mirror of https://github.com/msberends/AMR.git
set_mo_source
This commit is contained in:
parent
c6c3088e9f
commit
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@ -15,6 +15,7 @@
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^docs$
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^git_merge\.sh$
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^git_premaster\.sh$
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^git_siteonly\.sh$
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^index\.md$
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^installed_deps$
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^Meta$
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@ -20,5 +20,6 @@ vignettes/*.R
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^CRAN-RELEASE$
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git_premaster.sh
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git_merge.sh
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git_siteonly.sh
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packrat/lib*/
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packrat/src/
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.5.0.9010
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Date: 2019-01-17
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Version: 0.5.0.9011
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Date: 2019-01-21
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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@ -58,6 +58,7 @@ Imports:
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Suggests:
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covr (>= 3.0.1),
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ggplot2,
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readxl,
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rmarkdown,
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rstudioapi,
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testthat (>= 1.0.2)
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@ -77,6 +77,7 @@ export(full_join_microorganisms)
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export(g.test)
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export(geom_rsi)
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export(get_locale)
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export(get_mo_source)
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export(ggplot_rsi)
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export(ggplot_rsi_predict)
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export(guess_ab_col)
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@ -136,6 +137,7 @@ export(rsi_predict)
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export(scale_rsi_colours)
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export(scale_y_percent)
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export(semi_join_microorganisms)
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export(set_mo_source)
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export(skewness)
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export(theme_rsi)
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export(top_freq)
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2
NEWS.md
2
NEWS.md
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@ -6,6 +6,7 @@
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* New website: https://msberends.gitlab.io/AMR (built with the great [`pkgdown`](https://pkgdown.r-lib.org/))
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* Contains the complete manual of this package and all of its functions with an explanation of their parameters
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* Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis
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* 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
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* Support for the upcoming [`dplyr`](https://dplyr.tidyverse.org) version 0.8.0
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* New function `guess_ab_col()` to find an antibiotic column in a table
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* 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.
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@ -55,6 +56,7 @@
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* Removed parameter `output_logical`, the function will now always return a logical value
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* Renamed parameter `filter_specimen` to `specimen_group`, although using `filter_specimen` will still work
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* 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)
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* Merged data sets `microorganisms.certe` and `microorganisms.umcg` into `microorganisms.codes`
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* Function `mo_taxonomy()` now contains the kingdom too
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* Reduce false positives for `is.rsi.eligible()`
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* Summaries of class `mo` will now return the top 3 and the unique count, e.g. using `summary(mo)`
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24
R/data.R
24
R/data.R
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@ -148,7 +148,7 @@
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#' }
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#' @source [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
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#' @inheritSection AMR Read more on our website!
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#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.umcg}}
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#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.codes}}
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"microorganisms"
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#' Data set with old taxonomic data from ITIS
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@ -167,29 +167,17 @@
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#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}}
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"microorganisms.old"
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#' Translation table for UMCG
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#' Translation table for microorganism codes
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#'
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#' A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
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#' @format A \code{\link{data.frame}} with 1,095 observations and 2 variables:
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#' A data set containing commonly used codes for microorganisms. Define your own with \code{\link{set_mo_source}}.
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#' @format A \code{\link{data.frame}} with 3,303 observations and 2 variables:
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#' \describe{
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#' \item{\code{umcg}}{Code of microorganism according to UMCG MMB}
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#' \item{\code{certe}}{Code of microorganism according to Certe MMB}
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#' }
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#' @inheritSection AMR Read more on our website!
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#' @seealso \code{\link{as.mo}} \code{\link{microorganisms.certe}} \code{\link{microorganisms}}
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"microorganisms.umcg"
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#' Translation table for Certe
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#'
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#' A data set containing all bacteria codes of Certe MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
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#' @format A \code{\link{data.frame}} with 2,665 observations and 2 variables:
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#' \describe{
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#' \item{\code{certe}}{Code of microorganism according to Certe MMB}
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#' \item{\code{certe}}{Commonly used code of a microorganism}
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#' \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
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#' }
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#' @inheritSection AMR Read more on our website!
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#' @seealso \code{\link{as.mo}} \code{\link{microorganisms}}
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"microorganisms.certe"
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"microorganisms.codes"
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#' Data set with 2000 blood culture isolates of septic patients
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#'
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@ -54,11 +54,10 @@ globalVariables(c(".",
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"median",
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"mic",
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"microorganisms",
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"microorganisms.certe",
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"microorganisms.codes",
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"microorganisms.old",
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"microorganisms.oldDT",
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"microorganisms.prevDT",
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"microorganisms.umcg",
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"microorganisms.unprevDT",
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"microorganismsDT",
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"mo",
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56
R/mo.R
56
R/mo.R
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@ -30,7 +30,7 @@
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#'
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#' This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.
