth of a second).
#' @importFrom dplyr select everything
#' @export
#' @inheritSection AMR Read more on our website!
#' @examples
#' \dontrun{
#'
#' # imagine this Excel file (mo codes looked up in `microorganisms` data set):
#' # A B
#' # 1 our code mo
#' # 2 lab_mo_ecoli B_ESCHR_COL
#' # 3 lab_mo_kpneumoniae B_KLBSL_PNE
#'
#' # 1. We save it as 'home/me/ourcodes.xlsx'
#'
#' # 2. We use it for input:
#' set_mo_source("C:\path\ourcodes.xlsx")
#' #> Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#'
#' # 3. And use it in our functions:
#' as.mo("lab_mo_ecoli")
#' #> B_ESCHR_COL
#'
#' mo_genus("lab_mo_kpneumoniae")
#' #> "Klebsiella"
#'
#' # 4. It will look for changes itself:
#' # (add new row to the Excel file and save it)
#'
#' mo_genus("lab_mo_kpneumoniae")
#' #> Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#' #> "Klebsiella"
#' }
set_mo_source <- function(path) {
if (!is.character(path) | length(path) > 1) {
stop("`path` must be a character of length 1.")
}
if (path == "") {
options(mo_source = NULL)
options(mo_source_timestamp = NULL)
if (file.exists("~/.mo_source.rds")) {
unlink("~/.mo_source.rds")
message("Removed mo_source file '~/.mo_source.rds'.")
}
return(invisible())
}
if (!file.exists(path)) {
stop("File not found: ", path)
}
is_valid <- function(df) {
valid <- TRUE
if (!is.data.frame(df)) {
valid <- FALSE
} else if (!"mo" %in% colnames(df)) {
valid <- FALSE
} else if (!all(df$mo %in% AMR::microorganisms$mo)) {
valid <- FALSE
} else if (NCOL(df) < 2) {
valid <- FALSE
}
valid
}
if (path %like% '[.]rds$') {
df <- readRDS(path)
} else if (path %like% '[.]xlsx?$') {
# is Excel file (old or new)
if (!"readxl" %in% utils::installed.packages()) {
stop("Install the 'readxl' package first.")
}
if (path %like% '[.]xlsx$') {
df <- readxl::read_xlsx(path)
} else {
df <- readxl::read_xls(path)
}
} else {
# try comma first
try(
df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
silent = TRUE)
if (!is_valid(df)) {
# try pipe
try(
df <- utils::read.table(header = TRUE, sep = "|", stringsAsFactors = FALSE),
silent = TRUE)
}
}
if (!is_valid(df)) {
stop("File must contain a column with self-defined values and a reference column `mo` with valid values from the `microorganisms` data set.")
}
if (colnames(df)[1] == "mo") {
# put mo to the end
df <- df %>% select(-"mo", everything(), "mo")
}
df <- as.data.frame(df, stringAsFactors = FALSE)
# success
if (file.exists("~/.mo_source.rds")) {
action <- "Updated"
} else {
action <- "Created"
}
saveRDS(df, "~/.mo_source.rds")
options(mo_source = path)
options(mo_source_timestamp = as.character(file.info(path)$mtime))
message(action, " mo_source file '~/.mo_source.rds' from '", path, "'.")
}
#' @rdname mo_source
#' @export
get_mo_source <- function() {
if (is.null(getOption("mo_source", NULL))) {
return(NULL)
} else {
old_time <- as.POSIXct(getOption("mo_source_timestamp"))
new_time <- as.POSIXct(as.character(file.info(getOption("mo_source", ""))$mtime))
if (is.na(new_time)) {
# source file was deleted, remove reference too
set_mo_source("")
return(NULL)
}
if (new_time != old_time) {
# set updated source
set_mo_source(getOption("mo_source"))
}
}
readRDS("~/.mo_source.rds")
}

