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new col names for key_antibiotics
This commit is contained in:
parent
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.2.0.9013
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Date: 2018-07-17
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Version: 0.2.0.9014
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Date: 2018-07-19
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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1
NEWS.md
1
NEWS.md
@ -24,6 +24,7 @@
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#### Changed
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* Pretty printing for tibbles removed as it is not really the scope of this package
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* Improved speed of key antibiotics comparison for determining first isolates
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* Column names for the `key_antibiotics` function are now generic: 6 for broadspectrum ABs, 6 for Gram-positive specific and 6 for Gram-negative specific ABs
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* Printing of class `mic` now shows all MIC values
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* `%like%` now supports multiple patterns
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* Frequency tables are now actual `data.frame`s with altered console printing to make it look like a frequency table. Because of this, the parameter `toConsole` is not longer needed.
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@ -162,7 +162,7 @@ first_isolate <- function(tbl,
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}
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# remove testcodes
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if (!is.na(testcodes_exclude[1]) & testcodes_exclude[1] != '' & info == TRUE) {
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cat('Isolates from these test codes will be ignored:\n', toString(testcodes_exclude), '\n')
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cat('[Criteria] Excluded test codes:\n', toString(testcodes_exclude), '\n')
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}
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if (is.na(col_icu)) {
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@ -181,7 +181,7 @@ first_isolate <- function(tbl,
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if (!is.na(filter_specimen) & filter_specimen != '') {
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check_columns_existance(col_specimen, tbl)
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if (info == TRUE) {
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cat('Isolates other than of specimen group \'', filter_specimen, '\' will be ignored. ', sep = '')
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cat('[Criteria] Excluded other than specimen group \'', filter_specimen, '\'\n', sep = '')
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}
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} else {
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filter_specimen <- ''
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@ -209,8 +209,8 @@ first_isolate <- function(tbl,
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if (filter_specimen == '') {
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if (icu_exclude == FALSE) {
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if (info == TRUE) {
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cat('Isolates from ICU will *NOT* be ignored.\n')
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if (info == TRUE & !is.na(col_icu)) {
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cat('[Criteria] Included isolates from ICU.\n')
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}
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tbl <- tbl %>%
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arrange_at(c(col_patient_id,
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@ -221,7 +221,7 @@ first_isolate <- function(tbl,
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row.end <- nrow(tbl)
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} else {
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if (info == TRUE) {
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cat('Isolates from ICU will be ignored.\n')
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cat('[Criteria] Excluded isolates from ICU.\n')
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}
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tbl <- tbl %>%
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arrange_at(c(col_icu,
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@ -241,8 +241,8 @@ first_isolate <- function(tbl,
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} else {
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# sort on specimen and only analyse these row to save time
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if (icu_exclude == FALSE) {
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if (info == TRUE) {
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cat('Isolates from ICU will *NOT* be ignored.\n')
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if (info == TRUE & !is.na(col_icu)) {
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cat('[Criteria] Included isolates from ICU.\n')
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}
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tbl <- tbl %>%
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arrange_at(c(col_specimen,
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@ -258,7 +258,7 @@ first_isolate <- function(tbl,
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)
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} else {
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if (info == TRUE) {
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cat('Isolates from ICU will be ignored.\n')
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cat('[Criteria] Excluded isolates from ICU.\n')
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}
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tbl <- tbl %>%
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arrange_at(c(col_icu,
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@ -281,7 +281,7 @@ first_isolate <- function(tbl,
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if (abs(row.start) == Inf | abs(row.end) == Inf) {
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if (info == TRUE) {
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cat('No isolates found.\n')
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message('No isolates found.')
