# .col_spec_csv = "dccccccccccdDDD"
# .col_spec_xlsx = c("numeric",
# rep("text", 10),
# "numeric",
# "date",
# "date",
# "date")
#
# excel_date <- function (x, origin = "1900-01-01", ...) {
# ## from openxlsx::convertToDate
# x <- as.numeric(x)
# notNa <- !is.na(x)
# if (origin == "1900-01-01") {
# x[notNa] <- x[notNa] - 2
# }
# return(as.Date(x, origin = origin, ...))
# }
#
# column_convertors_xlsx <- function(){
# ## all columns remain as text except...
# list(
# "FINALID"=as.numeric,
# "age" = as.numeric,
# "Onsetdate" = excel_date,
# "specimen_date" = excel_date,
# "lab_report_date" = excel_date
# )
# }
#
# csvdate <- function(x){
# as.Date(x,format="%m/%d/%y")
#
# }
#
# column_convertors_csv <- function(){
# list(
# "Onsetdate" = csvdate,
# "specimen_date" = csvdate,
# "lab_report_date" = csvdate)
# }
#
read_casefile <- function(casefile){
# if(grepl("\\.xlsx$",casefile, ignore.case=TRUE)){
# cases <- readxl::read_xlsx(casefile, col_types="text")
# column_convertors = column_convertors_xlsx()
# }else if(grepl("\\.csv$",casefile, ignore.case=TRUE)){
# cases <- read.csv(casefile, stringsAsFactors=FALSE)
# column_convertors = column_convertors_csv()
# }else{
# stop("Unrecognised case file extension for ",casefile," - not CSV or XLSX")
# }
# cc = column_convertors
# for(col in names(cc)){
# cases[[col]] = cc[[col]](cases[[col]])
# }
cases <- read.csv(casefile, stringsAsFactors=FALSE)
return(cases)
}
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