141
_pkgdown.yml
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@ -19,7 +19,7 @@
# Visit our website for more info: https://msberends.gitab.io/AMR. # # Visit our website for more info: https://msberends.gitab.io/AMR. #
# ==================================================================== # # ==================================================================== #
url: https://msberends.gitlab.io/AMR url: 'https://msberends.gitlab.io/AMR'
title: 'AMR (for R)' title: 'AMR (for R)'
@ -74,74 +74,77 @@ navbar:
href: 'LICENSE-text.html' href: 'LICENSE-text.html'
reference: reference:
- title: 'Background information' - title: 'Background information'
desc: > desc: >
Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html) Some pages about our package and its external sources. Be sure to read our [How To's](./../articles/index.html)
for more information about how to work with functions in this package. for more information about how to work with functions in this package.
contents: contents:
- '`AMR`' - '`AMR`'
- '`ITIS`' - '`ITIS`'
- title: 'Cleaning your data' - title: 'Cleaning your data'
desc: > desc: >
Functions for cleaning and optimising your data, to be able Functions for cleaning and optimising your data, to be able to add
to add variables later on (like taxonomic properties) or to variables later on (like taxonomic properties) or to fix and extend
fix and extend antibiotic interpretations by applying [EUCAST rules](http://www.eucast.org/expert_rules_and_intrinsic_resistance/). antibiotic interpretations by applying [EUCAST rules](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
contents: contents:
- starts_with("as.") - starts_with("as.")
- '`eucast_rules`' - '`mo_source`'
- '`guess_ab_col`' - '`eucast_rules`'
- '`read.4D`' - '`guess_ab_col`'
- title: 'Adding variables to your data' - '`read.4D`'
desc: > - title: 'Adding variables to your data'
Functions to add new data to existing data, like the determination desc: >
of first isolates, Functions to add new data to existing data, like the determination
contents: of first isolates, multi-drug resistant microorganisms (MDRO), getting
- '`first_isolate`' properties of microorganisms or antibiotics and determining the age of
- '`mdro`' patients or divide ages into age groups.
- '`key_antibiotics`' contents:
- '`mo_property`' - '`first_isolate`'
- '`ab_property`' - '`mdro`'
- '`atc_property`' - '`key_antibiotics`'
- '`abname`' - '`mo_property`'
- '`age`' - '`ab_property`'
- '`age_groups`' - '`atc_property`'
- '`p.symbol`' - '`abname`'
- '`join`' - '`age`'
- title: 'Analysing your data' - '`age_groups`'
desc: > - '`p.symbol`'
Functions for conducting AMR analysis - '`join`'
contents: - title: 'Analysing your data'
- '`count`' desc: >
- '`portion`' Functions for conducting AMR analysis, like counting isolates, calculating
- '`freq`' resistance or susceptibility, creating frequency tables or make plots.
- '`g.test`' contents:
- '`ggplot_rsi`' - '`count`'
- '`kurtosis`' - '`portion`'
- '`resistance_predict`' - '`freq`'
- '`rsi`' - '`g.test`'
- '`skewness`' - '`ggplot_rsi`'
- title: 'Included data sets' - '`kurtosis`'
desc: > - '`resistance_predict`'
References for microorganisms and antibiotics, and even a - '`rsi`'
genuine data set with isolates from septic patients. - '`skewness`'
contents: - title: 'Included data sets'
- '`antibiotics`' desc: >
- '`microorganisms`' References for microorganisms and antibiotics, and even a
- '`septic_patients`' genuine data set with isolates from septic patients.
- '`microorganisms.certe`' contents:
- '`microorganisms.old`' - '`antibiotics`'
- '`microorganisms.umcg`' - '`microorganisms`'
- '`supplementary_data`' - '`septic_patients`'
- title: Other - '`microorganisms.codes`'
desc: > - '`microorganisms.old`'
These functions are mostly for internal use, but some of - '`supplementary_data`'
them may also be suitable for your analysis. Especially the - title: Other
'like' function can be useful: `if (x %like% y) {...}`. desc: >
contents: These functions are mostly for internal use, but some of
- '`get_locale`' them may also be suitable for your analysis. Especially the
- '`like`' 'like' function can be useful: `if (x %like% y) {...}`.
- '`mo_failures`' contents:
- '`mo_renamed`' - '`get_locale`'
- '`like`'
- '`mo_failures`'
- '`mo_renamed`'
authors: authors:
Matthijs S. Berends: Matthijs S. Berends:

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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="Released version">0.5.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span> </span>
</div> </div>

4
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@ -40,7 +40,7 @@
</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">0.5.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span> </span>
</div> </div>
@ -178,7 +178,7 @@
<h1>Benchmarks</h1> <h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4> <h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">17 January 2019</h4> <h4 class="date">21 January 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div> <div class="hidden name"><code>benchmarks.Rmd</code></div>

2
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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="Released version">0.5.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span> </span>
</div> </div>

2
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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="Released version">0.5.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span> </span>
</div> </div>