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#' @param allow_uncertain a logical to indicate whether the input should be checked for less possible results, see Details
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#' @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.
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#' @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).
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#' @rdname as.mo
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#' @aliases mo
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#' @keywords mo Becker becker Lancefield lancefield guess
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@ -139,7 +139,7 @@
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#' df <- df %>%
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#' mutate(mo = as.mo(paste(genus, species)))
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#' }
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as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = NULL) {
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as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = get_mo_source()) {
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mo <- mo_validate(x = x, property = "mo",
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Becker = Becker, Lancefield = Lancefield,
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allow_uncertain = allow_uncertain, reference_df = reference_df)
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@ -152,11 +152,11 @@ is.mo <- function(x) {
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identical(class(x), "mo")
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}
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#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated
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#' @importFrom dplyr %>% pull left_join n_distinct progress_estimated filter
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#' @importFrom data.table data.table as.data.table setkey
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#' @importFrom crayon magenta red italic
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exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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allow_uncertain = TRUE, reference_df = NULL,
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allow_uncertain = TRUE, reference_df = get_mo_source(),
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property = "mo", clear_options = TRUE) {
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if (!"AMR" %in% base::.packages()) {
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@ -206,11 +206,16 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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if (!is.data.frame(reference_df) | NCOL(reference_df) < 2) {
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stop('`reference_df` must be a data.frame with at least two columns.', call. = FALSE)
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}
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# remove factors, just keep characters
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if (!"mo" %in% colnames(reference_df)) {
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stop("`reference_df` must contain a column `mo` with values from the 'microorganisms' data set.", call. = FALSE)
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}
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reference_df <- reference_df %>% filter(!is.na(mo))
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# # remove factors, just keep characters
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suppressWarnings(
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reference_df[] <- lapply(reference_df, as.character)
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)
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}
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if (all(identical(trimws(x_input), "") | is.na(x_input))) {
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# all empty
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if (property == "mo") {
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@ -220,24 +225,25 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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} else {
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return(rep(NA_character_, length(x_input)))
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}
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} else if (all(x %in% microorganismsDT[["mo"]])) {
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# existing mo codes when not looking for property "mo", like mo_genus("B_ESCHR_COL")
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x <- microorganismsDT[data.table(mo = x), on = "mo", ..property][[1]]
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} else if (!is.null(reference_df)
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& all(x %in% reference_df[, 1])
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& all(reference_df[, 2] %in% microorganismsDT[["mo"]])) {
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# manually defined reference
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} else if (all(x %in% reference_df[, 1])
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& all(reference_df[, "mo"] %in% microorganismsDT[["mo"]])) {
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# all in reference df
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colnames(reference_df)[1] <- "x"
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colnames(reference_df)[2] <- "mo"
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suppressWarnings(
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x <- data.frame(x = x, stringsAsFactors = FALSE) %>%
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left_join(reference_df, by = "x") %>%
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left_join(microorganisms, by = "mo") %>%
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pull(property)
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)
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} else if (all(toupper(x) %in% microorganisms.certe[, "certe"])) {
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# old Certe codes
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y <- as.data.table(microorganisms.certe)[data.table(certe = toupper(x)), on = "certe", ]
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} else if (all(x %in% microorganismsDT[["mo"]])) {
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# existing mo codes when not looking for property "mo", like mo_genus("B_ESCHR_COL")
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x <- microorganismsDT[data.table(mo = x), on = "mo", ..property][[1]]
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} else if (all(toupper(x) %in% microorganisms.codes[, "code"])) {
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# commonly used MO codes
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y <- as.data.table(microorganisms.codes)[data.table(code = toupper(x)), on = "code", ]
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x <- microorganismsDT[data.table(mo = y[["mo"]]), on = "mo", ..property][[1]]
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} else if (!all(x %in% microorganismsDT[[property]])) {
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@ -419,28 +425,16 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
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}
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# TRY OTHER SOURCES ----
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if (toupper(x_backup[i]) %in% microorganisms.certe[, 1]) {
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mo_found <- microorganisms.certe[toupper(x_backup[i]) == microorganisms.certe[, 1], 2][1L]
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if (toupper(x_backup[i]) %in% microorganisms.codes[, 1]) {
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mo_found <- microorganisms.codes[toupper(x_backup[i]) == microorganisms.codes[, 1], "mo"][1L]
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if (length(mo_found) > 0) {
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x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
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next
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}
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}
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if (x_backup[i] %in% microorganisms.umcg[, 1]) {
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mo_umcg <- microorganisms.umcg[microorganisms.umcg[, 1] == x_backup[i], 2]
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mo_found <- microorganisms.certe[microorganisms.certe[, 1] == mo_umcg, 2][1L]
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if (length(mo_found) == 0) {
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# not found
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x[i] <- NA_character_
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failures <- c(failures, x_backup[i])
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} else {
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x[i] <- microorganismsDT[mo == mo_found, ..property][[1]][1L]
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}
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next
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}
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if (!is.null(reference_df)) {
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if (x_backup[i] %in% reference_df[, 1]) {
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ref_mo <- reference_df[reference_df[, 1] == x_backup[i], 2]
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ref_mo <- reference_df[reference_df[, 1] == x_backup[i], "mo"]
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if (ref_mo %in% microorganismsDT[, mo]) {
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x[i] <- microorganismsDT[mo == ref_mo, ..property][[1]][1L]
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next
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@ -0,0 +1,174 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitab.io/AMR. #
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# ==================================================================== #
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#' Use predefined reference data set
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#'
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#' 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}}.
