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rsi/mic fix

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MS Berends 2018-05-31 09:02:49 +02:00 committed by GitHub
parent 5593aee19e
commit 7a6d5fb6b7
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1 changed files with 16 additions and 11 deletions
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R/classes.R
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@ -42,12 +42,16 @@ as.rsi <- function(x) {
na_before <- x[is.na(x) | x == ''] %>% length() na_before <- x[is.na(x) | x == ''] %>% length()
# remove all spaces # remove all spaces
x <- gsub(' {2,55}', '', x) x <- gsub(' +', '', x)
# disallow more than 10 characters to start with # remove all MIC-like values: numbers, operators and periods
x[nchar(x) > 10] <- NA x <- gsub('[0-9.,<=>]+', '', x)
# disallow more than 3 characters
x[nchar(x) > 3] <- NA
# set to capitals
x <- toupper(x)
# remove all invalid characters # remove all invalid characters
x <- gsub('[^RSI]+', '', x %>% toupper()) x <- gsub('[^RSI]+', '', x)
# needed for UMCG in cases of "S;S" but also "S;I"; the latter will be NA: # in cases of "S;S" keep S, but in case of "S;I" make it NA
x <- gsub('^S+$', 'S', x) x <- gsub('^S+$', 'S', x)
x <- gsub('^I+$', 'I', x) x <- gsub('^I+$', 'I', x)
x <- gsub('^R+$', 'R', x) x <- gsub('^R+$', 'R', x)
@ -65,7 +69,7 @@ as.rsi <- function(x) {
list_missing, call. = FALSE) list_missing, call. = FALSE)
} }
x <- x %>% toupper() %>% factor(levels = c("S", "I", "R"), ordered = TRUE) x <- x %>% factor(levels = c("S", "I", "R"), ordered = TRUE)
class(x) <- c('rsi', 'ordered', 'factor') class(x) <- c('rsi', 'ordered', 'factor')
attr(x, 'package') <- 'AMR' attr(x, 'package') <- 'AMR'
attr(x, 'package.version') <- packageDescription('AMR')$Version attr(x, 'package.version') <- packageDescription('AMR')$Version
@ -147,7 +151,7 @@ plot.rsi <- function(x, ...) {
ylim = c(0, ymax), ylim = c(0, ymax),
ylab = 'Percentage', ylab = 'Percentage',
xlab = 'Antimicrobial Interpretation', xlab = 'Antimicrobial Interpretation',
main = paste('Susceptibilty Analysis of', x_name), main = paste('Susceptibility Analysis of', x_name),
axes = FALSE, axes = FALSE,
...) ...)
# x axis # x axis
@ -178,7 +182,7 @@ barplot.rsi <- function(height, ...) {
barplot(table(x), barplot(table(x),
col = c('green3', 'orange2', 'red3'), col = c('green3', 'orange2', 'red3'),
xlab = 'Antimicrobial Interpretation', xlab = 'Antimicrobial Interpretation',
main = paste('Susceptibilty Analysis of', x_name), main = paste('Susceptibility Analysis of', x_name),
ylab = 'Frequency', ylab = 'Frequency',
axes = FALSE, axes = FALSE,
...) ...)
@ -215,16 +219,17 @@ as.mic <- function(x, na.rm = FALSE) {
# comma to dot # comma to dot
x <- gsub(',', '.', x, fixed = TRUE) x <- gsub(',', '.', x, fixed = TRUE)
# starting dots must start with 0 # starting dots must start with 0
x <- gsub('^[.]', '0.', x) x <- gsub('^[.]+', '0.', x)
# <=0.2560.512 should be 0.512 # <=0.2560.512 should be 0.512
x <- gsub('.*[.].*[.]', '0.', x) x <- gsub('.*[.].*[.]', '0.', x)
# remove ending .0 # remove ending .0
x <- gsub('[.]0$', '', x) x <- gsub('[.]+0$', '', x)
# remove all after last digit # remove all after last digit
x <- gsub('[^0-9]$', '', x) x <- gsub('[^0-9]+$', '', x)
# remove last zeroes # remove last zeroes
x <- gsub('[.]?0+$', '', x) x <- gsub('[.]?0+$', '', x)
# these are alllowed MIC values and will be factor levels
lvls <- c("<0.002", "<=0.002", "0.002", ">=0.002", ">0.002", lvls <- c("<0.002", "<=0.002", "0.002", ">=0.002", ">0.002",
"<0.003", "<=0.003", "0.003", ">=0.003", ">0.003", "<0.003", "<=0.003", "0.003", ">=0.003", ">0.003",
"<0.004", "<=0.004", "0.004", ">=0.004", ">0.004", "<0.004", "<=0.004", "0.004", ">=0.004", ">0.004",