66
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@ -23,22 +23,22 @@
/* class for footer */ /* class for footer */
.university { .university {
background-image: url(logo_rug.png); background-image: url(logo_rug.png);
height: 40px; background-size: 200px;
background-size: 160px; background-repeat: no-repeat;
background-repeat: no-repeat; background-position: center right;
} }
/* Supports icons for brand using font-awesome */ /* Supports icons for brand using font-awesome */
.fab { .fab {
font-family: "Font Awesome 5 Brands" !important; font-family: "Font Awesome 5 Brands" !important;
} }
/* Remove the 'Read more on our website!' part from the manual pages */ /* Remove the 'Read more on our website!' part from the manual pages */
#read-more-on-our-website-, #read-more-on-our-website-,
#read-more-on-our-website- + p, #read-more-on-our-website- + p,
li a[href="#read-more-on-our-website-"] { li a[href="#read-more-on-our-website-"] {
display: none; display: none;
} }
/* make colour darker and better readable for links */ /* make colour darker and better readable for links */
@ -60,21 +60,33 @@ a pre[href], a pre[href]:hover, a pre[href]:focus {
/* syntax font */ /* syntax font */
pre, code { pre, code {
font-family: 'Courier New', monospace; font-family: 'Courier New', monospace;
font-size: 100% !important; font-size: 100% !important;
font-weight: bold; font-weight: bold;
background-color: transparent; background-color: transparent;
} }
pre { pre {
font-size: 90% !important; font-size: 90% !important;
} }
kbd {
display: inline-block;
padding: 0 4px;
box-shadow: 1px 1px 1px #2c3e50;
margin: 2px;
font-size: small;
vertical-align: text-bottom;
color: #2c3e50;
background: #eee;
font-weight: bold;
}
li, p { li, p {
line-height: 1.5; line-height: 1.5;
} }
/* slightly smaller blockquote */ /* slightly smaller blockquote */
blockquote { blockquote {
font-size: 98%; font-size: 98%;
} }
/* 2nd list in navigation should be smaller */ /* 2nd list in navigation should be smaller */
@ -91,11 +103,11 @@ help {
/* replace 'Developers' with 'Authors' */ /* replace 'Developers' with 'Authors' */
.developers h2 { .developers h2 {
display: none; display: none;
} }
.developers:before { .developers:before {
content: 'Authors'; content: 'Authors';
font-size: 1.5em; font-size: 1.5em;
} }
/* hide version label */ /* hide version label */
@ -105,11 +117,11 @@ help {
/* Date of vignettes */ /* Date of vignettes */
.template-article .date:before { .template-article .date:before {
content: 'Last updated: '; content: 'Last updated: ';
} }
.template-article .date { .template-article .date {
font-size: 14px; font-size: 14px;
padding-top: 40px; padding-top: 40px;
} }
/* more space between icon and text in top menu */ /* more space between icon and text in top menu */
@ -134,15 +146,21 @@ help {
padding: 4px !important; padding: 4px !important;
} }
thead { thead {
border-top: 2px solid black; border-top: 2px solid black;
border-bottom: 2px solid black; border-bottom: 2px solid black;
} }
tbody { thead ~ tbody {
border-bottom: 2px solid black; /* only when it has a header */
border-bottom: 2px solid black;
} }
table a:not(.btn), .table a:not(.btn) { table a:not(.btn), .table a:not(.btn) {
text-decoration: inherit; text-decoration: inherit;
} }
table a:not(.btn):hover, .table a:not(.btn):hover { table a:not(.btn):hover, .table a:not(.btn):hover {
text-decoration: underline; text-decoration: underline;
}
.template-reference-index h2 ~ p {
font-size: 110%;
/* font-weight: bold; */
} }

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@ -29,11 +29,19 @@ $('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" hr
// Edit footer // Edit footer
$( document ).ready(function() { $( document ).ready(function() {
// redirect to GitLab
var url_old = window.location.href;
var url_new = url_old.replace("github", "gitlab");
if (url_old != url_new) {
window.location.replace(url);
}
$('footer').html('<p>' + $('footer').html('<p>' +
$('footer .copyright p').html().replace("Developed by", $('footer .copyright p').html().replace("Developed by",
"<code>AMR</code> (for R). Developed at the University of Groningen.<br>Authors:") + '<code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl" target="_blank">University of Groningen</a>.<br>Authors:') +
'</p>'); '</p>');
//$('footer').prepend("<div class='university'/>"); $('footer').addClass("university");
// Edit title of manual // Edit title of manual
$('.template-reference-index h1').text('Manual'); $('.template-reference-index h1').text('Manual');

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@ -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="Released version">0.5.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span> </span>
</div> </div>
@ -191,6 +191,7 @@
<li>Research Microbiologists</li> <li>Research Microbiologists</li>
<li>Biomedical Researchers</li> <li>Biomedical Researchers</li>
<li>Research Pharmacologists</li> <li>Research Pharmacologists</li>
<li>Data Scientists / Data Analysts</li>
</ul> </ul>
<p>Veterinary Microbiology:</p> <p>Veterinary Microbiology:</p>
<ul> <ul>
@ -203,14 +204,6 @@
<li>Extremophile Researchers</li> <li>Extremophile Researchers</li>
<li>Astrobiologists</li> <li>Astrobiologists</li>
</ul> </ul>
<p>Other specialists in any of the above fields:</p>
<ul>
<li>Data Scientists/Data Analysts</li>
<li>Biotechnologists</li>
<li>Biochemists</li>
<li>Geneticists</li>
<li>Molecular Biologists/Microbiologists</li>
</ul>
<p>Developers:</p> <p>Developers:</p>
<ul> <ul>
<li>Package developers for R</li> <li>Package developers for R</li>
@ -222,7 +215,7 @@
<a href="#get-this-package" class="anchor"></a>Get this package</h3> <a href="#get-this-package" class="anchor"></a>Get this package</h3>
<p>This package is available on the official R network (CRAN), which has a peer-reviewed submission process. Install this package in R with:</p> <p>This package is available on the official R network (CRAN), which has a peer-reviewed submission process. Install this package in R with:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</a></code></pre></div> <div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"AMR"</span>)</a></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on menu <em>Tools</em> &gt; <em>Install Packages…</em>, then type in “AMR” and press <kbd>Install</kbd>.</p> <p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
</div> </div>
<div id="get-started" class="section level3"> <div id="get-started" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">