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#' @param path location of your reference file, see Details
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#' @rdname mo_source
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#' @name mo_source
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#' @aliases set_mo_source get_mo_source
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#' @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.
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#'
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#' \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 = ...)}.
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#'
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#' \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.
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#'
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#' 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).
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#' @importFrom dplyr select everything
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#' @export
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#' @inheritSection AMR Read more on our website!
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#' @examples
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#' \dontrun{
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#'
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#' # imagine this Excel file (mo codes looked up in `microorganisms` data set):
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#' # A B
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#' # 1 our code mo
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#' # 2 lab_mo_ecoli B_ESCHR_COL
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#' # 3 lab_mo_kpneumoniae B_KLBSL_PNE
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#'
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#' # 1. We save it as 'home/me/ourcodes.xlsx'
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#'
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#' # 2. We use it for input:
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#' set_mo_source("C:\path\ourcodes.xlsx")
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#' #> Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
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#'
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#' # 3. And use it in our functions:
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#' as.mo("lab_mo_ecoli")
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#' #> B_ESCHR_COL
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#'
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#' mo_genus("lab_mo_kpneumoniae")
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#' #> "Klebsiella"
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#'
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#' # 4. It will look for changes itself:
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#' # (add new row to the Excel file and save it)
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#'
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#' mo_genus("lab_mo_kpneumoniae")
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#' #> Updated mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
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#' #> "Klebsiella"
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#' }
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set_mo_source <- function(path) {
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if (!is.character(path) | length(path) > 1) {
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stop("`path` must be a character of length 1.")
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}
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if (path == "") {
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options(mo_source = NULL)
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options(mo_source_timestamp = NULL)
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if (file.exists("~/.mo_source.rds")) {
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unlink("~/.mo_source.rds")
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message("Removed mo_source file '~/.mo_source.rds'.")
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}
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return(invisible())
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}
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if (!file.exists(path)) {
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stop("File not found: ", path)
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}
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is_valid <- function(df) {
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valid <- TRUE
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if (!is.data.frame(df)) {
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valid <- FALSE
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} else if (!"mo" %in% colnames(df)) {
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valid <- FALSE
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} else if (!all(df$mo %in% AMR::microorganisms$mo)) {
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valid <- FALSE
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} else if (NCOL(df) < 2) {
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valid <- FALSE
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}
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valid
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}
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if (path %like% '[.]rds$') {
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df <- readRDS(path)
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} else if (path %like% '[.]xlsx?$') {
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# is Excel file (old or new)
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if (!"readxl" %in% utils::installed.packages()) {
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stop("Install the 'readxl' package first.")
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}
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if (path %like% '[.]xlsx$') {
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df <- readxl::read_xlsx(path)
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} else {
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df <- readxl::read_xls(path)
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}
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} else {
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||||
# 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
141
_pkgdown.yml
|
|
@ -19,7 +19,7 @@
|
|||
# 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)'
|
||||
|
||||
|
|
@ -74,74 +74,77 @@ navbar:
|
|||
href: 'LICENSE-text.html'
|
||||
|
||||
reference:
|
||||
- title: 'Background information'
|
||||
desc: >
|
||||
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.
|
||||
contents:
|
||||
- '`AMR`'
|
||||
- '`ITIS`'
|
||||
- title: 'Cleaning your data'
|
||||
desc: >
|
||||
Functions for cleaning and optimising your data, to be able
|
||||
to add variables later on (like taxonomic properties) or to
|
||||
fix and extend antibiotic interpretations by applying [EUCAST rules](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
|
||||
contents:
|
||||
- starts_with("as.")
