tests/testthat/test_NMscanInput.R

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

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

context("NMscanInput")

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$path.csv <- NULL
    meta.x$datafile$path.rds <- NULL
    meta.x$datafile$path.fst <- NULL
    meta.x$tables$file <- NULL
    meta.x$tables$file.mtime <- NULL
    setattr(x,"NMdata",meta.x)
}



NMdataConf(reset=TRUE)

test_that("basic",{

    fileRef <- "testReference/NMscanInput_01.rds"
    file.lst <- "testData/nonmem/xgxr004.lst"

    ## res1 <- NMscanInput(file=file.lst,applyFilters = T,as.fun="none")
### using as.data.table for as.fun is not recommended but still allowed
    res <-
        NMscanInput(file=file.lst,apply.filters = T,as.fun="data.table")
    fix.time(res)
    expect_equal_to_reference(res,fileRef,version=2)
})


### this one has NMdata meta data
test_that("input has NMdata meta data",{
    fileRef <- "testReference/NMscanInput_02.rds"
    ## load_all("c:/Users/delff/working_copies/NMdata")

    file.lst <- "testData/nonmem/xgxr011.lst"
    ## NMgetSection(file.lst,section="PROBLEM")
    ## NMgetSection(file.lst,section="DATA")
    

    res <- NMscanInput(file=file.lst,applyFilters = T,as.fun="data.table")
    fix.time(res)
    nm1 <- NMinfo(res)
    expect_equal_to_reference(nm1,fileRef,version=2)
    ## readRDS(fileRef)$tables; nm1$tables    
    
})


test_that("single = filter",{
    ## load_all("c:/Users/delff/working_copies/NMdata")


    file.lst <- "testData/nonmem/xgxr009.lst"
    ## NMgetSection(file.lst,section="PROBLEM")
    ## NMgetSection(file.lst,section="DATA")
    res <- NMscanInput(file=file.lst,apply.filters = T,as.fun="data.table")
    expect_equal(res[,unique(DOSE)],10)
    
})


test_that("Duplicate columns in input data",{
    fileRef <- "testReference/NMscanInput_03.rds"
    ## file.lst <- system.file("examples/nonmem/xgxr015.lst", package="NMdata")
    file.lst <- "testData/nonmem/xgxr015.lst"

    ## res <- NMscanData(file=file.lst)
    ## res <- NMscanData(file=file.lst)

    ## load_all("../../")
    ## debugonce(NMscanInput)
    res <- expect_warning(
        NMscanInput(file=file.lst)
    )
    
    fix.time(res)
    expect_equal_to_reference(res,fileRef,version=2)
})

test_that("single-char ignore",{
    NMdataConf(reset=T)
    fileRef <- "testReference/NMscanInput_04.rds"
    file.lst <- "testData/nonmem/estim_debug.lst"

    ## inpdat <- NMscanInput(file=file.lst,applyFilters=T,file.mod=function(x)sub("\\.lst$",".ctl",x))
    res <- NMscanInput(file=file.lst,apply.filters=T,file.mod=function(x)fnExtension(x,".ctl"))
    expect_equal(nrow(res),98)
    
    fix.time(res)
    expect_equal_to_reference(res,fileRef,version=2)

    if(F){
        ref <- readRDS(fileRef)
        NMinfo(res,"input.filters")
        NMinfo(ref,"input.filters")
    }
})



test_that(".mod with mix of space and , in $INPUT",{
    fileRef <- "testReference/NMscanInput_05.rds"
    file.lst <- "testData/nonmem/min036.mod"

    inpdat <- NMscanInput(file=file.lst)

    expect_equal_to_reference(colnames(inpdat),fileRef,version=2)
    
})


test_that("Erroneously basing a filter on translated column names",{
    ## user could be 
    expect_error(
        NMscanInput("testData/nonmem/min036mod.mod",applyFilters=TRUE)
    )
})

test_that("Including meta data",{
    NMdataConf(reset=T)
    fileRef <- "testReference/NMscanInput_06.rds"
    file.lst <- "testData/nonmem/xgxr004.lst"

    res <-
        NMscanInput(file=file.lst,applyFilters = T,details=T, as.fun="data.table")

    ## res$meta$details$file <- "file"
    ## res$meta$details$file.mtime <- NULL
    fix.time(res)    
    
    expect_equal_to_reference(res,fileRef,version=2)
    