5
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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="Released version">0.5.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span> </span>
</div> </div>
@ -235,6 +235,7 @@
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis</li> <li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis</li>
</ul> </ul>
</li> </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>
<li>New function <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> to find an antibiotic column in a table</li> <li>New function <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> to find an antibiotic column in a table</li>
<li>New function <code><a href="../reference/mo_failures.html">mo_failures()</a></code> to review values that could not be coerced to a valid MO code, using <code><a href="../reference/as.mo.html">as.mo()</a></code>. This latter function will now only show a maximum of 25 uncoerced values.</li> <li>New function <code><a href="../reference/mo_failures.html">mo_failures()</a></code> to review values that could not be coerced to a valid MO code, using <code><a href="../reference/as.mo.html">as.mo()</a></code>. This latter function will now only show a maximum of 25 uncoerced values.</li>
@ -297,6 +298,8 @@
</ul> </ul>
</li> </li>
<li>A note to the manual pages of the <code>portion</code> functions, that low counts can influence the outcome and that the <code>portion</code> functions may camouflage this, since they only return the portion (albeit being dependent on the <code>minimum</code> parameter)</li> <li>A note to the manual pages of the <code>portion</code> functions, that low counts can influence the outcome and that the <code>portion</code> functions may camouflage this, since they only return the portion (albeit being dependent on the <code>minimum</code> parameter)</li>
<li>Merged data sets <code>microorganisms.certe</code> and <code>microorganisms.umcg</code> into <code>microorganisms.codes</code>
</li>
<li>Function <code><a href="../reference/mo_property.html">mo_taxonomy()</a></code> now contains the kingdom too</li> <li>Function <code><a href="../reference/mo_property.html">mo_taxonomy()</a></code> now contains the kingdom too</li>
<li>Reduce false positives for <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code> <li>Reduce false positives for <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code>
</li> </li>

6
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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">0.5.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span> </span>
</div> </div>
@ -228,7 +228,7 @@
</div> </div>
<pre class="usage"><span class='fu'>as.mo</span>(<span class='no'>x</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <pre class="usage"><span class='fu'>as.mo</span>(<span class='no'>x</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='kw'>NULL</span>) <span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='fu'><a href='mo_source.html'>get_mo_source</a></span>())
<span class='fu'>is.mo</span>(<span class='no'>x</span>)</pre> <span class='fu'>is.mo</span>(<span class='no'>x</span>)</pre>
@ -255,7 +255,7 @@
</tr> </tr>
<tr> <tr>
<th>reference_df</th> <th>reference_df</th>
<td><p>a <code>data.frame</code> to use for extra reference when translating <code>x</code> to a valid <code>mo</code>. The first column can be any microbial name, code or ID (used in your analysis or organisation), the second column must be a valid <code>mo</code> as found in the <code><a href='microorganisms.html'>microorganisms</a></code> data set.</p></td> <td><p>a <code>data.frame</code> to use for extra reference when translating <code>x</code> to a valid <code>mo</code>. See <code><a href='mo_source.html'>set_mo_source</a></code> and <code><a href='mo_source.html'>get_mo_source</a></code> to automate the usage of your own codes (e.g. used in your analysis or organisation).</p></td>
</tr> </tr>
</table> </table>

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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="Released version">0.5.0.9010</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
</span> </span>
</div> </div>
@ -278,6 +278,12 @@
<td><p>Class 'rsi'</p></td> <td><p>Class 'rsi'</p></td>
</tr><tr> </tr><tr>
<td>
<p><code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> </p>
</td>
<td><p>Use predefined reference data set</p></td>
</tr><tr>
<td> <td>
<p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">EUCAST_rules()</a></code> <code><a href="eucast_rules.html">interpretive_reading()</a></code> </p> <p><code><a href="eucast_rules.html">eucast_rules()</a></code> <code><a href="eucast_rules.html">EUCAST_rules()</a></code> <code><a href="eucast_rules.html">interpretive_reading()</a></code> </p>
</td> </td>
@ -299,7 +305,7 @@
<tr> <tr>
<th colspan="2"> <th colspan="2">
<h2 id="section-adding-variables-to-your-data" class="hasAnchor"><a href="#section-adding-variables-to-your-data" class="anchor"></a>Adding variables to your data</h2> <h2 id="section-adding-variables-to-your-data" class="hasAnchor"><a href="#section-adding-variables-to-your-data" class="anchor"></a>Adding variables to your data</h2>
<p class="section-desc"><p>Functions to add new data to existing data, like the determination of first isolates,</p></p> <p class="section-desc"><p>Functions to add new data to existing data, like the determination of first isolates, multi-drug resistant microorganisms (MDRO), getting properties of microorganisms or antibiotics and determining the age of patients or divide ages into age groups.</p></p>
</th> </th>
</tr> </tr>
<tr> <tr>
@ -373,7 +379,7 @@
<tr> <tr>
<th colspan="2"> <th colspan="2">
<h2 id="section-analysing-your-data" class="hasAnchor"><a href="#section-analysing-your-data" class="anchor"></a>Analysing your data</h2> <h2 id="section-analysing-your-data" class="hasAnchor"><a href="#section-analysing-your-data" class="anchor"></a>Analysing your data</h2>
<p class="section-desc"><p>Functions for conducting AMR analysis</p></p> <p class="section-desc"><p>Functions for conducting AMR analysis, like counting isolates, calculating resistance or susceptibility, creating frequency tables or make plots.</p></p>
</th> </th>
</tr> </tr>
<tr> <tr>
@ -459,9 +465,9 @@
</tr><tr> </tr><tr>
<td> <td>
<p><code><a href="microorganisms.certe.html">microorganisms.certe</a></code> </p> <p><code><a href="microorganisms.codes.html">microorganisms.codes</a></code> </p>
</td> </td>
<td><p>Translation table for Certe</p></td> <td><p>Translation table for microorganism codes</p></td>
</tr><tr> </tr><tr>
<td> <td>
@ -470,12 +476,6 @@
<td><p>Data set with old taxonomic data from ITIS</p></td> <td><p>Data set with old taxonomic data from ITIS</p></td>
</tr><tr> </tr><tr>
<td>
<p><code><a href="microorganisms.umcg.html">microorganisms.umcg</a></code> </p>
</td>
<td><p>Translation table for UMCG</p></td>
</tr><tr>
<td> <td>
<p><code><a href="supplementary_data.html">microorganismsDT</a></code> <code><a href="supplementary_data.html">microorganisms.prevDT</a></code> <code><a href="supplementary_data.html">microorganisms.unprevDT</a></code> <code><a href="supplementary_data.html">microorganisms.oldDT</a></code> </p> <p><code><a href="supplementary_data.html">microorganismsDT</a></code> <code><a href="supplementary_data.html">microorganisms.prevDT</a></code> <code><a href="supplementary_data.html">microorganisms.unprevDT</a></code> <code><a href="supplementary_data.html">microorganisms.oldDT</a></code> </p>
</td> </td>