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}
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# NA's where genus is unavailable
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tbl <- tbl %>%
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@ -317,15 +317,15 @@ first_isolate <- function(tbl,
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if (col_keyantibiotics != '') {
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if (info == TRUE) {
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if (type == 'keyantibiotics') {
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cat('Key antibiotics for first weighted isolates will be compared (')
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cat('[Criteria] Inclusion based on key antibiotics, ')
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if (ignore_I == FALSE) {
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cat('NOT ')
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cat('not ')
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}
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cat('ignoring I).')
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cat('ignoring I.\n')
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}
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if (type == 'points') {
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cat(paste0('Comparing antibiotics for first weighted isolates (using points threshold of '
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, points_threshold, ')...\n'))
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cat(paste0('[Criteria] Inclusion based on key antibiotics, using points threshold of '
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, points_threshold, '.\n'))
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}
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}
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type_param <- type
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@ -350,9 +350,6 @@ first_isolate <- function(tbl,
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TRUE,
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FALSE))
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)
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if (info == TRUE) {
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cat('\n')
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}
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} else {
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# suppress warnings because dplyr want us to use library(dplyr) when using filter(row_number())
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suppressWarnings(
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@ -388,13 +385,13 @@ first_isolate <- function(tbl,
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pull(real_first_isolate)
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if (info == TRUE) {
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cat(paste0('\nFound ',
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message(paste0('Found ',
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all_first %>% sum(na.rm = TRUE),
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' first ', weighted.notice, 'isolates (',
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(all_first %>% sum(na.rm = TRUE) / scope.size) %>% percent(),
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' of isolates in scope [where genus was not empty] and ',
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(all_first %>% sum(na.rm = TRUE) / tbl %>% nrow()) %>% percent(),
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' of total)\n'))
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' of total)'))
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}
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if (output_logical == FALSE) {
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@ -22,14 +22,16 @@
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#' @param tbl table with antibiotics coloms, like \code{amox} and \code{amcl}.
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#' @param x,y characters to compare
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#' @inheritParams first_isolate
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#' @param amcl,amox,cfot,cfta,cfur,cipr,coli,eryt,gent,mero,oxac,pita,rifa,teic,tetr,tobr,trsu,vanc column names of antibiotics, case-insensitive
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#' @param universal_1,universal_2,universal_3,universal_4,universal_5,universal_6 column names of \strong{broad-spectrum} antibiotics, case-insensitive
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#' @param GramPos_1,GramPos_2,GramPos_3,GramPos_4,GramPos_5,GramPos_6 column names of antibiotics for \strong{Gram positives}, case-insensitive
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#' @param GramNeg_1,GramNeg_2,GramNeg_3,GramNeg_4,GramNeg_5,GramNeg_6 column names of antibiotics for \strong{Gram negatives}, case-insensitive
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#' @details The function \code{key_antibiotics} returns a character vector with antibiotic results.
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#'
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#' The antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
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#' amox, amcl, cfur, pita, cipr, trsu, vanc, teic, tetr, eryt, oxac, rifa.
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#' At default, the antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
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#' \code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"vanc"}, \code{"teic"}, \code{"tetr"}, \code{"eryt"}, \code{"oxac"}, \code{"rifa"}.
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#'
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#' The antibiotics that are used for \strong{Gram negative bacteria} are (colum names): \cr
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#' amox, amcl, cfur, pita, cipr, trsu, gent, tobr, coli, cfot, cfta, mero.
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#' At default, the antibiotics that are used for \strong{Gram negative bacteria} are (colum names): \cr
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#' \code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"gent"}, \code{"tobr"}, \code{"coli"}, \code{"cfot"}, \code{"cfta"}, \code{"mero"}.
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#'
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#'
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#' The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical value.
