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read.4D improvements
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commit
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@ -67,4 +67,4 @@ BugReports: https://gitlab.com/msberends/AMR/issues
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License: GPL-2 | file LICENSE
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 6.1.0
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RoxygenNote: 6.1.1
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@ -119,7 +119,7 @@ export(portion_S)
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export(portion_SI)
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export(portion_df)
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export(ratio)
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export(read_4D)
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export(read.4D)
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export(resistance_predict)
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export(right_join_microorganisms)
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export(rsi)
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@ -239,6 +239,6 @@ importFrom(stats,mad)
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importFrom(stats,pchisq)
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importFrom(stats,predict)
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importFrom(stats,sd)
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importFrom(utils,View)
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importFrom(utils,browseVignettes)
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importFrom(utils,installed.packages)
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importFrom(xml2,read_html)
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3
NEWS.md
3
NEWS.md
@ -5,7 +5,7 @@
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* Function `count_all` to get all available isolates (that like all `portion_*` and `count_*` functions also supports `summarise` and `group_by`), the old `n_rsi` is now an alias of `count_all`
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* Function `get_locale` to determine language for language-dependent output for some `mo_*` functions. This is now the default value for their `language` parameter, by which the system language will be used at default.
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* Data sets `microorganismsDT`, `microorganisms.prevDT`, `microorganisms.unprevDT` and `microorganisms.oldDT` to improve the speed of `as.mo`. They are for reference only, since they are primarily for internal use of `as.mo`.
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* Function `read_4D` to read from the 4D database of the MMB department of the UMCG
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* Function `read.4D` to read from the 4D database of the MMB department of the UMCG
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* Functions `mo_authors` and `mo_year` to get specific values about the scientific reference of a taxonomic entry
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#### Changed
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@ -57,6 +57,7 @@
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* Speed improvement for `is.rsi.eligible`, now 15-20 times faster
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* In `g.test`, when `sum(x)` is below 1000 or any of the expected values is below 5, Fisher's Exact Test will be suggested
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* `ab_name` will try to fall back on `as.atc` when no results are found
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* Removed the addin to view data sets
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#### Other
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* New dependency on package `crayon`, to support formatted text in the console
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@ -47,7 +47,7 @@ get_locale <- function() {
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} else if (grepl("^(Portuguese|Portugu.s|pt_|PT_)", lang, ignore.case = FALSE)) {
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"pt"
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} else {
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# other language, set to English
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# other language -> set to English
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"en"
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}
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}
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@ -49,6 +49,7 @@
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#'
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#' \code{ggplot_rsi} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\code{\%>\%}). See Examples.
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#' @rdname ggplot_rsi
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#' @importFrom utils installed.packages
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#' @export
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#' @examples
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#' library(dplyr)
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18
R/misc.R
18
R/misc.R
@ -26,24 +26,6 @@ addin_insert_like <- function() {
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rstudioapi::insertText(" %like% ")
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}
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# No export, no Rd
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#' @importFrom utils View
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addin_open_antibiotics <- function() {
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View(antibiotics)
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}
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# No export, no Rd
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#' @importFrom utils View
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addin_open_microorganisms <- function() {
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View(microorganisms)
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}
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# No export, no Rd
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#' @importFrom utils View
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addin_open_septic_patients <- function() {
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View(septic_patients)
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}
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# No export, no Rd
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percent <- function(x, round = 1, force_zero = FALSE, ...) {
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val <- base::round(x * 100, digits = round)
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16
R/mo.R
16
R/mo.R
@ -181,7 +181,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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x[is.null(x)] <- NA
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# support tidyverse selection like: df %>% select(colA)
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if (!is.vector(x)) {
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if (!is.vector(x) & !is.null(dim(x))) {
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x <- pull(x, 1)
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}
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}
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@ -360,9 +360,15 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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# next
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}
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if (x_backup[i] %in% AMR::microorganisms.umcg[, 1]) {
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ref_certe <- AMR::microorganisms.umcg[AMR::microorganisms.umcg[, 1] == x_backup[i], 2]
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ref_mo <- AMR::microorganisms.certe[AMR::microorganisms.certe[, 1] == ref_certe, 2]
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x[i] <- microorganismsDT[mo == ref_mo, ..property][[1]][1L]
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mo_umcg <- AMR::microorganisms.umcg[AMR::microorganisms.umcg[, 1] == x_backup[i], 2]
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mo_found <- AMR::microorganisms.certe[AMR::microorganisms.certe[, 1] == mo_umcg, 2]
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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 (x_backup[i] %in% reference_df[, 1]) {
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@ -575,7 +581,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
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failures <- failures[!failures %in% c(NA, NULL, NaN)]
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if (length(failures) > 0) {
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warning("These ", length(failures) , " values could not be coerced: ",
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warning("These ", length(failures) , " values could not be coerced to a valid MO code: ",
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paste('"', unique(failures), '"', sep = "", collapse = ', '),
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".",
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call. = FALSE)
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@ -18,11 +18,15 @@
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#' Read data from 4D database
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#'
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#' This function is only useful for the MMB department of the UMCG. Use this function to \strong{import data by just defining the \code{file} parameter}. It will automatically transform birth dates and calculate patients age, translate the data set to English, transform the \code{mo} with \code{\link{as.mo}} and transform all antimicrobial columns with \code{\link{as.rsi}}.