    
})


test_that("CYCLE=DROP",{

    fileRef <- "testReference/NMscanInput_07.rds"
### file.lst <- system.file("examples/nonmem/xgxr002.lst",package="NMdata")
    file.lst <- "testData/nonmem/xgxr002.lst"

    ## res <- NMscanInput(file=file.lst,applyFilters = T,as.fun="none")
### using as.data.table for as.fun is not recommended but still allowed
    res <-
        NMscanInput(file=file.lst,apply.filters = T,as.fun="data.table")

    fix.time(res)
    nm1 <- NMinfo(res)
    expect_equal_to_reference(nm1,fileRef,version=2)

    if(F){
        ref <- readRDS(fileRef)
        ref
        nm1
    }

    
})



test_that("No filters",{

    fileRef <- "testReference/NMscanInput_08.rds"

    inp <- NMscanInput("testData/nonmem/xgxr027.lst")
    inp <- fix.time(inp)

    expect_equal_to_reference(inp,fileRef,version=2)
})


test_that("Multiple filters on same column",{
    NMdataConf(as.fun="data.table")
    fileRef <- "testReference/NMscanInput_09.rds"

    inp.nofilt <- NMscanInput("testData/nonmem/xgxr029.mod",applyFilters=FALSE)[,data:="nofilt"]
    inp.filt <- NMscanInput("testData/nonmem/xgxr029.mod",applyFilters=TRUE)[,data:="filt"]
    inp <- rbind(inp.nofilt,inp.filt)
    
    tab.count <- dcast(
        inp[,.N,by=.(ID,data)]
       ,ID~data,value.var="N")

    expect_equal_to_reference(tab.count,fileRef,version=2)
})


test_that("ID only from pseudonym",{
    NMdataConf(as.fun="data.table")
    fileRef <- "testReference/NMscanInput_10.rds"
    file.mod <- "testData/nonmem/pred030.mod"
    NMreadSection(file.mod,section="input")
    NMextractDataFile(file.mod)$path.csv |> readLines(n=3)

    inp <- NMscanInput(file.mod)
    inp2 <- NMscanInput(file.mod,translate=F)
    
    inp <- fix.time(inp)    
    
    expect_equal_to_reference(inp,fileRef,version=2)
    expect_equal(
        setdiff(colnames(inp),c(colnames(inp2)))
       ,c("ID","DV"))

    if(F){
        ref <- readRDS(fileRef)
        ref
        inp
        inp2
        NMinfo(inp,"input.colnames")
        NMinfo(ref,"input.colnames")
    }
    
    inp3 <- NMscanInput(file.mod,translate=T,recover.cols = FALSE)
    expect_equal(colnames(inp),colnames(inp3))

})


test_that("Missing control stream",{

    expect_error(NMscanInput("testData/nonmem/doesnotexist.mod"))
})

test_that("apply.filters=F and recover.rows=FALSE",{
    NMdataConf(as.fun="data.table")

    fileRef <- "testReference/NMscanInput_11.rds"
    ##file.lst <- system.file("examples/nonmem/xgxr002.lst",package="NMdata")
    file.lst <- "testData/nonmem/xgxr002.lst"

    ## res <- NMscanInput(file=file.lst,applyFilters = T,as.fun="none")
### using as.data.table for as.fun is not recommended but still allowed
    res <-
        NMscanInput(file=file.lst,apply.filters = F,as.fun="data.table",recover.cols=FALSE)

    fix.time(res)
    nm1 <- NMinfo(res)
    expect_equal_to_reference(nm1,fileRef,version=2)

    if(F){
        ref <- readRDS(fileRef)
        ref
        nm1
    }

})

test_that("Space CYCLE =DROP",{
    NMdataConf(reset=TRUE)
    fileRef <- "testReference/NMscanInput_12.rds"
    file.mod <- "testData/nonmem/xgxr030.mod"

    ## res <- NMscanInput(file=file.lst,applyFilters = T,as.fun="none")
### using as.data.table for as.fun is not recommended but still allowed
    res <-
        NMscanInput(file=file.mod,file.mod=identity,apply.filters = F,as.fun="data.table",recover.cols=FALSE)

    fix.time(res)
    nm1 <- NMinfo(res)
    expect_equal_to_reference(nm1,fileRef,version=2)

    if(F){
        ref <- readRDS(fileRef)
        ref
        nm1
    }

})


test_that("Combinations of translate and recover.cols",{
    NMdataConf(reset=TRUE)
    fileRef <- "testReference/NMscanInput_13.rds"
    file.mod <- "testData/nonmem/xgxr030.mod"