|
||||
- '`eucast_rules`'
|
||||
- '`guess_ab_col`'
|
||||
- '`read.4D`'
|
||||
- title: 'Adding variables to your data'
|
||||
desc: >
|
||||
Functions to add new data to existing data, like the determination
|
||||
of first isolates,
|
||||
contents:
|
||||
- '`first_isolate`'
|
||||
- '`mdro`'
|
||||
- '`key_antibiotics`'
|
||||
- '`mo_property`'
|
||||
- '`ab_property`'
|
||||
- '`atc_property`'
|
||||
- '`abname`'
|
||||
- '`age`'
|
||||
- '`age_groups`'
|
||||
- '`p.symbol`'
|
||||
- '`join`'
|
||||
- title: 'Analysing your data'
|
||||
desc: >
|
||||
Functions for conducting AMR analysis
|
||||
contents:
|
||||
- '`count`'
|
||||
- '`portion`'
|
||||
- '`freq`'
|
||||
- '`g.test`'
|
||||
- '`ggplot_rsi`'
|
||||
- '`kurtosis`'
|
||||
- '`resistance_predict`'
|
||||
- '`rsi`'
|
||||
- '`skewness`'
|
||||
- title: 'Included data sets'
|
||||
desc: >
|
||||
References for microorganisms and antibiotics, and even a
|
||||
genuine data set with isolates from septic patients.
|
||||
contents:
|
||||
- '`antibiotics`'
|
||||
- '`microorganisms`'
|
||||
- '`septic_patients`'
|
||||
- '`microorganisms.certe`'
|
||||
- '`microorganisms.old`'
|
||||
- '`microorganisms.umcg`'
|
||||
- '`supplementary_data`'
|
||||
- title: Other
|
||||
desc: >
|
||||
These functions are mostly for internal use, but some of
|
||||
them may also be suitable for your analysis. Especially the
|
||||
'like' function can be useful: `if (x %like% y) {...}`.
|
||||
contents:
|
||||
- '`get_locale`'
|
||||
- '`like`'
|
||||
- '`mo_failures`'
|
||||
- '`mo_renamed`'
|
||||
- title: 'Background information'
|
||||
desc: >
|
||||
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.
|
||||
contents:
|
||||
- '`AMR`'
|
||||
- '`ITIS`'
|
||||
- title: 'Cleaning your data'
|
||||
desc: >
|
||||
Functions for cleaning and optimising your data, to be able to add
|
||||
variables later on (like taxonomic properties) or to fix and extend
|
||||
antibiotic interpretations by applying [EUCAST rules](http://www.eucast.org/expert_rules_and_intrinsic_resistance/).
|
||||
contents:
|
||||
- starts_with("as.")
|
||||
- '`mo_source`'
|
||||
- '`eucast_rules`'
|
||||
- '`guess_ab_col`'
|
||||
- '`read.4D`'
|
||||
- title: 'Adding variables to your data'
|
||||
desc: >
|
||||
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.
|
||||
contents:
|
||||
- '`first_isolate`'
|
||||
- '`mdro`'
|
||||
- '`key_antibiotics`'
|
||||
- '`mo_property`'
|
||||
- '`ab_property`'
|
||||
- '`atc_property`'
|
||||
- '`abname`'
|
||||
- '`age`'
|
||||
- '`age_groups`'
|
||||
- '`p.symbol`'
|
||||
- '`join`'
|
||||
- title: 'Analysing your data'
|
||||
desc: >
|
||||
Functions for conducting AMR analysis, like counting isolates, calculating
|
||||
resistance or susceptibility, creating frequency tables or make plots.
|
||||
contents:
|
||||
- '`count`'
|
||||
- '`portion`'
|
||||
- '`freq`'
|
||||
- '`g.test`'
|
||||
- '`ggplot_rsi`'
|
||||
- '`kurtosis`'
|
||||
- '`resistance_predict`'
|
||||
- '`rsi`'
|
||||
- '`skewness`'
|
||||
- title: 'Included data sets'
|
||||
desc: >
|
||||
References for microorganisms and antibiotics, and even a
|
||||
genuine data set with isolates from septic patients.
|
||||
contents:
|
||||
- '`antibiotics`'
|
||||
- '`microorganisms`'
|
||||
- '`septic_patients`'
|
||||
- '`microorganisms.codes`'
|
||||
- '`microorganisms.old`'
|
||||
- '`supplementary_data`'
|
||||
- title: Other
|
||||
desc: >
|
||||
These functions are mostly for internal use, but some of
|
||||
them may also be suitable for your analysis. Especially the
|
||||
'like' function can be useful: `if (x %like% y) {...}`.
|
||||
contents:
|
||||
- '`get_locale`'
|
||||
- '`like`'
|
||||
- '`mo_failures`'
|
||||
- '`mo_renamed`'
|
||||
|
||||
authors:
|
||||
Matthijs S. Berends:
|
||||
|
|
|
|||
Binary file not shown.
