tests/testthat/test_NMscanData.R
In philipdelff/NMdata: Preparation, Checking and Post-Processing Data for PK/PD Modeling
## library(devtools)
## setwd("tests/testthat")
## load_all()
context("NMscanData")
library(data.table)
data.table::setDTthreads(1)
## 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$path.csv <- NULL
meta.x$datafile$path.rds <- NULL
meta.x$datafile$path.fst <- NULL
meta.x$tables$file <- NULL
meta.x$tables$file.mtime <- NULL
setattr(x,"NMdata",meta.x)
invisible(x)
}
NMdataConf(reset=TRUE)
test_that("basic",{
fileRef <- "testReference/NMscanData1.rds"
resRef <- if(file.exists(fileRef)) readRDS(fileRef) else NULL
## file.lst <- "../../inst/examples/nonmem/run001.lst"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr001.lst")
## file.lst <- system.file("examples/nonmem/xgxr001.lst" ,package="NMdata")
file.lst <- "testData/nonmem/xgxr001.lst"
## NMreadSection(NMdata_filepath("examples/nonmem/run001.lst"),section="DATA")
res <- NMscanData(file=file.lst, quiet=T, order.columns = F, merge.by.row=FALSE, check.time = FALSE)
## res2 <- NMscanData(file=file.lst, quiet=T, order.columns = F, merge.by.row=FALSE, check.time = FALSE,rep.count=T)
## dim(res)
fix.time(res)
expect_equal_to_reference(res,fileRef,version=2)
## without meta
## expect_equal(unNMdata(res),unNMdata(readRDS(fileRef)))
## data.table(attributes(readRDS(fileRef))$meta$variables$variable,attributes(res1)$meta$variables$variable)
})
test_that("Modifications to column names in $INPUT",{
fileRef <- "testReference/NMscanData2.rds"
## res.ref <- readRDS(fileRef)
## file.lst <- NMdata_filepath("examples/nonmem/xgxr002.lst")
file.lst <- "testData/nonmem/xgxr002.lst"
res1 <- NMscanData(file=file.lst, check.time = FALSE, merge.by.row=FALSE, quiet=T)
res <- list(
NMinfo(res1,"input.colnames"),
NMinfo(res1,"columns"),
colnames(res1)
)
expect_equal_to_reference(res,fileRef,version=2)
## without meta
## expect_equal(unNMdata(res),unNMdata(readRDS(fileRef)))
})
test_that("No translation of column names in $INPUT",{
fileRef <- "testReference/NMscanData2b.rds"
## res.ref <- readRDS(fileRef)
file.lst <- "testData/nonmem/xgxr002.lst"
res1 <- NMscanData(file=file.lst, check.time = FALSE, merge.by.row=FALSE, translate.input = T, quiet=T)
res2 <- NMscanData(file=file.lst, check.time = FALSE, merge.by.row=FALSE, translate.input = F, quiet=T)
dt.cnames <- data.table(colnames(res1),colnames(res2))
expect_equal_to_reference(dt.cnames,fileRef,version=2)
})
test_that("Multiple output table formats",{
NMdataConf(reset=TRUE)
fileRef <- "testReference/NMscanData_03.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr003.lst")
file.lst <- "testData/nonmem/xgxr003.lst"
## res <- NMscanData(file=file.lst)
res <- NMscanData(file=file.lst, check.time = FALSE, merge.by.row=FALSE, quiet=T)
fix.time(res)
expect_equal_to_reference(res,fileRef,version=2)
## without meta
## expect_equal(unNMdata(res),unNMdata(readRDS(fileRef)))
## only meta
## expect_equal(NMinfo(res),NMinfo(readRDS(fileRef)))
})
test_that("Interpret IGNORE statement",{
NMdataConf(reset=TRUE)
fileRef <- "testReference/NMscanData4.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr004.lst")
file.lst <- "testData/nonmem/xgxr004.lst"
## res <- NMscanData(file=file.lst)
## res <- NMscanData(file=file.lst)
res <- NMscanData(file=file.lst,merge.by.row=FALSE,check.time = FALSE, quiet=T)
fix.time(res)
## names(res$row)
expect_equal_to_reference(res,fileRef,version=2)
## without meta
## expect_equal(unNMdata(res),unNMdata(readRDS(fileRef)))
})
test_that("List of ACCEPT statements and vs separate statements",{
NMdataConf(reset=T)
NMdataConf(as.fun="data.table")
## file1.lst <- NMdata_filepath("examples/nonmem/xgxr006.lst")
## file2.lst <- NMdata_filepath("examples/nonmem/xgxr007.lst")
file1.lst <- "testData/nonmem/xgxr006.lst"
file2.lst <- "testData/nonmem/xgxr007.lst"
NMreadSection(file1.lst,section="PROBLEM")
NMreadSection(file2.lst,section="PROBLEM")
res1 <- NMscanData(file=file1.lst,merge.by.row=FALSE,col.model=NULL,check.time = FALSE, quiet=T)
res2 <- NMscanData(file=file2.lst,merge.by.row=FALSE,col.model=NULL,check.time = FALSE, quiet=T)
setattr(res1,"NMdata",NULL)
setattr(res2,"NMdata",NULL)
expect_identical(res1,res2)
})
test_that("merge by filters or not",{
## fileRef <- "testReference/NMscanData4.rds"
## file1.lst <- NMdata_filepath("examples/nonmem/xgxr006.lst")
## file2.lst <- NMdata_filepath("examples/nonmem/xgxr008.lst")
file1.lst <- "testData/nonmem/xgxr006.lst"
file2.lst <- "testData/nonmem/xgxr008.lst"
## NMreadSection(file1.lst,section="PROBLEM")
## NMreadSection(file2.lst,section="PROBLEM")
res1 <- NMscanData(file=file1.lst,merge.by.row=FALSE,col.model=NULL,check.time = FALSE, quiet=T)
res2 <- NMscanData(file=file2.lst,merge.by.row=FALSE,col.model=NULL,check.time = FALSE, quiet=T)
setnames(res2,"EFF0","eff0",skip_absent=T)
setcolorder(res1,colnames(res2))