### using as.data.table for as.fun is not recommended but still allowed
    res1 <-
        NMscanInput(file=file.mod,file.mod=identity,apply.filters = F,as.fun="data.table",
                    translate=FALSE,recover.cols=FALSE)
    ## colnames(res1)
    ## NMinfo(res1,"input.colnames")

    res2 <-
        NMscanInput(file=file.mod,file.mod=identity,apply.filters = F,as.fun="data.table",
                    translate=FALSE,recover.cols=TRUE)
    ## colnames(res2)
    ## NMinfo(res2,"input.colnames")

    res3 <-
        NMscanInput(file=file.mod,file.mod=identity,apply.filters = F,as.fun="data.table",
                    translate=TRUE,recover.cols=FALSE)
    ## colnames(res3)
    ## NMinfo(res3,"input.colnames")


    res4 <-
        NMscanInput(file=file.mod,file.mod=identity,apply.filters = F,as.fun="data.table",
                    translate=TRUE,recover.cols=TRUE)
    ## colnames(res4)
    ## NMinfo(res4,"input.colnames")


    all.res <- list(res1,res2,res3,res4)
    all.res <- lapply(all.res,fix.time)

    expect_equal_to_reference(all.res,fileRef,version=2)

    if(FALSE){
        ref <- readRDS(fileRef)
        ref[[1]]
        all.res[[1]]

        NMinfo(ref[[3]])
        NMinfo(all.res[[3]])
    }
    
})

test_that("Copy pseudonym when translate=T and recover.cols=TRUE",{
    NMdataConf(reset=TRUE)
    fileRef <- "testReference/NMscanInput_14.rds"
    file.mod <- "testData/nonmem/xgxr054.mod"

    res1 <-
        NMscanInput(file=file.mod,file.mod=identity,
                    apply.filters = FALSE,as.fun="data.table",
                    translate=TRUE,recover.cols=FALSE)
    fix.time(res1)
    ## res1
    expect_equal_to_reference(res1,fileRef,version=2)

    if(F){
        ref <- readRDS(fileRef)
        ref
        res1
    }
})



test_that("The first DV is renamed to DV_DROP. DOSE=DV results in DV and DOSE.",{
    NMdataConf(reset=TRUE)
    fileRef <- "testReference/NMscanInput_15.rds"

    ## $INPUT ROW ID NOMTIME TIME EVID CMT AMT DV=DROP FLAG STUDY
    ## BLQ CYCLE=DROP DOSE=DV PART PROFDAY PROFTIME BBW eff0

    file.mod <- "testData/nonmem/xgxr057.mod"

    res <-
        NMscanInput(file=file.mod,apply.filters = T,as.fun="data.table")
    fix.time(res)
    colnames(res)

    expect_equal_to_reference(res,fileRef,version=2)

    if(FALSE){
        ref <- readRDS(fileRef)
        NMinfo(ref,"input.colnames")
        NMinfo(res,"input.colnames")
        res
        ref
        res
    }

})

test_that("overlap with data file",{
    NMdataConf(reset=TRUE)
    fileRef <- "testReference/NMscanInput_16.rds"

    ## like 057, but with overlap with data file
    file.mod <- "testData/nonmem/xgxr058.mod"

    res <- expect_warning(
        NMscanInput(file=file.mod,apply.filters = T,as.fun="data.table")
    )
    fix.time(res)
    
    colnames(res)
    head(res)

    expect_equal_to_reference(res,fileRef,version=2)

    if(F){
        ref <- readRDS(fileRef)

        compareCols(ref,res)
        colnames(ref)
        colnames(res)
        head(ref)
        head(res)
        NMinfo(ref,"input.colnames")
        NMinfo(res,"input.colnames")
    }

})


test_that("overlap with data file",{
    NMdataConf(reset=TRUE)
    fileRef <- "testReference/NMscanInput_17.rds"

    ## like 057, but with overlap with data file
    file.mod <- "testData/nonmem/xgxr059.mod"

    res <- expect_warning(
        NMscanInput(file=file.mod,apply.filters = T,as.fun="data.table")
    )
    fix.time(res)
    
    colnames(res)
    head(res)

    expect_equal_to_reference(res,fileRef,version=2)

    if(F){
        ref <- readRDS(fileRef)
        ref
        res
        colnames(ref)
        colnames(res)
}

})