mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 06:06:12 +01:00
dr. M.S. (Matthijs) Berends
53464ff1c8
- Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore) - Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS - Renamed dataset `bactlist` to `microorganisms`
53 lines
2.3 KiB
R
53 lines
2.3 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# AUTHORS #
|
|
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# LICENCE #
|
|
# This program is free software; you can redistribute it and/or modify #
|
|
# it under the terms of the GNU General Public License version 2.0, #
|
|
# as published by the Free Software Foundation. #
|
|
# #
|
|
# This program is distributed in the hope that it will be useful, #
|
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
|
# GNU General Public License for more details. #
|
|
# ==================================================================== #
|
|
|
|
# No export, no Rd
|
|
"%like%" <- function(vector, pattern) {
|
|
# Source: https://github.com/Rdatatable/data.table/blob/master/R/like.R
|
|
# But made it case insensitive
|
|
if (is.factor(vector)) {
|
|
as.integer(vector) %in% grep(pattern, levels(vector), ignore.case = TRUE)
|
|
} else {
|
|
grepl(pattern, vector, ignore.case = TRUE)
|
|
}
|
|
}
|
|
|
|
# No export, no Rd
|
|
percent <- function(x, round = 1, ...) {
|
|
base::paste0(base::round(x * 100, digits = round), "%")
|
|
}
|
|
|
|
# No export, no Rd
|
|
quasiquotate <- function(deparsed, parsed) {
|
|
# when text: remove first and last "
|
|
if (any(deparsed %like% '^".+"$' | deparsed %like% "^'.+'$")) {
|
|
deparsed <- deparsed %>% substr(2, nchar(.) - 1)
|
|
}
|
|
# apply if needed
|
|
if (any(!deparsed %like% '[[$:()]'
|
|
& !deparsed %in% c('""', "''", "", # empty text
|
|
".", ".data", # dplyr references
|
|
"TRUE", "FALSE", # logicals
|
|
"NA", "NaN", "NULL", # empty values
|
|
ls(.GlobalEnv)))) {
|
|
deparsed
|
|
} else {
|
|
parsed
|
|
}
|
|
}
|