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<title>Translation table for microorganism codes — microorganisms.codes • AMR (for R)</title>
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<h1>Translation table for microorganism codes</h1>
<div class="hidden name"><code>microorganisms.codes.Rd</code></div>
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<p>A data set containing commonly used codes for microorganisms. Define your own with <code><a href='mo_source.html'>set_mo_source</a></code>.</p>
</div>
<pre class="usage"><span class='no'>microorganisms.codes</span></pre>
<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 3,303 observations and 2 variables:</p><dl class='dl-horizontal'>
<dt><code>certe</code></dt><dd><p>Commonly used code of a microorganism</p></dd>
<dt><code>mo</code></dt><dd><p>Code of microorganism in <code><a href='microorganisms.html'>microorganisms</a></code></p></dd>
</dl>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='microorganisms.html'>microorganisms</a></code></p></div>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='mo_property.html'>mo_property</a></code> <code><a href='microorganisms.umcg.html'>microorganisms.umcg</a></code></p></div> <div class='dont-index'><p><code><a href='as.mo.html'>as.mo</a></code> <code><a href='mo_property.html'>mo_property</a></code> <code><a href='microorganisms.codes.html'>microorganisms.codes</a></code></p></div>
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<h1>Use predefined reference data set</h1>
<div class="hidden name"><code>mo_source.Rd</code></div>
</div>
<div class="ref-description">
<p>These functions can be used to predefine your own reference to be used in <code><a href='as.mo.html'>as.mo</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus</a></code> and <code><a href='mo_property.html'>mo_gramstain</a></code>.</p>
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<pre class="usage"><span class='fu'>set_mo_source</span>(<span class='no'>path</span>)
<span class='fu'>get_mo_source</span>()</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>path</th>
<td><p>location of your reference file, see Details</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>The reference file can be a text file seperated with commas (CSV) or pipes, an Excel file (old 'xls' format or new 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the <code>readxl</code> package installed.</p>
<p><code>set_mo_source</code> will check the file for validity: it must be a <code>data.frame</code>, must have a column named <code>"mo"</code> which contains values from <code>microorganisms$mo</code> and must have a reference column with your own defined values. If all tests pass, <code>set_mo_source</code> will read the file into R and export it to <code>"~/.mo_source.rds"</code>. This compressed data file will then be used at default for MO determination (function <code><a href='as.mo.html'>as.mo</a></code> and consequently all <code>mo_*</code> functions like <code><a href='mo_property.html'>mo_genus</a></code> and <code><a href='mo_property.html'>mo_gramstain</a></code>). The location of the original file will be saved as option with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options</a>(mo_source = path)</code>. Its timestamp will be saved with <code><a href='https://www.rdocumentation.org/packages/base/topics/options'>options</a>(mo_source_datetime = ...)</code>.</p>
<p><code>get_mo_source</code> will return the data set by reading <code>"~/.mo_source.rds"</code> with <code><a href='https://www.rdocumentation.org/packages/base/topics/readRDS'>readRDS</a></code>. If the original file has changed (the file defined with <code>path</code>), it will call <code>set_mo_source</code> to update the data file automatically.</p>
<p>Reading an Excel file (<code>.xlsx</code>) with only one row has a size of 8-9 kB. The compressed file will have a size of 0.1 kB and can be read by <code>get_mo_source</code> in only a couple of microseconds (a millionth of a second).</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"># NOT RUN {
# imagine this Excel file (mo codes looked up in `microorganisms` data set):
# A B
# 1 our code mo
# 2 lab_mo_ecoli B_ESCHR_COL
# 3 lab_mo_kpneumoniae B_KLBSL_PNE
# 1. We save it as 'home/me/ourcodes.xlsx'
# 2. We use it for input:
set_mo_source("C:\path\ourcodes.xlsx")
#> Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
# 3. And use it in our functions:
as.mo("lab_mo_ecoli")
#> B_ESCHR_COL
mo_genus("lab_mo_kpneumoniae")
#> "Klebsiella"
# 4. It will look for changes itself:
# (add new row to the Excel file and save it)
mo_genus("lab_mo_kpneumoniae")
#> Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#> "Klebsiella"
# }
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#details">Details</a></li>
<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
<li><a href="#examples">Examples</a></li>
</ul>
</div>
</div>
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
</div>
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
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<script>
docsearch({
apiKey: 'f737050abfd4d726c63938e18f8c496e',
indexName: 'amr',
inputSelector: 'input#search-input.form-control',
transformData: function(hits) {
return hits.map(function (hit) {
hit.url = updateHitURL(hit);
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8
docs/sitemap.xml
View File

