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mirror of https://github.com/msberends/AMR.git synced 2024-12-25 20:06:12 +01:00

keyab automatic

This commit is contained in:
dr. M.S. (Matthijs) Berends 2018-12-10 15:14:29 +01:00
parent 9478ab71be
commit 5ab7eb07bc
4 changed files with 37 additions and 10 deletions

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@ -11,7 +11,7 @@ R 3:
# install dependencies for package # install dependencies for package
- apt-get install --yes --no-install-recommends libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev - apt-get install --yes --no-install-recommends libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev
- Rscript -e 'install.packages(c("devtools", "rlang"))' - Rscript -e 'install.packages(c("devtools", "rlang"))'
- Rscript -e 'devtools::install_deps(dependencies = c("Depends", "Imports", "Suggests"), repos = "https://cran.rstudio.com")' - Rscript -e 'devtools::install_dev_deps(repos = "https://cran.rstudio.com")'
# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
- rm -rf vignettes - rm -rf vignettes
- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")' - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'

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@ -12,6 +12,9 @@
* There will be looked for uncertain results at default - these results will be returned with an informative warning * There will be looked for uncertain results at default - these results will be returned with an informative warning
* Manual now contains more info about the algorithms * Manual now contains more info about the algorithms
* Progress bar will be shown when it takes more than 3 seconds to get results * Progress bar will be shown when it takes more than 3 seconds to get results
* Function `first_isolate`:
* Will now use a column named like "patid" for the patient ID (parameter `col_patientid`), when this parameter was left blank
* Will now use a column named like "key(...)ab" or "key(...)antibiotics" for the key antibiotics (parameter `col_keyantibiotics`), when this parameter was left blank
* Function `first_isolate` will now use a column named like "patid" for the patient ID, when this parameter was left blank * Function `first_isolate` will now use a column named like "patid" for the patient ID, when this parameter was left blank
* 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)`

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@ -21,12 +21,12 @@
#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. #' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.
#' @param tbl a \code{data.frame} containing isolates. #' @param tbl a \code{data.frame} containing isolates.
#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of class \code{Date} #' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of class \code{Date}
#' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' (case insensitive) #' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)
#' @param col_mo column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}. #' @param col_mo column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.
#' @param col_testcode column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation. #' @param col_testcode column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.
#' @param col_specimen column name of the specimen type or group #' @param col_specimen column name of the specimen type or group
#' @param col_icu column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU) #' @param col_icu column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)
#' @param col_keyantibiotics column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. Supports tidyverse-like quotation. #' @param col_keyantibiotics column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. Supports tidyverse-like quotation. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use \code{col_keyantibiotics = FALSE} to prevent this.
#' @param episode_days episode in days after which a genus/species combination will be determined as 'first isolate' again #' @param episode_days episode in days after which a genus/species combination will be determined as 'first isolate' again
#' @param testcodes_exclude character vector with test codes that should be excluded (case-insensitive) #' @param testcodes_exclude character vector with test codes that should be excluded (case-insensitive)
#' @param icu_exclude logical whether ICU isolates should be excluded #' @param icu_exclude logical whether ICU isolates should be excluded
@ -158,20 +158,44 @@ first_isolate <- function(tbl,
col_mo <- colnames(tbl)[lapply(tbl, class) == "mo"][1] col_mo <- colnames(tbl)[lapply(tbl, class) == "mo"][1]
message("NOTE: Using column `", col_mo, "` as input for `col_mo`.") message("NOTE: Using column `", col_mo, "` as input for `col_mo`.")
} }
# -- date # -- date
if (is.null(col_date) & "Date" %in% lapply(tbl, class)) { if (is.null(col_date)) {
col_date <- colnames(tbl)[lapply(tbl, class) == "Date"][1] for (i in 1:ncol(tbl)) {
message("NOTE: Using column `", col_date, "` as input for `col_date`.") if ("Date" %in% class(tbl %>% pull(i)) | "POSIXct" %in% class(tbl %>% pull(i))) {
col_date <- colnames(tbl)[i]
message("NOTE: Using column `", col_date, "` as input for `col_date`.")
break
}
}
} }
if (is.null(col_date)) {
stop("`col_date` must be set.", call. = FALSE)
}
# convert to Date
tbl[, col_date] <- as.Date(tbl[, col_date])
# -- patient id # -- patient id
if (is.null(col_patient_id) & any(colnames(tbl) %like% "^(patient|patid)")) { if (is.null(col_patient_id) & any(colnames(tbl) %like% "^(patient|patid)")) {
col_patient_id <- colnames(tbl)[colnames(tbl) %like% "^(patient|patid)"][1] col_patient_id <- colnames(tbl)[colnames(tbl) %like% "^(patient|patid)"][1]
message("NOTE: Using column `", col_patient_id, "` as input for `col_patient_id`.") message("NOTE: Using column `", col_patient_id, "` as input for `col_patient_id`.")
} }
if (is.null(col_patient_id)) {
stop("`col_patient_id` must be set.", call. = FALSE)
}
# bactid OR genus+species must be available # -- key antibiotics
if (is.null(col_keyantibiotics) & any(colnames(tbl) %like% "^key.*(ab|antibiotics)")) {
col_keyantibiotics <- colnames(tbl)[colnames(tbl) %like% "^key.*(ab|antibiotics)"][1]
message("NOTE: Using column `", col_keyantibiotics, "` as input for `col_keyantibiotics`.")
}
if (isFALSE(col_keyantibiotics)) {
col_keyantibiotics <- NULL
}
# col_mo OR col_genus+col_species must be available
if (is.null(col_mo) & (is.null(col_genus) | is.null(col_species))) { if (is.null(col_mo) & (is.null(col_genus) | is.null(col_species))) {
stop('`col_mo` or both `col_genus` and `col_species` must be available.') stop("`col_mo` or both `col_genus` and `col_species` must be set.", call. = FALSE)
} }

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@ -21,7 +21,7 @@ first_isolate(tbl, col_date = NULL, col_patient_id = NULL,
\item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column of class \code{Date}} \item{col_date}{column name of the result date (or date that is was received on the lab), defaults to the first column of class \code{Date}}
\item{col_patient_id}{column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' (case insensitive)} \item{col_patient_id}{column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)}
\item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.} \item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.}
@ -31,7 +31,7 @@ first_isolate(tbl, col_date = NULL, col_patient_id = NULL,
\item{col_icu}{column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)} \item{col_icu}{column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)}
\item{col_keyantibiotics}{column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. Supports tidyverse-like quotation.} \item{col_keyantibiotics}{column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. Supports tidyverse-like quotation. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use \code{col_keyantibiotics = FALSE} to prevent this.}
\item{episode_days}{episode in days after which a genus/species combination will be determined as 'first isolate' again} \item{episode_days}{episode in days after which a genus/species combination will be determined as 'first isolate' again}