Binary file not shown.
Binary file not shown.
|
|
@ -78,7 +78,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -40,7 +40,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -178,7 +178,7 @@
|
|||
<h1>Benchmarks</h1>
|
||||
<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>
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -23,22 +23,22 @@
|
|||
|
||||
/* class for footer */
|
||||
.university {
|
||||
background-image: url(logo_rug.png);
|
||||
height: 40px;
|
||||
background-size: 160px;
|
||||
background-repeat: no-repeat;
|
||||
background-image: url(logo_rug.png);
|
||||
background-size: 200px;
|
||||
background-repeat: no-repeat;
|
||||
background-position: center right;
|
||||
}
|
||||
|
||||
/* Supports icons for brand using font-awesome */
|
||||
.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 */
|
||||
#read-more-on-our-website-,
|
||||
#read-more-on-our-website- + p,
|
||||
li a[href="#read-more-on-our-website-"] {
|
||||
display: none;
|
||||
display: none;
|
||||
}
|
||||
|
||||
/* 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 */
|
||||
pre, code {
|
||||
font-family: 'Courier New', monospace;
|
||||
font-size: 100% !important;
|
||||
font-weight: bold;
|
||||
background-color: transparent;
|
||||
font-family: 'Courier New', monospace;
|
||||
font-size: 100% !important;
|
||||
font-weight: bold;
|
||||
background-color: transparent;
|
||||
}
|
||||
pre {
|
||||
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 {
|
||||
line-height: 1.5;
|
||||
line-height: 1.5;
|
||||
}
|
||||
|
||||
/* slightly smaller blockquote */
|
||||
blockquote {
|
||||
font-size: 98%;
|
||||
font-size: 98%;
|
||||
}
|
||||
|
||||
/* 2nd list in navigation should be smaller */
|
||||
|
|
@ -91,11 +103,11 @@ help {
|
|||
|
||||
/* replace 'Developers' with 'Authors' */
|
||||
.developers h2 {
|
||||
display: none;
|
||||
display: none;
|
||||
}
|
||||
.developers:before {
|
||||
content: 'Authors';
|
||||
font-size: 1.5em;
|
||||
content: 'Authors';
|
||||
font-size: 1.5em;
|
||||
}
|
||||
|
||||
/* hide version label */
|
||||
|
|
@ -105,11 +117,11 @@ help {
|
|||
|
||||
/* Date of vignettes */
|
||||
.template-article .date:before {
|
||||
content: 'Last updated: ';
|
||||
content: 'Last updated: ';
|
||||
}
|
||||
.template-article .date {
|
||||
font-size: 14px;
|
||||
padding-top: 40px;
|
||||
font-size: 14px;
|
||||
padding-top: 40px;
|
||||
}
|
||||
|
||||
/* more space between icon and text in top menu */
|
||||
|
|
@ -134,15 +146,21 @@ help {
|
|||
padding: 4px !important;
|
||||
}
|
||||
thead {
|
||||
border-top: 2px solid black;
|
||||
border-bottom: 2px solid black;
|
||||
border-top: 2px solid black;
|
||||
border-bottom: 2px solid black;
|
||||
}
|
||||
tbody {
|
||||
border-bottom: 2px solid black;
|
||||
thead ~ tbody {
|
||||
/* only when it has a header */
|
||||
border-bottom: 2px solid black;
|
||||
}
|
||||
table a:not(.btn), .table a:not(.btn) {
|
||||
text-decoration: inherit;
|
||||
text-decoration: inherit;
|
||||
}
|
||||
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; */
|
||||
}
|
||||
|
|
|
|||
|
|
@ -29,11 +29,19 @@ $('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" hr
|
|||
|
||||
// Edit footer
|
||||
$( 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>' +
|
||||
$('footer .copyright p').html().replace("Developed by",
|
||||
"<code>AMR</code> (for R). Developed at the University of Groningen.<br>Authors:") +
|
||||
'<code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl" target="_blank">University of Groningen</a>.<br>Authors:') +
|
||||
'</p>');
|
||||
//$('footer').prepend("<div class='university'/>");
|
||||
$('footer').addClass("university");
|
||||
|
||||
// Edit title of manual
|
||||
$('.template-reference-index h1').text('Manual');
|
||||
|
|
|
|||
|
|
@ -42,7 +42,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -191,6 +191,7 @@
|
|||
<li>Research Microbiologists</li>
|
||||
<li>Biomedical Researchers</li>
|
||||
<li>Research Pharmacologists</li>
|
||||
<li>Data Scientists / Data Analysts</li>
|
||||
</ul>
|
||||
<p>Veterinary Microbiology:</p>
|
||||
<ul>
|
||||
|
|
@ -203,14 +204,6 @@
|
|||
<li>Extremophile Researchers</li>
|
||||
<li>Astrobiologists</li>
|
||||
</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>
|
||||
<ul>
|
||||
<li>Package developers for R</li>
|
||||
|
|
@ -222,7 +215,7 @@
|
|||
<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>
|
||||
<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> > <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> > <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