@ -85,14 +85,11 @@
<loc>https://msberends.gitlab.io/AMR/reference/microorganisms.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/microorganisms.html</loc>
</url> </url>
<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/microorganisms.certe.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/microorganisms.codes.html</loc>
</url> </url>
<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/microorganisms.old.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/microorganisms.old.html</loc>
</url> </url>
<url>
<loc>https://msberends.gitlab.io/AMR/reference/microorganisms.umcg.html</loc>
</url>
<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/mo_failures.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/mo_failures.html</loc>
</url> </url>
@ -102,6 +99,9 @@
<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/mo_renamed.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/mo_renamed.html</loc>
</url> </url>
<url>
<loc>https://msberends.gitlab.io/AMR/reference/mo_source.html</loc>
</url>
<url> <url>
<loc>https://msberends.gitlab.io/AMR/reference/p.symbol.html</loc> <loc>https://msberends.gitlab.io/AMR/reference/p.symbol.html</loc>
</url> </url>

11
index.md
View File

@ -17,6 +17,7 @@ Medical Microbiology:
* Research Microbiologists * Research Microbiologists
* Biomedical Researchers * Biomedical Researchers
* Research Pharmacologists * Research Pharmacologists
* Data Scientists / Data Analysts
Veterinary Microbiology: Veterinary Microbiology:
@ -29,14 +30,6 @@ Microbial Ecology:
* Extremophile Researchers * Extremophile Researchers
* Astrobiologists * Astrobiologists
Other specialists in any of the above fields:
* Data Scientists/Data Analysts
* Biotechnologists
* Biochemists
* Geneticists
* Molecular Biologists/Microbiologists
Developers: Developers:
* Package developers for R * Package developers for R
@ -51,7 +44,7 @@ This package is available on the official R network (CRAN), which has a peer-rev
install.packages("AMR") install.packages("AMR")
``` ```
It will be downloaded and installed automatically. For RStudio, click on menu *Tools* > *Install Packages...*, then type in "AMR" and press <kbd>Install</kbd>. It will be downloaded and installed automatically. For RStudio, click on the menu *Tools* > *Install Packages...* and then type in "AMR" and press <kbd>Install</kbd>.
### Get started ### Get started

4
man/as.mo.Rd
View File

@ -7,7 +7,7 @@
\title{Transform to microorganism ID} \title{Transform to microorganism ID}
\usage{ \usage{
as.mo(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, as.mo(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
reference_df = NULL) reference_df = get_mo_source())
is.mo(x) is.mo(x)
} }
@ -24,7 +24,7 @@ is.mo(x)
\item{allow_uncertain}{a logical to indicate whether the input should be checked for less possible results, see Details} \item{allow_uncertain}{a logical to indicate whether the input should be checked for less possible results, see Details}
\item{reference_df}{a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. The first column can be any microbial name, code or ID (used in your analysis or organisation), the second column must be a valid \code{mo} as found in the \code{\link{microorganisms}} data set.} \item{reference_df}{a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. See \code{\link{set_mo_source}} and \code{\link{get_mo_source}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
} }
\value{ \value{
Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}. Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.

2
man/microorganisms.Rd
View File

@ -48,6 +48,6 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
} }
\seealso{ \seealso{
\code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}} \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.codes}}
} }
\keyword{datasets} \keyword{datasets}

14
man/microorganisms.certe.Rd → man/microorganisms.codes.Rd
View File

@ -1,19 +1,19 @@
% Generated by roxygen2: do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R % Please edit documentation in R/data.R
\docType{data} \docType{data}
\name{microorganisms.certe} \name{microorganisms.codes}
\alias{microorganisms.certe} \alias{microorganisms.codes}
\title{Translation table for Certe} \title{Translation table for microorganism codes}
\format{A \code{\link{data.frame}} with 2,665 observations and 2 variables: \format{A \code{\link{data.frame}} with 3,303 observations and 2 variables:
\describe{ \describe{
\item{\code{certe}}{Code of microorganism according to Certe MMB} \item{\code{certe}}{Commonly used code of a microorganism}
\item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}} \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
}} }}
\usage{ \usage{
microorganisms.certe microorganisms.codes
} }
\description{ \description{
A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}. A data set containing commonly used codes for microorganisms. Define your own with \code{\link{set_mo_source}}.
} }
\section{Read more on our website!}{ \section{Read more on our website!}{

27