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@ -54,24 +56,24 @@
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#' }
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key_antibiotics <- function(tbl,
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col_bactid = "bactid",
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amcl = "amcl",
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amox = "amox",
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cfot = "cfot",
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cfta = "cfta",
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cfur = "cfur",
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cipr = "cipr",
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coli = "coli",
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eryt = "eryt",
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gent = "gent",
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mero = "mero",
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oxac = "oxac",
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pita = "pita",
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rifa = "rifa",
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teic = "teic",
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tetr = "tetr",
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tobr = "tobr",
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trsu = "trsu",
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vanc = "vanc",
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universal_1 = "amox",
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universal_2 = "amcl",
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universal_3 = "cfur",
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universal_4 = "pita",
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universal_5 = "cipr",
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universal_6 = "trsu",
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GramPos_1 = "vanc",
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GramPos_2 = "teic",
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GramPos_3 = "tetr",
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GramPos_4 = "eryt",
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GramPos_5 = "oxac",
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GramPos_6 = "rifa",
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GramNeg_1 = "gent",
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GramNeg_2 = "tobr",
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GramNeg_3 = "coli",
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GramNeg_4 = "cfot",
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GramNeg_5 = "cfta",
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GramNeg_6 = "mero",
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info = TRUE) {
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if (!col_bactid %in% colnames(tbl)) {
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@ -79,37 +81,40 @@ key_antibiotics <- function(tbl,
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}
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# check columns
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col.list <- c(amcl, amox, cfot, cfta, cfur, cipr,
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coli, eryt, gent, mero, oxac, pita,
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rifa, teic, tetr, tobr, trsu, vanc)
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col.list <- c(universal_1, universal_2, universal_3, universal_4, universal_5, universal_6,
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GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6,
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GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6)
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col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info)
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amcl <- col.list[amcl]
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amox <- col.list[amox]
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cfot <- col.list[cfot]
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cfta <- col.list[cfta]
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cfur <- col.list[cfur]
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cipr <- col.list[cipr]
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coli <- col.list[coli]
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eryt <- col.list[eryt]
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gent <- col.list[gent]
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mero <- col.list[mero]
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oxac <- col.list[oxac]
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pita <- col.list[pita]
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rifa <- col.list[rifa]
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teic <- col.list[teic]
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tetr <- col.list[tetr]
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tobr <- col.list[tobr]
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trsu <- col.list[trsu]
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vanc <- col.list[vanc]
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universal_1 <- col.list[universal_1]
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universal_2 <- col.list[universal_2]
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universal_3 <- col.list[universal_3]
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universal_4 <- col.list[universal_4]
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universal_5 <- col.list[universal_5]
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universal_6 <- col.list[universal_6]
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GramPos_1 <- col.list[GramPos_1]
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GramPos_2 <- col.list[GramPos_2]
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GramPos_3 <- col.list[GramPos_3]
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GramPos_4 <- col.list[GramPos_4]
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GramPos_5 <- col.list[GramPos_5]
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GramPos_6 <- col.list[GramPos_6]
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GramNeg_1 <- col.list[GramNeg_1]
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GramNeg_2 <- col.list[GramNeg_2]
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GramNeg_3 <- col.list[GramNeg_3]
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GramNeg_4 <- col.list[GramNeg_4]
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GramNeg_5 <- col.list[GramNeg_5]
