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age_groups fix

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dr. M.S. (Matthijs) Berends
2019-02-27 11:36:12 +01:00
parent 4ba2ff68e0
commit 54162522bd
41 changed files with 450 additions and 386 deletions
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15
R/mo_source.R
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@ -26,13 +26,13 @@
#' @rdname mo_source
#' @name mo_source
#' @aliases set_mo_source get_mo_source
#' @details The reference file can be a text file seperated with commas (CSV) or pipes, an Excel file (old 'xls' format or new 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the \code{readxl} package installed.
#' @details The reference file can be a text file seperated with commas (CSV) or tabs or pipes, an Excel file (either 'xls' or 'xlsx' format) or an R object file (extension '.rds'). To use an Excel file, you need to have the \code{readxl} package installed.
#'
#' \code{set_mo_source} will check the file for validity: it must be a \code{data.frame}, must have a column named \code{"mo"} which contains values from \code{microorganisms$mo} and must have a reference column with your own defined values. If all tests pass, \code{set_mo_source} will read the file into R and export it to \code{"~/.mo_source.rds"}. This compressed data file will then be used at default for MO determination (function \code{\link{as.mo}} and consequently all \code{mo_*} functions like \code{\link{mo_genus}} and \code{\link{mo_gramstain}}). The location of the original file will be saved as option with \code{\link{options}(mo_source = path)}. Its timestamp will be saved with \code{\link{options}(mo_source_datetime = ...)}.
#'
#' \code{get_mo_source} will return the data set by reading \code{"~/.mo_source.rds"} with \code{\link{readRDS}}. If the original file has changed (the file defined with \code{path}), it will call \code{set_mo_source} to update the data file automatically.
#'
#' Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file will have a size of 0.1 kB and can be read by \code{get_mo_source} in only a couple of microseconds (a millionth of a second).
#' Reading an Excel file (\code{.xlsx}) with only one row has a size of 8-9 kB. The compressed file used by this package will have a size of 0.1 kB and can be read by \code{get_mo_source} in only a couple of microseconds (a millionth of a second).
#' @importFrom dplyr select everything
#' @export
#' @inheritSection AMR Read more on our website!
@ -48,7 +48,7 @@
#' # 1. We save it as 'home/me/ourcodes.xlsx'
#'
#' # 2. We use it for input:
#' set_mo_source("C:\path\ourcodes.xlsx")
#' set_mo_source("home/me/ourcodes.xlsx")
#' #> Created mo_source file '~/.mo_source.rds' from 'home/me/ourcodes.xlsx'.
#'
#' # 3. And use it in our functions:
@ -109,11 +109,20 @@ set_mo_source <- function(path) {
}
df <- readxl::read_excel(path)
} else if (path %like% '[.]tsv$') {
df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE)
} else {
# try comma first
try(
df <- utils::read.table(header = TRUE, sep = ",", stringsAsFactors = FALSE),
silent = TRUE)
if (!is_valid(df)) {
# try tab
try(
df <- utils::read.table(header = TRUE, sep = "\t", stringsAsFactors = FALSE),
silent = TRUE)
}
if (!is_valid(df)) {
# try pipe
try(