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#' This function is only useful for the MMB department of the UMCG. Use this function to \strong{import data by just defining the \code{file} parameter}. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the \code{mo} with \code{\link{as.mo}} and transform all antimicrobial columns with \code{\link{as.rsi}}.
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#' @inheritParams utils::read.table
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#' @param info a logical to indicate whether info about the import should be printed, defaults to \code{TRUE} in interactive sessions
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#' @details Column names will be transformed, but the original column names are set as a "label" attribute and can be seen in e.g. RStudio Viewer.
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#' @export
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read_4D <- function(file,
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read.4D <- function(file,
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info = interactive(),
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header = TRUE,
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row.names = NULL,
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sep = "\t",
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quote = "\"'",
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dec = ",",
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@ -36,7 +40,11 @@ read_4D <- function(file,
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fileEncoding = "UTF-8",
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encoding = "UTF-8") {
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if (info == TRUE) {
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message("Importing data... ", appendLF = FALSE)
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}
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data_4D <- utils::read.table(file = file,
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row.names = row.names,
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header = header,
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sep = sep,
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quote = quote,
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@ -57,7 +65,7 @@ read_4D <- function(file,
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posixlt <- as.POSIXlt(date_regular)
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# born after today will be born 100 years ago
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# based on https://stackoverflow.com/a/3312971/4575331
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posixlt[date_regular > Sys.Date()]$year <- posixlt[date_regular > Sys.Date()]$year - 100
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posixlt[date_regular > Sys.Date() & !is.na(posixlt)]$year <- posixlt[date_regular > Sys.Date() & !is.na(posixlt)]$year - 100
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as.Date(posixlt)
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}
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to_age_4D <- function(from, to) {
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@ -71,6 +79,15 @@ read_4D <- function(file,
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age - 1, age)
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}
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if (info == TRUE) {
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message("OK\nTransforming column names... ", appendLF = FALSE)
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}
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if ("row.names" %in% colnames(data_4D) & all(is.na(data_4D[, ncol(data_4D)]))) {
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# remove first column name "row.names" and remove last empty column
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colnames(data_4D) <- c(colnames(data_4D)[2:ncol(data_4D)], "_skip_last")
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data_4D <- data_4D[, -ncol(data_4D)]
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}
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colnames(data_4D) <- tolower(colnames(data_4D))
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if (all(c("afnamedat", "gebdatum") %in% colnames(data_4D))) {
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# add age
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@ -91,6 +108,10 @@ read_4D <- function(file,
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# order of columns
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data_4D <- data_4D[, cols_wanted]
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# backup original column names
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colnames.bak <- toupper(colnames(data_4D))
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colnames.bak[colnames.bak == "AGE"] <- NULL
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# rename of columns
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colnames(data_4D) <- gsub("patientnr", "patient_id", colnames(data_4D), fixed = TRUE)
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colnames(data_4D) <- gsub("gebdatum", "date_birth", colnames(data_4D), fixed = TRUE)
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@ -104,6 +125,9 @@ read_4D <- function(file,
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colnames(data_4D) <- gsub("mat", "specimen_group", colnames(data_4D), fixed = TRUE)
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colnames(data_4D) <- gsub("mocode", "mo", colnames(data_4D), fixed = TRUE)
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if (info == TRUE) {
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message("OK\nTransforming dates and age... ", appendLF = FALSE)
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}
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if ("date_birth" %in% colnames(data_4D)) {
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data_4D$date_birth <- to_date_4D(data_4D$date_birth)
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@ -117,6 +141,10 @@ read_4D <- function(file,
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if ("gender" %in% colnames(data_4D)) {
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data_4D$gender[data_4D$gender == "V"] <- "F"
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}
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if (info == TRUE) {
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message("OK\nTransforming MO codes... ", appendLF = FALSE)
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}
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if ("mo" %in% colnames(data_4D)) {
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data_4D$mo <- as.mo(data_4D$mo)
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# column right of mo is:
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@ -129,6 +157,18 @@ read_4D <- function(file,
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}
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}
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# set original column names as label (can be seen in RStudio Viewer)
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if (info == TRUE) {
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message("OK\nSetting original column names as label... ", appendLF = FALSE)
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}