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GramNeg_6 <- col.list[GramNeg_6]
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gram_positive = c(amox, amcl, cfur, pita, cipr, trsu,
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# specific for G+:
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vanc, teic, tetr, eryt, oxac, rifa)
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universal <- c(universal_1, universal_2, universal_3,
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universal_4, universal_5, universal_6)
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gram_positive = c(universal,
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GramPos_1, GramPos_2, GramPos_3,
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GramPos_4, GramPos_5, GramPos_6)
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gram_positive <- gram_positive[!is.na(gram_positive)]
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gram_negative = c(amox, amcl, cfur, pita, cipr, trsu,
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# specific for G-:
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gent, tobr, coli, cfot, cfta, mero)
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gram_negative = c(universal,
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GramNeg_1, GramNeg_2, GramNeg_3,
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GramNeg_4, GramNeg_5, GramNeg_6)
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gram_negative <- gram_negative[!is.na(gram_negative)]
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# join microorganisms
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@ -5,12 +5,13 @@
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\alias{key_antibiotics_equal}
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\title{Key antibiotics for first \emph{weighted} isolates}
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\usage{
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key_antibiotics(tbl, col_bactid = "bactid", amcl = "amcl", amox = "amox",
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cfot = "cfot", cfta = "cfta", cfur = "cfur", cipr = "cipr",
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coli = "coli", eryt = "eryt", gent = "gent", mero = "mero",
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oxac = "oxac", pita = "pita", rifa = "rifa", teic = "teic",
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tetr = "tetr", tobr = "tobr", trsu = "trsu", vanc = "vanc",
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info = TRUE)
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key_antibiotics(tbl, col_bactid = "bactid", universal_1 = "amox",
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universal_2 = "amcl", universal_3 = "cfur", universal_4 = "pita",
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universal_5 = "cipr", universal_6 = "trsu", GramPos_1 = "vanc",
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GramPos_2 = "teic", GramPos_3 = "tetr", GramPos_4 = "eryt",
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GramPos_5 = "oxac", GramPos_6 = "rifa", GramNeg_1 = "gent",
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GramNeg_2 = "tobr", GramNeg_3 = "coli", GramNeg_4 = "cfot",
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GramNeg_5 = "cfta", GramNeg_6 = "mero", info = TRUE)
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key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
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ignore_I = TRUE, points_threshold = 2, info = FALSE)
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@ -20,7 +21,11 @@ key_antibiotics_equal(x, y, type = c("keyantibiotics", "points"),
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\item{col_bactid}{column name of the unique IDs of the microorganisms (should occur in the \code{\link{microorganisms}} dataset). Get your bactid's with the function \code{\link{guess_bactid}}, that takes microorganism names as input.}
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\item{amcl, amox, cfot, cfta, cfur, cipr, coli, eryt, gent, mero, oxac, pita, rifa, teic, tetr, tobr, trsu, vanc}{column names of antibiotics, case-insensitive}
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\item{universal_1, universal_2, universal_3, universal_4, universal_5, universal_6}{column names of \strong{broad-spectrum} antibiotics, case-insensitive}
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\item{GramPos_1, GramPos_2, GramPos_3, GramPos_4, GramPos_5, GramPos_6}{column names of antibiotics for \strong{Gram positives}, case-insensitive}
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\item{GramNeg_1, GramNeg_2, GramNeg_3, GramNeg_4, GramNeg_5, GramNeg_6}{column names of antibiotics for \strong{Gram negatives}, case-insensitive}
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\item{info}{print progress}
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@ -38,11 +43,11 @@ These function can be used to determine first isolates (see \code{\link{first_is
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\details{
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The function \code{key_antibiotics} returns a character vector with antibiotic results.
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The antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
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amox, amcl, cfur, pita, cipr, trsu, vanc, teic, tetr, eryt, oxac, rifa.
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At default, the antibiotics that are used for \strong{Gram positive bacteria} are (colum names): \cr
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\code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"vanc"}, \code{"teic"}, \code{"tetr"}, \code{"eryt"}, \code{"oxac"}, \code{"rifa"}.
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The antibiotics that are used for \strong{Gram negative bacteria} are (colum names): \cr
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amox, amcl, cfur, pita, cipr, trsu, gent, tobr, coli, cfot, cfta, mero.
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At default, the antibiotics that are used for \strong{Gram negative bacteria} are (colum names): \cr
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\code{"amox"}, \code{"amcl"}, \code{"cfur"}, \code{"pita"}, \code{"cipr"}, \code{"trsu"} (until here is universal), \code{"gent"}, \code{"tobr"}, \code{"coli"}, \code{"cfot"}, \code{"cfta"}, \code{"mero"}.
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The function \code{key_antibiotics_equal} checks the characters returned by \code{key_antibiotics} for equality, and returns a logical value.
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