radar2/global.R

103 lines
3.2 KiB
R

# WELCOME TO RadaR
#RadaR is licensed under the GNU General Public License (GPL) v2.0 (https://github.com/ceefluz/radar/blob/master/LICENSE)
# LIST OF REQUIRED PACKAGES -----------------------------------------------
library(shiny)
library(shinydashboard)
library(shinydashboardPlus)
library(dashboardthemes)
library(shinyWidgets)
library(shinycssloaders)
library(shinyjs)
library(DT)
library(tidyverse)
library(ggtext)
library(AMR)
library(cleaner)
library(scales)
library(ggiraph)
source('interfaces.R')
trsns <- read_tsv("translations.txt", lazy = FALSE)
# to do: make system settings dependent
trnslt <- function(english, new_lang = "nl", file = trsns) {
if (english %in% trsns[, 1, drop = TRUE]) {
trsns[match(english, trsns[, 1, drop = TRUE]), new_lang, drop = TRUE]
} else {
english
}
}
pathogens <- read_csv("data/grouping microorganisms.csv")
# created by calling createAbMapping()
tAntibiotics = readxl::read_xlsx('data/ab_mapping.xlsx') %>%
select(Mnemonic, Naam, `EARS-Net.Mnemonic`, `EARS-Net.Name`)
# radar_data <- readGlimsArchive(ymdStartDate = ymdStartDate,
# ymdEndDate = ymdEndDate,
# readPreprocessed = T)
radar_data <- readGlimsFinalResults() %>%
mutate_if(is.rsi, as.sir)
if (!'CRO' %in% colnames(radar_data))
radar_data <- radar_data %>% add_column('CRO' = '')
if (!'OXA' %in% colnames(radar_data))
radar_data <- radar_data %>% add_column('OXA' = '')
specialties <- read_csv("data/specialties.csv", lazy = FALSE)
specialties <- specialties %>%
mutate(specialty_shiny = if_else(specialty != "Outpatients", paste0(specialty, " (", str_replace_all(specialism, ";", ", "), ")"), "Outpatients"),
department = if_else(is.na(department), "NO DEPARTMENT GIVEN", department))
specialties <- separate_rows(specialties, specialism, sep = ";")
specialties <- separate_rows(specialties, department, sep = ";")
radar_data <- radar_data %>%
left_join(specialties) %>%
mutate(specialty = if_else(is.na(specialty), "NO SPECIALTY GIVEN", specialty),
specialty_shiny = if_else(is.na(specialty_shiny), "NO SPECIALTY GIVEN", specialty_shiny),
name = mo_name(mo),
FLC = OXA) %>%
left_join(pathogens)
lab_ab <- c("CFCC", "CFCL", "CFOC", "CFSC", "CFTC", "COCL", "GEHI", "QUDA")
radar_data <- radar_data %>%
select_at(vars(!contains(lab_ab))) %>%
rename_if(is.rsi, function(x) ifelse(is.na(suppressWarnings(as.ab(x))),
x,
suppressWarnings(as.ab(x)))) %>%
mutate(group_all = 1) # dummy variable to disable grouping
radar_data <- radar_data %>%
mutate(CRO = if_else(is.na(CRO) & !is.na(CTX), CTX, CRO))
suppressMessages(
radar_data_first <- radar_data %>%
filter_first_isolate(col_patient_id = "patientid", episode_days = 365, info = FALSE) %>%
mutate(mo = as.mo(mo, Becker = TRUE))
)
intrinsic_info <- AMR::intrinsic_resistant %>%
mutate(#mo = as.mo(microorganism),
intrinsic_r = TRUE)
download_box <- function(exportname, plot) {
downloadHandler(
filename = function() {
paste(exportname, Sys.Date(), ".png", sep = "")
},
content = function(file) {
ggsave(file, plot = plot, device = "png", width = 8)
}
)
}