## the var tables are different because ROW is input in one,
## output in the other. This is as expected.
## cbind(attr(res1,"var"),attr(res2,"var"))
setattr(res1,"NMdata",NULL)
setattr(res2,"NMdata",NULL)
expect_equal(res1,res2)
})
### BUG 011. NA rows used for fo table. 0 IDs.
#### it is the rare situation where
##### there is only first-only output (nmout=FALSE everywhere)
##### col.id is not in first-only table
##### nmout does not exactly represent the split we need here. We need
##### to know which rows were enriched by output.
test_that("Only a firstonly without ID but with ROW",{
### This should work because ROW is in firstonly table.
NMdataConf(reset=TRUE)
## NMdataConf(as.fun="data.table")
fileRef <- "testReference/NMscanData_11.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr011.lst")
file.lst <- "testData/nonmem/xgxr011.lst"
## NMreadSection(NMdata_filepath("examples/nonmem/run001.lst"),section="DATA")
### notice that DV PRED RES WRES are returned in firstonly. This is horrible.
## tabs <- NMscanTables(file.lst)
## tabs
### impossible with filters at the moment. Cannot be implemented because id level cannot be merged onto row level input.
expect_error(
expect_warning(
NMscanData(file=file.lst,merge.by.row=FALSE,col.row="ROW",check.time = FALSE, quiet=T)
)
)
## merge.by.row should be able to merge.
res <-
expect_warning(
NMscanData(file=file.lst,merge.by.row=TRUE,col.row="ROW",check.time = FALSE, quiet=T)
)
fix.time(res)
expect_equal_to_reference(res,fileRef,version=2)
## without meta
## expect_equal(unNMdata(res),unNMdata(readRDS(fileRef)))
## ref <- readRDS(fileRef)
})
test_that("Only a firstonly, no ID, no ROW",{
### use.input= TRUE, cbind.by.filters=FALSE.
## This should give an error because input cannot be used even though it is requested
## this one only outputs a firstonly that cannot be merged onto
## input. use.input=T so input data should be returned.
fileRef <- "testReference/NMscanData12.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr012.lst")
file.lst <- "testData/nonmem/xgxr012.lst"
## NMreadSection(file.lst,section="DATA")
## NMreadSection(file.lst,section="PROBLEM")
## NMreadSection(file.lst,section="TABLE")
expect_error(
expect_warning(
res1 <- NMscanData(file=file.lst,check.time = FALSE, quiet=T)
)
)
})
test_that("FO and row-level output. No ID, no row.",{
#### merge.by.row = "ifAvailable" or FALSE
## Only row-level output returned because cbind.by.filters=F, and firstonly is without ID and row. Warning that firstonly is dropped. Correct.
fileRef <- "testReference/NMscanData_13.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr013.lst")
file.lst <- "testData/nonmem/xgxr013.lst"
NMreadSection(file.lst,section="PROBLEM")
## NMreadSection(NMdata_filepath("examples/nonmem/run001.lst"),section="DATA")
NMreadSection(file.lst,section="TABLE")
## tabs <- NMscanTables(file=file.lst)
res1 <- expect_warning(
NMscanData(file=file.lst,check.time = FALSE, quiet=T)
)
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
## merge.by.row=F cannot combine and returns output. OK
res2 <- expect_warning(
NMscanData(file=file.lst,check.time = FALSE,merge.by.row=T, quiet=T)
)
## if we leave use.input out and can only get row level. OK
res2 <- expect_warning(
NMscanData(file=file.lst,check.time = FALSE,use.input=F, quiet=T)
)
})
### uses ACCEPT: DOSE.GT.20 explining only 731 rows
test_that("FO and row-level output. No ID, no row. cbind.by.filters=T",{
## row-level output+input returned because cbind.by.filters=T, and firstonly is without ID and row. Correct.
fileRef <- "testReference/NMscanData_14.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr013.lst")
file.lst <- "testData/nonmem/xgxr013.lst"
NMreadSection(file.lst,section="PROBLEM")
## tabs <- NMscanTables(file=file.lst)
res1 <- expect_warning(
NMscanData(file=file.lst,merge.by.row=FALSE,check.time = FALSE, quiet=T)
)
fix.time(res1)
summary(res1)$variables
summary(res1)$tables
summary(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
})
## bug. This should return a meaningful error msg
## "bug" confirmed after release of 0.0.16.
test_that("Only a firstonly without ID but with ROW",{
### cbind.by.filters is TRUE, so ROW is not used to recover firstonly data.
fileRef <- "testReference/NMscanData15.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr011.lst")
file.lst <- "testData/nonmem/xgxr011.lst"
NMreadSection(file.lst,section="DATA")
NMreadSection(file.lst,section="TABLE")