|
||||
</div>
|
||||
<div id="get-started" class="section level3">
|
||||
<h3 class="hasAnchor">
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -235,6 +235,7 @@
|
|||
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis</li>
|
||||
</ul>
|
||||
</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>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>
|
||||
|
|
@ -297,6 +298,8 @@
|
|||
</ul>
|
||||
</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>Reduce false positives for <code><a href="../reference/as.rsi.html">is.rsi.eligible()</a></code>
|
||||
</li>
|
||||
|
|
|
|||
|
|
@ -80,7 +80,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -228,7 +228,7 @@
|
|||
</div>
|
||||
|
||||
<pre class="usage"><span class='fu'>as.mo</span>(<span class='no'>x</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>allow_uncertain</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
|
||||
<span class='kw'>reference_df</span> <span class='kw'>=</span> <span class='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>
|
||||
|
||||
|
|
@ -255,7 +255,7 @@
|
|||
</tr>
|
||||
<tr>
|
||||
<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>
|
||||
</table>
|
||||
|
||||
|
|
|
|||
|
|
@ -78,7 +78,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<a class="navbar-link" href="../index.html">AMR (for R)</a>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9010</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9011</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
@ -278,6 +278,12 @@
|
|||
<td><p>Class 'rsi'</p></td>
|
||||
</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>
|
||||
<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>
|
||||
|
|
@ -299,7 +305,7 @@
|
|||
<tr>
|
||||
<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>
|
||||
<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>
|
||||
</tr>
|
||||
<tr>
|
||||
|
|
@ -373,7 +379,7 @@
|
|||
<tr>
|
||||
<th colspan="2">
|
||||
<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>
|
||||
</tr>
|
||||
<tr>
|
||||
|
|
@ -459,9 +465,9 @@
|
|||
</tr><tr>
|
||||
|
||||
<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><p>Translation table for Certe</p></td>
|
||||
<td><p>Translation table for microorganism codes</p></td>
|
||||
</tr><tr>
|
||||
|
||||
<td>
|
||||
|
|
@ -470,12 +476,6 @@
|
|||
<td><p>Data set with old taxonomic data from ITIS</p></td>
|
||||
</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>
|
||||
<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>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,297 @@
|
|||
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Conduct AMR analysis
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||||
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Predict antimicrobial resistance
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||||
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Apply EUCAST rules
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||||
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Get properties of a microorganism
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Get properties of an antibiotic
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Create frequency tables
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Use the G-test
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Other: benchmarks
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<div class="page-header">
|
||||
<h1>Translation table for microorganism codes</h1>
|
||||
|
||||
<div class="hidden name"><code>microorganisms.codes.Rd</code></div>
|
||||
</div>
|
||||
|
||||
<div class="ref-description">
|
||||
|
||||
<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>
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<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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<h1>Use predefined reference data set</h1>
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<div class="hidden name"><code>mo_source.Rd</code></div>
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<div class="ref-description">
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||||
<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>)
|
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||||
<span class='fu'>get_mo_source</span>()</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>path</th>
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<td><p>location of your reference file, see Details</p></td>
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</tr>