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for (i in 1:ncol(data_4D)) {
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attr(data_4D[, i], "label") <- colnames.bak[i]
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}
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if (info == TRUE) {
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message("OK")
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}
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data_4D
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}
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@ -5,15 +5,3 @@ Interactive: false
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Name: Insert %like%
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Binding: addin_insert_like
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Interactive: false
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Name: View 'antibiotics' data set
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Binding: addin_open_antibiotics
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Interactive: false
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Name: View 'microorganisms' data set
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Binding: addin_open_microorganisms
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Interactive: false
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Name: View 'septic_patients' data set
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Binding: addin_open_septic_patients
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Interactive: false
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@ -1,13 +1,13 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/read_4d.R
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\name{read_4D}
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\alias{read_4D}
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% Please edit documentation in R/read.4d.R
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\name{read.4D}
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\alias{read.4D}
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\title{Read data from 4D database}
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\usage{
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read_4D(file, header = TRUE, sep = "\\t", quote = "\\"'",
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dec = ",", na.strings = c("NA", "", "."), skip = 2,
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check.names = TRUE, strip.white = TRUE, fill = TRUE,
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blank.lines.skip = TRUE, stringsAsFactors = FALSE,
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read.4D(file, info = interactive(), header = TRUE, row.names = NULL,
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sep = "\\t", quote = "\\"'", dec = ",", na.strings = c("NA", "",
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"."), skip = 2, check.names = TRUE, strip.white = TRUE,
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fill = TRUE, blank.lines.skip = TRUE, stringsAsFactors = FALSE,
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fileEncoding = "UTF-8", encoding = "UTF-8")
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}
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\arguments{
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@ -32,12 +32,29 @@ read_4D(file, header = TRUE, sep = "\\t", quote = "\\"'",
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\code{\link{url}}.)
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}
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\item{info}{a logical to indicate whether info about the import should be printed, defaults to \code{TRUE} in interactive sessions}
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\item{header}{a logical value indicating whether the file contains the
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names of the variables as its first line. If missing, the value is
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determined from the file format: \code{header} is set to \code{TRUE}
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if and only if the first row contains one fewer field than the
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number of columns.}
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\item{row.names}{a vector of row names. This can be a vector giving
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the actual row names, or a single number giving the column of the
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table which contains the row names, or character string giving the
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name of the table column containing the row names.
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If there is a header and the first row contains one fewer field than
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the number of columns, the first column in the input is used for the
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row names. Otherwise if \code{row.names} is missing, the rows are
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numbered.
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Using \code{row.names = NULL} forces row numbering. Missing or
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\code{NULL} \code{row.names} generate row names that are considered
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to be \sQuote{automatic} (and not preserved by \code{\link{as.matrix}}).
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}
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\item{sep}{the field separator character. Values on each line of the
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file are separated by this character. If \code{sep = ""} (the
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default for \code{read.table}) the separator is \sQuote{white space},
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@ -100,5 +117,8 @@ read_4D(file, header = TRUE, sep = "\\t", quote = "\\"'",
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}
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}
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\description{
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This function is only useful for the MMB department of the UMCG. Use this function to \strong{import data by just defining the \code{file} parameter}. It will automatically transform birth dates and calculate patients age, translate the data set to English, transform the \code{mo} with \code{\link{as.mo}} and transform all antimicrobial columns with \code{\link{as.rsi}}.
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This function is only useful for the MMB department of the UMCG. Use this function to \strong{import data by just defining the \code{file} parameter}. It will automatically transform birth dates and calculate patients age, translate the column names to English, transform the \code{mo} with \code{\link{as.mo}} and transform all antimicrobial columns with \code{\link{as.rsi}}.
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}
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\details{
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Column names will be transformed, but the original column names are set as a "label" attribute and can be seen in e.g. RStudio Viewer.
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}
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