### notice that DV PRED RES WRES are returned in firstonly. This is horrible.
## tabs <- NMscanTables(file.lst)
## tabs
res1 <- expect_error(
#expect_warning(
NMscanData(file=file.lst,merge.by.row=FALSE,check.time = FALSE, quiet=T)
## )
)
## tabs=NMscanTables(file=file.lst)
## tabs
})
test_that("Only a firstonly without ID but with ROW. Using merge.by.row=TRUE.",{
### ROW is used to recover firstonly data.
## NMdataConf(as.fun="data.table")
## NMdataConf(as.fun=NULL)
NMdataConf(reset=TRUE)
fileRef <- "testReference/NMscanData_15b.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr011.lst")
file.lst <- "testData/nonmem/xgxr011.lst"
NMreadSection(file.lst,section="DATA")
NMreadSection(file.lst,section="TABLE")
### notice that DV PRED RES WRES are returned in firstonly. This is horrible.
## tabs <- NMscanTables(file.lst)
## tabs
res1 <- expect_warning(
NMscanData(file=file.lst,col.row="ROW",merge.by.row=TRUE,check.time = FALSE, quiet=T)
)
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
})
### recoverRows without a row identifier
test_that("recoverRows without a row identifier",{
fileRef <- "testReference/NMscanData_16.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr004.lst")
file.lst <- "testData/nonmem/xgxr004.lst"
NMreadSection(file.lst,section="DATA")
NMreadSection(file.lst,section="TABLE")
### notice that DV PRED RES WRES are returned in firstonly.
## tabs <- NMscanTables(file.lst)
## tabs
res1 <- NMscanData(file=file.lst,merge.by.row=FALSE,recover.rows = T,as.fun="data.table",check.time = FALSE, quiet=T)
dim(res1)
res1[,table(nmout,DOSE)]
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
})
### get a data.frame
test_that("use as.fun to get a data.frame",{
### cbind.by.filters is TRUE, so ROW is used to recover firstonly data.
fileRef <- "testReference/NMscanData_17.rds"
file.lst <- "testData/nonmem/xgxr004.lst"
NMreadSection(file.lst,section="DATA")
NMreadSection(file.lst,section="TABLE")
res1 <- NMscanData(file=file.lst,merge.by.row=FALSE,recover.rows = T,as.fun=as.data.frame,check.time = FALSE, quiet=T)
dim(res1)
class(res1)
with(res1,table(nmout,DOSE))
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
#### explore
## ref <- readRDS(fileRef)
## compareCols(res1,ref)
## setorder(ref,ROW)
## expect_equal(
## res1,ref
## )
## ref <- readRDS(fileRef)
## names(attributes(res1))
## names(attributes(ref))
})
### get a tibble
test_that("use as.fun to get a tibble",{
### cbind.by.filters is TRUE, so ROW is used to recover firstonly data.
fileRef <- "testReference/NMscanData_18.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr004.lst")
file.lst <- "testData/nonmem/xgxr004.lst"
NMreadSection(file.lst,section="DATA")
NMreadSection(file.lst,section="TABLE")
### notice that DV PRED RES WRES are returned in firstonly.
## tabs <- NMscanTables(file.lst)
## tabs
res1 <- NMscanData(file=file.lst,merge.by.row=FALSE,recover.rows = T,as.fun=tibble::as_tibble,check.time = FALSE, quiet=T)
dim(res1)
class(res1)
## fix.time(res1)
## expect_equal_to_reference(
## res1,fileRef,version=2
## )
expect_true(tibble::is_tibble(res1))
expect_equal(dim(res1),c(1502,35))
###### explore diffs
## ref <- readRDS(fileRef)
## compareCols(res1,ref)
## setorder(ref,ROW)
## expect_equal(
## unNMdata(res1),unNMdata(ref)
## )
## ref <- readRDS(fileRef)
## names(attributes(res1))
## names(attributes(ref))
## class(res1)
## class(ref)
})
## test the dir structure with input.txt/output.txt
test_that("dir structure with input.txt/output.txt",{
## options(NMdata.as.fun="none")
## options(NMdata.file.mod=function(file) file.path(dirname(file),"input.txt"))
## options(NMdata.modelname=function(file) basename(dirname(normalizePath(file))))
NMdataConf(reset=TRUE)
NMdataConf(as.fun="data.table")
## NMdataConf(file.mod=function(file) file.path(dirname(file),"input.txt"))
NMdataConf(file.mod=identity)
NMdataConf(modelname=function(file) basename(dirname(normalizePath(file))))
## filedir.lst <- file.nm("xgxr001dir/output.txt")
filedir.lst <- "testData/nonmem/xgxr001dir/output.txt"
res1dir <- NMscanData(filedir.lst,check.time = FALSE,merge.by.row=F, quiet=T)
## test model names from NMinfo and in result data
expect_equal(NMinfo(res1dir,"details")$model,"xgxr001dir")
umod <- unique(res1dir[,model])
expect_equal(length(umod),1)
expect_equal(umod,"xgxr001dir")
})