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</table>
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<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>
|
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<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>
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<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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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>
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<li><a href="#arguments">Arguments</a></li>
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<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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|
||||
<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>
|
||||
|
||||
<div class="pkgdown">
|
||||
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
|
||||
</div>
|
||||
</footer>
|
||||
</div>
|
||||
|
||||
|
||||
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script>
|
||||
<script>
|
||||
docsearch({
|
||||
|
||||
|
||||
apiKey: 'f737050abfd4d726c63938e18f8c496e',
|
||||
indexName: 'amr',
|
||||
inputSelector: 'input#search-input.form-control',
|
||||
transformData: function(hits) {
|
||||
return hits.map(function (hit) {
|
||||
hit.url = updateHitURL(hit);
|
||||
return hit;
|
||||
});
|
||||
}
|
||||
});
|
||||
</script>
|
||||
|
||||
|
||||
</body>
|
||||
</html>
|
||||
|
||||
|
|
@ -85,14 +85,11 @@
|
|||
<loc>https://msberends.gitlab.io/AMR/reference/microorganisms.html</loc>
|
||||
</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>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/microorganisms.old.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/microorganisms.umcg.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/mo_failures.html</loc>
|
||||
</url>
|
||||
|
|
@ -102,6 +99,9 @@
|
|||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/mo_renamed.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/mo_source.html</loc>
|
||||
</url>
|
||||
<url>
|
||||
<loc>https://msberends.gitlab.io/AMR/reference/p.symbol.html</loc>
|
||||
</url>
|
||||
|
|
|
|||
11
index.md
11
index.md
|
|
@ -17,6 +17,7 @@ Medical Microbiology:
|
|||
* Research Microbiologists
|
||||
* Biomedical Researchers
|
||||
* Research Pharmacologists
|
||||
* Data Scientists / Data Analysts
|
||||
|
||||
Veterinary Microbiology:
|
||||
|
||||
|
|
@ -29,14 +30,6 @@ Microbial Ecology:
|
|||
* Extremophile Researchers
|
||||
* Astrobiologists
|
||||
|
||||
Other specialists in any of the above fields:
|
||||
|
||||
* Data Scientists/Data Analysts
|
||||
* Biotechnologists
|
||||
* Biochemists
|
||||
* Geneticists
|
||||
* Molecular Biologists/Microbiologists
|
||||
|
||||
Developers:
|
||||
|
||||
* 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")
|
||||
```
|
||||
|
||||
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
|
||||
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@
|
|||
\title{Transform to microorganism ID}
|
||||
\usage{
|
||||
as.mo(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
|
||||
reference_df = NULL)
|
||||
reference_df = get_mo_source())
|
||||
|
||||
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{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{
|
||||
Character (vector) with class \code{"mo"}. Unknown values will return \code{NA}.
|
||||
|
|
|
|||
|
|
@ -48,6 +48,6 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
|
|||
}
|
||||
|
||||
\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}
|
||||
|
|
|
|||
|
|
@ -1,19 +1,19 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/data.R
|
||||
\docType{data}
|
||||
\name{microorganisms.certe}
|
||||
\alias{microorganisms.certe}
|
||||
\title{Translation table for Certe}
|
||||
\format{A \code{\link{data.frame}} with 2,665 observations and 2 variables:
|
||||
\name{microorganisms.codes}
|
||||
\alias{microorganisms.codes}
|
||||
\title{Translation table for microorganism codes}
|
||||
\format{A \code{\link{data.frame}} with 3,303 observations and 2 variables:
|
||||
\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}}}
|
||||
}}
|
||||
\usage{
|
||||
microorganisms.certe
|
||||
microorganisms.codes
|
||||
}
|
||||
\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}$mo} (using \code{\link{left_join_microorganisms}}). GLIMS codes can also be translated to valid \code{MO}s with \code{\link{guess_mo}}.
|
||||
A data set containing commonly used codes for microorganisms. Define your own with \code{\link{set_mo_source}}.