man/microorganisms.umcg.Rd
View File

@ -1,27 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{microorganisms.umcg}
\alias{microorganisms.umcg}
\title{Translation table for UMCG}
\format{A \code{\link{data.frame}} with 1,095 observations and 2 variables:
\describe{
\item{\code{umcg}}{Code of microorganism according to UMCG MMB}
\item{\code{certe}}{Code of microorganism according to Certe MMB}
}}
\usage{
microorganisms.umcg
}
\description{
A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
}
\section{Read more on our website!}{
\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a omprehensive tutorial} about how to conduct AMR analysis and find \href{https://msberends.gitlab.io/AMR/reference}{the complete documentation of all functions}, which reads a lot easier than in R.
}
\seealso{
\code{\link{as.mo}} \code{\link{microorganisms.certe}} \code{\link{microorganisms}}
}
\keyword{datasets}

63
man/mo_source.Rd Normal file
View File

@ -0,0 +1,63 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mo_source.R
\name{mo_source}
\alias{mo_source}
\alias{set_mo_source}
\alias{get_mo_source}
\title{Use predefined reference data set}
\usage{
set_mo_source(path)
get_mo_source()
}
\arguments{
\item{path}{location of your reference file, see Details}
}
\description{
These functions can be used to predefine your own reference to be used in \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}.
}
\details{
The reference file can be a text file seperated with commas (CSV) or pipes, an Excel file (old 'xls' format or new 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the \code{readxl} package installed.
\code{set_mo_source} will check the file for validity: it must be a \code{data.frame}, must have a column named \code{"mo"} which contains values from \code{microorganisms$mo} and must have a reference column with your own defined values. If all tests pass, \code{set_mo_source} will read the file into R and export it to \code{"~/.mo_source.rds"}. This compressed data file will then be used at default for MO determination (function \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}). The location of the original file will be saved as option with \code{\link{options}(mo_source = path)}. Its timestamp will be saved with \code{\link{options}(mo_source_datetime = ...)}.
\code{get_mo_source} will return the data set by reading \code{"~/.mo_source.rds"} with \code{\link{readRDS}}. If the original file has changed (the file defined with \code{path}), it will call \code{set_mo_source} to update the data file automatically.
Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file will have a size of 0.1 kB and can be read by \code{get_mo_source} in only a couple of microseconds (a millionth of a second).
}
\section{Read more on our website!}{
\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a omprehensive tutorial} about how to conduct AMR analysis and find \href{https://msberends.gitlab.io/AMR/reference}{the complete documentation of all functions}, which reads a lot easier than in R.
}
\examples{
\dontrun{
# imagine this Excel file (mo codes looked up in `microorganisms` data set):
# A B
# 1 our code mo
# 2 lab_mo_ecoli B_ESCHR_COL
# 3 lab_mo_kpneumoniae B_KLBSL_PNE
# 1. We save it as 'home/me/ourcodes.xlsx'
# 2. We use it for input:
set_mo_source("C:\\path\\ourcodes.xlsx")
#> Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
# 3. And use it in our functions:
as.mo("lab_mo_ecoli")
#> B_ESCHR_COL
mo_genus("lab_mo_kpneumoniae")
#> "Klebsiella"
# 4. It will look for changes itself:
# (add new row to the Excel file and save it)
mo_genus("lab_mo_kpneumoniae")
#> Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#> "Klebsiella"
}
}

66
pkgdown/extra.css
View File

@ -23,22 +23,22 @@
/* class for footer */ /* class for footer */
.university { .university {
background-image: url(logo_rug.png); background-image: url(logo_rug.png);
height: 40px; background-size: 200px;
background-size: 160px; background-repeat: no-repeat;
background-repeat: no-repeat; background-position: center right;
} }
/* Supports icons for brand using font-awesome */ /* Supports icons for brand using font-awesome */
.fab { .fab {
font-family: "Font Awesome 5 Brands" !important; font-family: "Font Awesome 5 Brands" !important;
} }
/* Remove the 'Read more on our website!' part from the manual pages */ /* Remove the 'Read more on our website!' part from the manual pages */
#read-more-on-our-website-, #read-more-on-our-website-,
#read-more-on-our-website- + p, #read-more-on-our-website- + p,
li a[href="#read-more-on-our-website-"] { li a[href="#read-more-on-our-website-"] {
display: none; display: none;
} }
/* make colour darker and better readable for links */ /* make colour darker and better readable for links */
@ -60,21 +60,33 @@ a pre[href], a pre[href]:hover, a pre[href]:focus {
/* syntax font */ /* syntax font */
pre, code { pre, code {
font-family: 'Courier New', monospace; font-family: 'Courier New', monospace;
font-size: 100% !important; font-size: 100% !important;
font-weight: bold; font-weight: bold;