#### compare mod/lst vs input/output
## this test isn't ready.
### Todo: Delete components from NMinfo and then test equality
test_that("input.txt/output.txt - unset modelname",{
NMdataConf(reset=TRUE)
NMdataConf(as.fun="data.table")
## NMdataConf(file.mod=function(file) file.path(dirname(file),"input.txt"))
NMdataConf(file.mod=identity)
NMdataConf(modelname=function(file) basename(dirname(normalizePath(file))))
## filedir.lst <- file.nm("xgxr001dir/output.txt")
filedir.lst <- "testData/nonmem/xgxr001dir/output.txt"
res1dir <- NMscanData(filedir.lst,check.time = FALSE,merge.by.row=T, quiet=T)
NMdataConf(file.mod="default")
NMdataConf(modelname=NULL)
## file.lst <- NMdata_filepath("examples/nonmem/xgxr001.lst")
file.lst <- "testData/nonmem/xgxr001.lst"
res1 <- NMscanData(file=file.lst,check.time = FALSE, quiet=T)
## unNMdata(res1)
## unNMdata(res1dir)
## this test isn't ready. How do I execute the input.txt/output.txt model?
els.details <- c("call","model","file.lst","file.mod")
for(elem in els.details){
attributes(res1)$NMdata$details[elem] <- NULL
attributes(res1dir)$NMdata$details[elem] <- NULL
}
attributes(res1)$NMdata$datafile$DATA <- NULL
attributes(res1dir)$NMdata$datafile$DATA <- NULL
attributes(res1)$NMdata$datafile$string <- NULL
attributes(res1dir)$NMdata$datafile$string <- NULL
fix.time(res1)
meta.res1 <- NMinfo(res1)
meta.res1$details$logtime.lst <- NULL
setattr(res1,"NMdata",meta.res1)
fix.time(res1dir)
meta.res1dir <- NMinfo(res1dir)
meta.res1dir$details$logtime.lst <- NULL
setattr(res1dir,"NMdata",meta.res1dir)
## these differ a little in the two estimates
cols.differ <- c("TVKA","TVCL","TVV3","TVQ","KA","CL","V3","Q","V2","IPRED","PRED","RES","WRES")
res1[,(cols.differ):=NULL]
res1dir[,(cols.differ):=NULL]
expect_equal(unNMdata(res1[,!("model")]),unNMdata(res1dir[,!("model")]))
## NMinfo(res1,"tables")
## NMinfo(res1dir,"tables")
NMdataConf(as.fun=NULL)
})
test_that("output.txt, file.mod=identity - NMinfo file.mod=output.txt?",{
NMdataConf(reset=TRUE)
NMdataConf(as.fun="data.table")
NMdataConf(file.mod=identity)
NMdataConf(modelname=function(file) basename(dirname(normalizePath(file))))
## filedir.lst <- file.nm("xgxr001dir/output.txt")
filedir.lst <- "testData/nonmem/xgxr001dir/output.txt"
res1 <- NMscanData(filedir.lst,check.time = FALSE,merge.by.row=F, quiet=T)
expect_equal(basename(NMinfo(res1,"details")$file.lst),"output.txt")
})
##
test_that("Duplicate columns in input data",{
NMdataConf(reset=TRUE)
fileRef <- "testReference/NMscanData_20.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr015.lst")
file.lst <- "testData/nonmem/xgxr015.lst"
## debugonce(NMscanData)
res <- expect_warning(
NMscanData(file=file.lst,merge.by.row=FALSE,check.time = FALSE, quiet=T)
)
fix.time(res)
## names(res$row)
expect_equal_to_reference(res,fileRef,version=2)
})
### this is not a real test. Need to be able to test how the merges were performed.
## test_that("col.row and merge.by.row=TRUE from NMdataConf",{
## NMdataConf(reset=TRUE)
## NMdataConf(col.row="ROW", merge.by.row=TRUE)
## NMdataConf()
## file.lst <- system.file("examples/nonmem/xgxr001.lst" ,package="NMdata")
## res1 <- NMscanData(file=file.lst)
## })
test_that("Modifying row identifier",{
NMdataConf(reset=TRUE)
## file.lst <- NMdata_filepath("examples/nonmem/xgxr016.lst")
file.lst <- "testData/nonmem/xgxr016.lst"
res <-
expect_error(
NMscanData(file=file.lst,merge.by.row=TRUE,check.time = FALSE, quiet=T)
)
})
test_that("merge.by.row=ifAvailable when available",{
NMdataConf(reset=TRUE)
fileRef <- "testReference/NMscanData_21.rds"
file.lst <- system.file("examples/nonmem/xgxr001.lst" ,package="NMdata")
res1 <- NMscanData(file=file.lst,merge.by.row="ifAvailable",check.time=FALSE, quiet=T)
## dim(res1)
### we don't need metadata for this test
unNMdata(res1)
expect_equal_to_reference(res1,fileRef,version=2)
})
test_that("merge.by.row=ifAvailable when not available",{
fileRef <- "testReference/NMscanData_22.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr004.lst")
file.lst <- "testData/nonmem/xgxr004.lst"
res1 <- NMscanData(file=file.lst,merge.by.row="ifAvailable",recover.rows = T,as.fun="data.table",check.time = FALSE, quiet=T)
dim(res1)
res1[,table(nmout,DOSE)]
fix.time(res1)
## compareCols(readRDS(fileRef),res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
##### explore diffs
## ref <- readRDS(fileRef)
## compareCols(res1,ref)
## setorder(ref,ROW)
## expect_equal(
## unNMdata(res1),unNMdata(ref)
## )
})