|
||||
}
|
||||
\section{Read more on our website!}{
|
||||
|
||||
|
|
@ -1,27 +0,0 @@
|
|||
% Generated by roxygen2: do not edit by hand
|
||||
% Please edit documentation in R/data.R
|
||||
\docType{data}
|
||||
\name{microorganisms.umcg}
|
||||
\alias{microorganisms.umcg}
|
||||
\title{Translation table for UMCG}
|
||||
\format{A \code{\link{data.frame}} with 1,095 observations and 2 variables:
|
||||
\describe{
|
||||
\item{\code{umcg}}{Code of microorganism according to UMCG MMB}
|
||||
\item{\code{certe}}{Code of microorganism according to Certe MMB}
|
||||
}}
|
||||
\usage{
|
||||
microorganisms.umcg
|
||||
}
|
||||
\description{
|
||||
A data set containing all bacteria codes of UMCG MMB. These codes can be joined to data with an ID from \code{\link{microorganisms}$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}
|
||||
|
|
@ -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"
|
||||
}
|
||||
}
|
||||
|
|
@ -23,22 +23,22 @@
|
|||
|
||||
/* class for footer */
|
||||
.university {
|
||||
background-image: url(logo_rug.png);
|
||||
height: 40px;
|
||||
background-size: 160px;
|
||||
background-repeat: no-repeat;
|
||||
background-image: url(logo_rug.png);
|
||||
background-size: 200px;
|
||||
background-repeat: no-repeat;
|
||||
background-position: center right;
|
||||
}
|
||||
|
||||
/* Supports icons for brand using font-awesome */
|
||||
.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 */
|
||||
#read-more-on-our-website-,
|
||||
#read-more-on-our-website- + p,
|
||||
li a[href="#read-more-on-our-website-"] {
|
||||
display: none;
|
||||
display: none;
|
||||
}
|
||||
|
||||
/* 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 */
|
||||
pre, code {
|
||||
font-family: 'Courier New', monospace;
|
||||
font-size: 100% !important;
|
||||
font-weight: bold;
|
||||
background-color: transparent;
|
||||
font-family: 'Courier New', monospace;
|
||||
font-size: 100% !important;
|
||||
font-weight: bold;
|
||||
background-color: transparent;
|
||||
}
|
||||
pre {
|
||||
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 {
|
||||
line-height: 1.5;
|
||||
line-height: 1.5;
|
||||
}
|
||||
|
||||
/* slightly smaller blockquote */
|
||||
blockquote {
|
||||
font-size: 98%;
|
||||
font-size: 98%;
|
||||
}
|
||||
|
||||
/* 2nd list in navigation should be smaller */
|
||||
|
|
@ -91,11 +103,11 @@ help {
|
|||
|
||||
/* replace 'Developers' with 'Authors' */
|
||||
.developers h2 {
|
||||
display: none;
|
||||
display: none;
|
||||
}
|
||||
.developers:before {
|
||||
content: 'Authors';
|
||||
font-size: 1.5em;
|
||||
content: 'Authors';
|
||||
font-size: 1.5em;
|
||||
}
|
||||
|
||||
/* hide version label */
|
||||
|
|
@ -105,11 +117,11 @@ help {
|
|||
|
||||
/* Date of vignettes */
|
||||
.template-article .date:before {
|
||||
content: 'Last updated: ';
|
||||
content: 'Last updated: ';
|
||||
}
|
||||
.template-article .date {
|
||||
font-size: 14px;
|
||||
padding-top: 40px;
|
||||
font-size: 14px;
|
||||
padding-top: 40px;
|
||||
}
|
||||
|
||||
/* more space between icon and text in top menu */
|
||||
|
|
@ -134,15 +146,21 @@ help {
|
|||
padding: 4px !important;
|
||||
}
|
||||
thead {
|
||||
border-top: 2px solid black;
|
||||
border-bottom: 2px solid black;
|
||||
border-top: 2px solid black;
|
||||
border-bottom: 2px solid black;
|
||||
}
|
||||
tbody {
|
||||
border-bottom: 2px solid black;
|
||||
thead ~ tbody {
|
||||
/* only when it has a header */
|
||||
border-bottom: 2px solid black;
|
||||
}
|
||||
table a:not(.btn), .table a:not(.btn) {
|
||||
text-decoration: inherit;
|
||||
text-decoration: inherit;
|
||||
}
|
||||
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; */
|
||||
}
|
||||
|
|
|
|||
|
|
@ -29,11 +29,19 @@ $('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" hr
|
|||
|
||||
// Edit footer
|
||||
$( 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>' +
|
||||
$('footer .copyright p').html().replace("Developed by",
|
||||
"<code>AMR</code> (for R). Developed at the University of Groningen.<br>Authors:") +
|
||||
'<code>AMR</code> (for R). Developed at the <a href="https://www.rug.nl" target="_blank">University of Groningen</a>.<br>Authors:') +
|
||||
'</p>');
|
||||
//$('footer').prepend("<div class='university'/>");
|
||||
$('footer').addClass("university");
|
||||
|
||||
// Edit title of manual
|
||||
$('.template-reference-index h1').text('Manual');
|
||||
|
|
|
|||
|
|
@ -194,7 +194,7 @@ test_that("as.mo works", {
|
|||
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLA")
|
||||
# - Didymosphaeria spartinae (unprevalent)
|
||||
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)))),
|
||||
"F_LPTSP_OBI")
|
||||
|
||||
|
|
@ -205,15 +205,15 @@ test_that("as.mo works", {
|
|||
|
||||
# predefined reference_df
|
||||
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")
|
||||
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"))
|
||||
expect_warning(as.mo("TestingOwnID", reference_df = NULL))
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||||
expect_error(as.mo("E. coli", reference_df = data.frame(a = "TestingOwnID")))
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expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
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# combination of existing mo and certe
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# combination of existing mo and other code
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||||
expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
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c("B_ESCHR_COL", "B_ESCHR_COL"))
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue