tests/testthat/test_NMscanMultiple.R

In philipdelff/NMdata: Preparation, Checking and Post-Processing Data for PK/PD Modeling

## library(devtools)
## setwd("tests/testthat")
## load_all()

context("NMscanMultiple")
## NMdata_filepath <- function(...) {
##     system.file(..., package = "NMdata")
## }

## file.nm <- function(...) NMdata_filepath("examples/nonmem",...)
## file.data <- function(...) NMdata_filepath("examples/data",...)

fix.time <- function(x){
    meta.x <- attr(x,"NMdata")
    ## meta.x$time.call <- as.POSIXct("2020-02-01 00:01:01",tz="UTC")
    meta.x$details$time.NMscanData <- NULL
    meta.x$details$file.lst <- NULL
    meta.x$details$file.mod <- NULL
    meta.x$details$file.input <- NULL
    meta.x$details$mtime.input <- NULL
    meta.x$details$mtime.lst <- NULL
    meta.x$details$mtime.mod <- NULL
    meta.x$datafile$path <- NULL
    meta.x$datafile$path.rds <- NULL
    meta.x$tables$file <- NULL
    meta.x$tables$file.mtime <- NULL
    setattr(x,"NMdata",meta.x)
    invisible(x)
}



NMdataConf(reset=TRUE)
test_that("basic",{

    fileRef <- "testReference/NMscanMultiple_01.rds"
    resRef <- if(file.exists(fileRef)) readRDS(fileRef) else NULL

### we do this in two steps because not all systems will find the files in same order apparently
    lsts <- list.files(path="testData/nonmem/",pattern="xgxr00[1-9]\\.lst",full.names=TRUE)
    lsts <- sort(lsts)
    res <- NMscanMultiple(lsts, check.time = FALSE,quiet=TRUE)
    ## dim(res)

    ## ref <- readRDS(fileRef)
    ## as.data.table(res)[,.N,by=.(model)]
    ## as.data.table(ref)[,.N,by=.(model)]
    
    
    ## res <- lapply(res,fix.time)
    res <- as.data.frame(res)
    unNMdata(res)


    expect_equal_to_reference(res,fileRef,version=2)
    ## without meta
    ##    expect_equal(unNMdata(res1),unNMdata(readRDS(fileRef)))
    ## data.table(attributes(readRDS(fileRef))$meta$variables$variable,attributes(res1)$meta$variables$variable)
})