test_that("col.row does not exist, but merge.by.row==TRUE",{
### col.row does not exist, but merge.by.row==TRUE
fileRef <- "testReference/NMscanData_22b.rds"
NMdataConf(reset=T)
NMdataConf(check.time=F)
file.lst <- system.file("examples/nonmem/xgxr001.lst" ,package="NMdata")
## warning becauses the merge was not possible even though merge.by.row
res1 <-
expect_warning(
NMscanData(file=file.lst,col.row="NONEXIST",merge.by.row=TRUE, quiet=T)
)
fix.time(res1)
expect_equal_to_reference(res1,fileRef)
##### explore diffs
## ref <- readRDS(fileRef)
## indices( attributes(res1)$NMdata$tables)
## indices(attributes(ref)$NMdata$tables)
})
test_that("col.row is NULL, but merge.by.row==TRUE",{
### col.row is NULL, but merge.by.row==TRUE
file.lst <- system.file("examples/nonmem/xgxr001.lst" ,package="NMdata")
## error is that it's not in output. It's not in input either though
expect_error(
res1=NMscanData(file=file.lst,col.row=NULL,merge.by.row=TRUE, quiet=T)
)
})
test_that("A filter without operator",{
fileRef <- "testReference/NMscanData_23.rds"
file.lst <- "testData/nonmem/xgxr010.lst"
res1 <- NMscanData(file=file.lst,merge.by.row="ifAvailable",as.fun="data.table",check.time = FALSE, quiet=T)
res1[,.N,by=.(DOSE)]
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
})
test_that("Including a redundant output table",{
NMdataConf(reset=T)
NMdataConf(as.fun="data.table")
fileRef <- "testReference/NMscanData_24.rds"
## file.lst <- file.nm("xgxr019.lst")
file.lst <- "testData/nonmem/xgxr019.lst"
## notice no cols are taken from the redundant table - correct
res1 <- NMscanData(file=file.lst,merge.by.row="ifAvailable",as.fun="data.table",check.time = FALSE, quiet=T)
## tabs1 <- NMscanTables(file=file.lst,as.fun="data.table",details=T,rep.count=F)
## tabs1$meta
## tabs1$data[[4]]
## NMinfo(res1,"tables")
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
## inp1 <- NMscanInput(file=file.lst)
}
)
## this one has a commented DATA section and an extra DV in output table
test_that("redundant output",{
NMdataConf(reset=T)
NMdataConf(as.fun="data.table")
### ctl file naming is supported by default now
## NMdataConf(file.mod=function(x)sub("\\.lst$",".ctl",x))
NMdataConf(check.time=FALSE)
fileRef <- "testReference/NMscanData_25.rds"
file.lst <- "testData/nonmem/estim_debug.ctl"
## notice no cols are taken from the redundant table - correct
res1 <- expect_message(
NMscanData(file=file.lst, quiet=T)
)
## tabs1 <- NMscanTables(file=file.lst,as.fun="data.table",details=T,rep.count=F)
## tabs1$meta
## tabs1$data[[4]]
## NMinfo(res1,"tables")
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
## inp1 <- NMscanInput(file=file.lst)
}
)
## check.time (warning)
### I'm afraid this could give warnings when run in check or on CRAN.
if(FALSE){
test_that("check time warning",{
NMdataConf(reset=T)
fileRef <- "testReference/NMscanData26.rds"
## file.lst <- "testData/nonmem/xgxr001.lst"
dir.test <- "testData/nonmem/check.time"
if(dir.exists(dir.test)) unlink(dir.test,recursive=TRUE)
dir.create(dir.test)
file.copy("testData/nonmem/xgxr001.lst",dir.test)
file.copy("testData/nonmem/xgxr001_res.txt",dir.test)
file.copy("testData/nonmem/xgxr001.mod",dir.test)
file.lst <- file.path(dir.test,"xgxr001.lst")
file.mod <- fnExtension(file.lst,".mod")
data.new <- sub("../data","../../data",NMreadSection(file.mod,section="data"))
NMwriteSection(file.mod,section="data",newlines=data.new)
res1 <- expect_warning(
NMscanData(file=file.lst, quiet=F, order.columns = F, merge.by.row=FALSE, quiet=T)
)
## dim(res1)'
## without meta
expect_equal_to_reference(unNMdata(res1),fileRef)
## data.table(attributes(readRDS(fileRef))$meta$variables$variable,attributes(res1)$meta$variables$variable)
})
}
test_that("$INPUT copy",{
NMdataConf(reset=T)
NMdataConf(check.time=FALSE)
file.lst.1 <- "testData/nonmem/xgxr022.lst"
res.1 <- NMscanData(file.lst.1, quiet=T)
## NMinfo(res,"input.colname")
NMinfo(res.1,"input.colnames")
NMinfo(res.1,"columns")
file.lst.2 <- "testData/nonmem/xgxr001.lst"
res.2 <- NMscanData(file.lst.2, quiet=T)
expect_equal(ncol(res.1)-ncol(res.2),1)
expect_equal(setdiff(colnames(res.1),colnames(res.2)),c("COMP","EFF0"))
cols.1 <- NMinfo(res.1,"columns")
cols.2 <- NMinfo(res.2,"columns")
expect_equal(setdiff(cols.1$variable,cols.2$variable),c("COMP","EFF0"))
expect_equal(setdiff(cols.2$variable,cols.1$variable),c("eff0"))
})
test_that("only firstonly. Has col.id, no col.row.",{
###### trickers this
## use.input&&!any(tables$meta$full.length)
NMdataConf(reset=T)
NMdataConf(check.time=FALSE)
fileRef <- "testReference/NMscanData_27.rds"
file.lst <- "testData/nonmem/xgxr023.lst"
res <- NMscanData(file.lst,quiet=TRUE)
res <- fix.time(res)
expect_equal_to_reference(res,fileRef)
})
test_that("Two firstonly, one full-length",{
fileRef <- "testReference/NMscanData_28.rds"
file.lst <- "testData/nonmem/xgxr025.lst"
res <- NMscanData(file=file.lst,check.time=F, quiet=T)
res <- fix.time(res)
## ref <- readRDS(fileRef)
expect_equal_to_reference(res,fileRef,version=2)
})
test_that("Two firstonly, one full-length with col.nmrep",{
NMdataConf(reset=TRUE)
#### NMREP is now added to the number of columns taken from the
#### output table that has NMREP. Is that what we want? Or +1? +1 is
#### very complicated for user. Maybe better: if col.nmrep, it is treated like any other column, but in NMinfo(,"tables") there is a column, hasTABLENO
fileRef <- "testReference/NMscanData_28b.rds"
file.lst <- "testData/nonmem/xgxr025.lst"
res <- NMscanData(file=file.lst,check.time=F,col.nmrep=T, quiet=T)
res <- fix.time(res)
## ref <- readRDS(fileRef)
expect_equal_to_reference(res,fileRef,version=2)
})
test_that("Input data as character",{
fileRef <- "testReference/NMscanData29.rds"
file.lst <- "testData/nonmem/xgxr026.lst"
expect_error(NMscanData(file=file.lst,check.time=F))
res <- NMscanData(file=file.lst,check.time=F,use.rds=F, quiet=T)
sapply(res,class)
res <- NMscanData(file=file.lst,check.time=F,use.rds=T,merge.by.row = F, quiet=T)
sapply(res,class)
## res <- fix.time(res)
## ## ref <- readRDS(fileRef)
## expect_equal_to_reference(res,fileRef,version=2)
})
test_that("Input control stream missing",{
NMdataConf(reset=TRUE)
NMdataConf(file.mod="doesNotExist.mod")
fileRef <- "testReference/NMscanData_30.rds"
file.lst <- "testData/nonmem/xgxr001.lst"
res <- NMscanData(file=file.lst,use.input=F, quiet=T)
## check file.mod wasn't used. Notice, merge.by.row is still "ifAvailable" - this was never needed because use.input=FALSE.
## NMinfo(res1a,"details")
fix.time(res)
expect_equal_to_reference(res,fileRef,version=2)
})
test_that("simulation model with subproblems",{
NMdataConf(reset=TRUE)
fileRef <- "testReference/NMscanData_31.rds"
### sim a model with subproblems
## library(devtools)
## load_all("~/wdirs/NMexec")
## file.mod <- "testData/nonmem/xgxr014.mod"
## ## NMexec(file.mod,sge=FALSE,wait=T)
## doses <- NMcreateDoses(TIME=0,AMT=data.table(AMT=c(10,100),DOSE=c(10,100)))
## simdat <- addEVID2(doses,time.sim=1:24,CMT=2)
## simdat[,DV:=NA][
## ,ROW:=.I]
## NMcheckData(simdat)
## NMdataConf(as.fun="data.table")
## sim1 <- NMsim(file.mod,data=simdat,
## suffix.sim="testsim1",dir.sim="testData/simulations"
## ,seed=343108,subproblems=100,nmquiet=T)
### NMsim saves serialized rds. Resaving as version 2
## res.sim <- readRDS("testData/simulations/NMsimData_xgxr014_testsim1.rds")
## saveRDS(res.sim,"testData/simulations/NMsimData_xgxr014_testsim1.rds",version=2)
##### sim done
res <- NMscanData("testData/simulations/xgxr014_testsim1.lst",check.time=F, quiet=T)
fix.time(res)
meta.x <- attr(res,"NMdata")
meta.x$details$time.ok <- NULL
setattr(res,"NMdata",meta.x)
expect_equal_to_reference(res,fileRef,version=2)
}
)
test_that("csv vs rds vs fst",{
fileRef <- "testReference/NMscanData_32.rds"
file.lst <- "testData/nonmem/xgxr014.lst"
res.csv <- NMscanData(file=file.lst, order.columns = F, merge.by.row=FALSE, check.time = FALSE,formats.read=cc(csv), quiet=T)
res.rds <- NMscanData(file=file.lst, order.columns = F, merge.by.row=FALSE, check.time = FALSE,formats.read=cc(rds,csv), quiet=T)
res.fst <- NMscanData(file=file.lst, order.columns = F, merge.by.row=FALSE, check.time = FALSE,formats.read=cc(fst,csv), quiet=T)
res <- dims(res.csv,res.rds,res.fst)
expect_equal_to_reference(res,fileRef,version=2)
})
test_that("inside lappy",{
### there are issues running NMdata functions in lapply - probably due to getArgs
lsts <- c( "testData/nonmem/xgxr014.lst", "testData/nonmem/xgxr032.lst")
res1 <- NMscanData(lsts[1],as.fun="data.table",check.time=FALSE,quiet=TRUE)
res2 <- NMscanData(lsts[2],as.fun="data.table",check.time=FALSE,quiet=TRUE)
res.all <- rbindlist(lapply(lsts,NMscanData,as.fun="data.table",check.time=FALSE,quiet=TRUE),fill=T )
dims1 <- dims(
rbind(res1,res2,fill=T)
,
res.all
)
expect_equal(dims1[,uniqueN(nrows)],1)
expect_equal(dims1[,uniqueN(ncols)],1)
})
philipdelff/NMdata documentation built on March 5, 2025, 12:20 a.m.
R Package Documentation
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## library(devtools)
## setwd("tests/testthat")
## load_all()
context("NMscanData")
library(data.table)
data.table::setDTthreads(1)
## NMdata_filepath <- function(...) {
## system.file(..., package = "NMdata")
## }
## file.nm <- function(...) NMdata_filepath("examples/nonmem",...)
## file.data <- function(...) NMdata_filepath("examples/data",...)
fix.time <- function(x){
meta.x <- attr(x,"NMdata")
## meta.x$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.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)
invisible(x)
}
NMdataConf(reset=TRUE)
test_that("basic",{
fileRef <- "testReference/NMscanData1.rds"
resRef <- if(file.exists(fileRef)) readRDS(fileRef) else NULL
## file.lst <- "../../inst/examples/nonmem/run001.lst"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr001.lst")
## file.lst <- system.file("examples/nonmem/xgxr001.lst" ,package="NMdata")
file.lst <- "testData/nonmem/xgxr001.lst"
## NMreadSection(NMdata_filepath("examples/nonmem/run001.lst"),section="DATA")
res <- NMscanData(file=file.lst, quiet=T, order.columns = F, merge.by.row=FALSE, check.time = FALSE)
## res2 <- NMscanData(file=file.lst, quiet=T, order.columns = F, merge.by.row=FALSE, check.time = FALSE,rep.count=T)
## dim(res)
fix.time(res)
expect_equal_to_reference(res,fileRef,version=2)
## without meta
## expect_equal(unNMdata(res),unNMdata(readRDS(fileRef)))
## data.table(attributes(readRDS(fileRef))$meta$variables$variable,attributes(res1)$meta$variables$variable)
})
test_that("Modifications to column names in $INPUT",{
fileRef <- "testReference/NMscanData2.rds"
## res.ref <- readRDS(fileRef)
## file.lst <- NMdata_filepath("examples/nonmem/xgxr002.lst")
file.lst <- "testData/nonmem/xgxr002.lst"
res1 <- NMscanData(file=file.lst, check.time = FALSE, merge.by.row=FALSE, quiet=T)
res <- list(
NMinfo(res1,"input.colnames"),
NMinfo(res1,"columns"),
colnames(res1)
)
expect_equal_to_reference(res,fileRef,version=2)
## without meta
## expect_equal(unNMdata(res),unNMdata(readRDS(fileRef)))
})
test_that("No translation of column names in $INPUT",{
fileRef <- "testReference/NMscanData2b.rds"
## res.ref <- readRDS(fileRef)
file.lst <- "testData/nonmem/xgxr002.lst"
res1 <- NMscanData(file=file.lst, check.time = FALSE, merge.by.row=FALSE, translate.input = T, quiet=T)
res2 <- NMscanData(file=file.lst, check.time = FALSE, merge.by.row=FALSE, translate.input = F, quiet=T)
dt.cnames <- data.table(colnames(res1),colnames(res2))
expect_equal_to_reference(dt.cnames,fileRef,version=2)
})
test_that("Multiple output table formats",{
NMdataConf(reset=TRUE)
fileRef <- "testReference/NMscanData_03.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr003.lst")
file.lst <- "testData/nonmem/xgxr003.lst"
## res <- NMscanData(file=file.lst)
res <- NMscanData(file=file.lst, check.time = FALSE, merge.by.row=FALSE, quiet=T)
fix.time(res)
expect_equal_to_reference(res,fileRef,version=2)
## without meta
## expect_equal(unNMdata(res),unNMdata(readRDS(fileRef)))
## only meta
## expect_equal(NMinfo(res),NMinfo(readRDS(fileRef)))
})
test_that("Interpret IGNORE statement",{
NMdataConf(reset=TRUE)
fileRef <- "testReference/NMscanData4.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr004.lst")
file.lst <- "testData/nonmem/xgxr004.lst"
## res <- NMscanData(file=file.lst)
## res <- NMscanData(file=file.lst)
res <- NMscanData(file=file.lst,merge.by.row=FALSE,check.time = FALSE, quiet=T)
fix.time(res)
## names(res$row)
expect_equal_to_reference(res,fileRef,version=2)
## without meta
## expect_equal(unNMdata(res),unNMdata(readRDS(fileRef)))
})
test_that("List of ACCEPT statements and vs separate statements",{
NMdataConf(reset=T)
NMdataConf(as.fun="data.table")
## file1.lst <- NMdata_filepath("examples/nonmem/xgxr006.lst")
## file2.lst <- NMdata_filepath("examples/nonmem/xgxr007.lst")
file1.lst <- "testData/nonmem/xgxr006.lst"
file2.lst <- "testData/nonmem/xgxr007.lst"
NMreadSection(file1.lst,section="PROBLEM")
NMreadSection(file2.lst,section="PROBLEM")
res1 <- NMscanData(file=file1.lst,merge.by.row=FALSE,col.model=NULL,check.time = FALSE, quiet=T)
res2 <- NMscanData(file=file2.lst,merge.by.row=FALSE,col.model=NULL,check.time = FALSE, quiet=T)
setattr(res1,"NMdata",NULL)
setattr(res2,"NMdata",NULL)
expect_identical(res1,res2)
})
test_that("merge by filters or not",{
## fileRef <- "testReference/NMscanData4.rds"
## file1.lst <- NMdata_filepath("examples/nonmem/xgxr006.lst")
## file2.lst <- NMdata_filepath("examples/nonmem/xgxr008.lst")
file1.lst <- "testData/nonmem/xgxr006.lst"
file2.lst <- "testData/nonmem/xgxr008.lst"
## NMreadSection(file1.lst,section="PROBLEM")
## NMreadSection(file2.lst,section="PROBLEM")
res1 <- NMscanData(file=file1.lst,merge.by.row=FALSE,col.model=NULL,check.time = FALSE, quiet=T)
res2 <- NMscanData(file=file2.lst,merge.by.row=FALSE,col.model=NULL,check.time = FALSE, quiet=T)
setnames(res2,"EFF0","eff0",skip_absent=T)
setcolorder(res1,colnames(res2))
