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note about portions

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dr. M.S. (Matthijs) Berends 2018-12-14 07:23:25 +01:00
parent 01a6d56334
commit 81af7be36e
6 changed files with 14 additions and 9 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.5.0.9003 Version: 0.5.0.9004
Date: 2018-12-10 Date: 2018-12-14
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(

1
NEWS.md
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@ -15,6 +15,7 @@
* Function `first_isolate`: * 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 "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 * 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
* A note to the manual pages of the `portion` functions, that low counts can infuence the outcome and that the `portion` functions may camouflage this, since they only return the portion (albeit being dependent on the `minimum` parameter)
* Function `mo_taxonomy` now contains the kingdom too * Function `mo_taxonomy` now contains the kingdom too
* 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`

10
R/first_isolate.R
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@ -23,10 +23,10 @@
#' @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' or 'patid' (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 = NULL} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored.
#' @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. 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 col_keyantibiotics column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. 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
@ -187,7 +187,7 @@ first_isolate <- function(tbl,
# -- key antibiotics # -- key antibiotics
if (is.null(col_keyantibiotics) & any(colnames(tbl) %like% "^key.*(ab|antibiotics)")) { if (is.null(col_keyantibiotics) & any(colnames(tbl) %like% "^key.*(ab|antibiotics)")) {
col_keyantibiotics <- colnames(tbl)[colnames(tbl) %like% "^key.*(ab|antibiotics)"][1] col_keyantibiotics <- colnames(tbl)[colnames(tbl) %like% "^key.*(ab|antibiotics)"][1]
message("NOTE: Using column `", col_keyantibiotics, "` as input for `col_keyantibiotics`.") message("NOTE: Using column `", col_keyantibiotics, "` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.")
} }
if (isFALSE(col_keyantibiotics)) { if (isFALSE(col_keyantibiotics)) {
col_keyantibiotics <- NULL col_keyantibiotics <- NULL
@ -205,6 +205,10 @@ first_isolate <- function(tbl,
stop('Please check tbl for existance.') stop('Please check tbl for existance.')
} }
if (is.na(column)) {
column <- NULL
}
if (!is.null(column)) { if (!is.null(column)) {
if (!(column %in% colnames(tblname))) { if (!(column %in% colnames(tblname))) {
stop('Column `', column, '` not found.') stop('Column `', column, '` not found.')

2
R/portion.R
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@ -30,7 +30,7 @@
#' @param combine_IR a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible) #' @param combine_IR a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)
#' @details \strong{Remember that you should filter your table to let it contain only first isolates!} Use \code{\link{first_isolate}} to determine them in your data set. #' @details \strong{Remember that you should filter your table to let it contain only first isolates!} Use \code{\link{first_isolate}} to determine them in your data set.
#' #'
#' These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. If a column has been transformed with \code{\link{as.rsi}}, just use e.g. \code{isolates[isolates == "R"]} to get the resistant ones. You could then calculate the \code{\link{length}} of it. #' These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the \code{\link[AMR]{count}} functions to count isolates. \emph{Low counts can infuence the outcome - these \code{portion} functions may camouflage this, since they only return the portion albeit being dependent on the \code{minimum} parameter.}
#' #'
#' \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}. #' \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
#' #'

4
man/first_isolate.Rd
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@ -25,13 +25,13 @@ first_isolate(tbl, col_date = NULL, col_patient_id = NULL,
\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}}.}
\item{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.} \item{col_testcode}{column name of the test codes. Use \code{col_testcode = NULL} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored.}
\item{col_specimen}{column name of the specimen type or group} \item{col_specimen}{column name of the specimen type or group}
\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. 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{col_keyantibiotics}{column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. 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}

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man/portion.Rd
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@ -59,7 +59,7 @@ These functions can be used to calculate the (co-)resistance of microbial isolat
\details{ \details{
\strong{Remember that you should filter your table to let it contain only first isolates!} Use \code{\link{first_isolate}} to determine them in your data set. \strong{Remember that you should filter your table to let it contain only first isolates!} Use \code{\link{first_isolate}} to determine them in your data set.
These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. If a column has been transformed with \code{\link{as.rsi}}, just use e.g. \code{isolates[isolates == "R"]} to get the resistant ones. You could then calculate the \code{\link{length}} of it. These functions are not meant to count isolates, but to calculate the portion of resistance/susceptibility. Use the \code{\link[AMR]{count}} functions to count isolates. \emph{Low counts can infuence the outcome - these \code{portion} functions may camouflage this, since they only return the portion albeit being dependent on the \code{minimum} parameter.}
\code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}. \code{portion_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and calculates the portions R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.