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New mo algorithm, prepare for 2.0

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Dr. Matthijs Berends
2022-10-05 09:12:22 +02:00
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parent 63fe160322
commit cd2acc4a29
182 changed files with 4054 additions and 90905 deletions
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16
R/disk.R
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@ -1,12 +1,16 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2022 Berends MS, Luz CF et al. #
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
@ -72,14 +76,14 @@ as.disk <- function(x, na.rm = FALSE) {
if (na.rm == TRUE) {
x <- x[!is.na(x)]
}
x[trimws(x) == ""] <- NA
x[trimws2(x) == ""] <- NA
x.bak <- x
na_before <- length(x[is.na(x)])
# heavily based on cleaner::clean_double():
clean_double2 <- function(x, remove = "[^0-9.,-]", fixed = FALSE) {
x <- gsub(",", ".", x)
x <- gsub(",", ".", x, fixed = TRUE)
# remove ending dot/comma
x <- gsub("[,.]$", "", x)
# only keep last dot/comma
@ -131,7 +135,7 @@ all_valid_disks <- function(x) {
x_disk <- tryCatch(suppressWarnings(as.disk(x[!is.na(x)])),
error = function(e) NA
)
!any(is.na(x_disk)) && !all(is.na(x))
!anyNA(x_disk) && !all(is.na(x))
}
#' @rdname as.disk