background-color: transparent; background-color: transparent;
} }
pre { pre {
font-size: 90% !important; font-size: 90% !important;
} }
kbd {
display: inline-block;
padding: 0 4px;
box-shadow: 1px 1px 1px #2c3e50;
margin: 2px;
font-size: small;
vertical-align: text-bottom;
color: #2c3e50;
background: #eee;
font-weight: bold;
}
li, p { li, p {
line-height: 1.5; line-height: 1.5;
} }
/* slightly smaller blockquote */ /* slightly smaller blockquote */
blockquote { blockquote {
font-size: 98%; font-size: 98%;
} }
/* 2nd list in navigation should be smaller */ /* 2nd list in navigation should be smaller */
@ -91,11 +103,11 @@ help {
/* replace 'Developers' with 'Authors' */ /* replace 'Developers' with 'Authors' */
.developers h2 { .developers h2 {
display: none; display: none;
} }
.developers:before { .developers:before {
content: 'Authors'; content: 'Authors';
font-size: 1.5em; font-size: 1.5em;
} }
/* hide version label */ /* hide version label */
@ -105,11 +117,11 @@ help {
/* Date of vignettes */ /* Date of vignettes */
.template-article .date:before { .template-article .date:before {
content: 'Last updated: '; content: 'Last updated: ';
} }
.template-article .date { .template-article .date {
font-size: 14px; font-size: 14px;
padding-top: 40px; padding-top: 40px;
} }
/* more space between icon and text in top menu */ /* more space between icon and text in top menu */
@ -134,15 +146,21 @@ help {
padding: 4px !important; padding: 4px !important;
} }
thead { thead {
border-top: 2px solid black; border-top: 2px solid black;
border-bottom: 2px solid black; border-bottom: 2px solid black;
} }
tbody { thead ~ tbody {
border-bottom: 2px solid black; /* only when it has a header */
border-bottom: 2px solid black;
} }
table a:not(.btn), .table a:not(.btn) { table a:not(.btn), .table a:not(.btn) {
text-decoration: inherit; text-decoration: inherit;
} }
table a:not(.btn):hover, .table a:not(.btn):hover { table a:not(.btn):hover, .table a:not(.btn):hover {
text-decoration: underline; text-decoration: underline;
}
.template-reference-index h2 ~ p {
font-size: 110%;
/* font-weight: bold; */
} }

12
pkgdown/extra.js
View File

@ -29,11 +29,19 @@ $('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" hr
// Edit footer // Edit footer
$( document ).ready(function() { $( document ).ready(function() {
// redirect to GitLab
var url_old = window.location.href;
var url_new = url_old.replace("github", "gitlab");
if (url_old != url_new) {
window.location.replace(url);
}
$('footer').html('<p>' + $('footer').html('<p>' +
$('footer .copyright p').html().replace("Developed by", $('footer .copyright p').html().replace("Developed by",
"<code>AMR</code> (for R). Developed at the University of Groningen.<br>Authors:") + '<code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl" target="_blank">University of Groningen</a>.<br>Authors:') +
'</p>'); '</p>');
//$('footer').prepend("<div class='university'/>"); $('footer').addClass("university");
// Edit title of manual // Edit title of manual
$('.template-reference-index h1').text('Manual'); $('.template-reference-index h1').text('Manual');

10
tests/testthat/test-mo.R
View File

@ -194,7 +194,7 @@ test_that("as.mo works", {
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLA") expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLA")
# - Didymosphaeria spartinae (unprevalent) # - Didymosphaeria spartinae (unprevalent)
expect_warning(suppressMessages(as.mo("D spartin", allow_uncertain = TRUE))) expect_warning(suppressMessages(as.mo("D spartin", allow_uncertain = TRUE)))
# - was renames to Leptosphaeria obiones # - was renamed to Leptosphaeria obiones
expect_equal(suppressWarnings(suppressMessages(as.character(as.mo("D spartin", allow_uncertain = TRUE)))), expect_equal(suppressWarnings(suppressMessages(as.character(as.mo("D spartin", allow_uncertain = TRUE)))),
"F_LPTSP_OBI") "F_LPTSP_OBI")
@ -205,15 +205,15 @@ test_that("as.mo works", {
# predefined reference_df # predefined reference_df
expect_equal(as.character(as.mo("TestingOwnID", expect_equal(as.character(as.mo("TestingOwnID",
reference_df = data.frame(a = "TestingOwnID", b = "B_ESCHR_COL"))), reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COL"))),
"B_ESCHR_COL") "B_ESCHR_COL")
expect_equal(as.character(as.mo(c("TestingOwnID", "E. coli"), expect_equal(as.character(as.mo(c("TestingOwnID", "E. coli"),
reference_df = data.frame(a = "TestingOwnID", b = "B_ESCHR_COL"))), reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COL"))),
c("B_ESCHR_COL", "B_ESCHR_COL")) c("B_ESCHR_COL", "B_ESCHR_COL"))
expect_warning(as.mo("TestingOwnID", reference_df = NULL)) expect_warning(as.mo("TestingOwnID", reference_df = NULL))
expect_error(as.mo("E. coli", reference_df = data.frame(a = "TestingOwnID"))) expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
# combination of existing mo and certe # combination of existing mo and other code
expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))), expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
c("B_ESCHR_COL", "B_ESCHR_COL")) c("B_ESCHR_COL", "B_ESCHR_COL"))