## the var tables are different because ROW is input in one,
## output in the other. This is as expected.
## cbind(attr(res1,"var"),attr(res2,"var"))
setattr(res1,"NMdata",NULL)
setattr(res2,"NMdata",NULL)
expect_equal(res1,res2)
})
### BUG 011. NA rows used for fo table. 0 IDs.
#### it is the rare situation where
##### there is only first-only output (nmout=FALSE everywhere)
##### col.id is not in first-only table
##### nmout does not exactly represent the split we need here. We need
##### to know which rows were enriched by output.
test_that("Only a firstonly without ID but with ROW",{
### This should work because ROW is in firstonly table.
NMdataConf(reset=TRUE)
## NMdataConf(as.fun="data.table")
fileRef <- "testReference/NMscanData_11.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr011.lst")
file.lst <- "testData/nonmem/xgxr011.lst"
## NMreadSection(NMdata_filepath("examples/nonmem/run001.lst"),section="DATA")
### notice that DV PRED RES WRES are returned in firstonly. This is horrible.
## tabs <- NMscanTables(file.lst)
## tabs
### impossible with filters at the moment. Cannot be implemented because id level cannot be merged onto row level input.
expect_error(
expect_warning(
NMscanData(file=file.lst,merge.by.row=FALSE,col.row="ROW",check.time = FALSE, quiet=T)
)
)
## merge.by.row should be able to merge.
res <-
expect_warning(
NMscanData(file=file.lst,merge.by.row=TRUE,col.row="ROW",check.time = FALSE, quiet=T)
)
fix.time(res)
expect_equal_to_reference(res,fileRef,version=2)
## without meta
## expect_equal(unNMdata(res),unNMdata(readRDS(fileRef)))
## ref <- readRDS(fileRef)
})
test_that("Only a firstonly, no ID, no ROW",{
### use.input= TRUE, cbind.by.filters=FALSE.
## This should give an error because input cannot be used even though it is requested
## this one only outputs a firstonly that cannot be merged onto
## input. use.input=T so input data should be returned.
fileRef <- "testReference/NMscanData12.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr012.lst")
file.lst <- "testData/nonmem/xgxr012.lst"
## NMreadSection(file.lst,section="DATA")
## NMreadSection(file.lst,section="PROBLEM")
## NMreadSection(file.lst,section="TABLE")
expect_error(
expect_warning(
res1 <- NMscanData(file=file.lst,check.time = FALSE, quiet=T)
)
)
})
test_that("FO and row-level output. No ID, no row.",{
#### merge.by.row = "ifAvailable" or FALSE
## Only row-level output returned because cbind.by.filters=F, and firstonly is without ID and row. Warning that firstonly is dropped. Correct.
fileRef <- "testReference/NMscanData_13.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr013.lst")
file.lst <- "testData/nonmem/xgxr013.lst"
NMreadSection(file.lst,section="PROBLEM")
## NMreadSection(NMdata_filepath("examples/nonmem/run001.lst"),section="DATA")
NMreadSection(file.lst,section="TABLE")
## tabs <- NMscanTables(file=file.lst)
res1 <- expect_warning(
NMscanData(file=file.lst,check.time = FALSE, quiet=T)
)
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
## merge.by.row=F cannot combine and returns output. OK
res2 <- expect_warning(
NMscanData(file=file.lst,check.time = FALSE,merge.by.row=T, quiet=T)
)
## if we leave use.input out and can only get row level. OK
res2 <- expect_warning(
NMscanData(file=file.lst,check.time = FALSE,use.input=F, quiet=T)
)
})
### uses ACCEPT: DOSE.GT.20 explining only 731 rows
test_that("FO and row-level output. No ID, no row. cbind.by.filters=T",{
## row-level output+input returned because cbind.by.filters=T, and firstonly is without ID and row. Correct.
fileRef <- "testReference/NMscanData_14.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr013.lst")
file.lst <- "testData/nonmem/xgxr013.lst"
NMreadSection(file.lst,section="PROBLEM")
## tabs <- NMscanTables(file=file.lst)
res1 <- expect_warning(
NMscanData(file=file.lst,merge.by.row=FALSE,check.time = FALSE, quiet=T)
)
fix.time(res1)
summary(res1)$variables
summary(res1)$tables
summary(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
})
## bug. This should return a meaningful error msg
## "bug" confirmed after release of 0.0.16.
test_that("Only a firstonly without ID but with ROW",{
### cbind.by.filters is TRUE, so ROW is not used to recover firstonly data.
fileRef <- "testReference/NMscanData15.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr011.lst")
file.lst <- "testData/nonmem/xgxr011.lst"
NMreadSection(file.lst,section="DATA")
NMreadSection(file.lst,section="TABLE")
### notice that DV PRED RES WRES are returned in firstonly. This is horrible.
## tabs <- NMscanTables(file.lst)
## tabs
res1 <- expect_error(
#expect_warning(
NMscanData(file=file.lst,merge.by.row=FALSE,check.time = FALSE, quiet=T)
## )
)
## tabs=NMscanTables(file=file.lst)
## tabs
})
test_that("Only a firstonly without ID but with ROW. Using merge.by.row=TRUE.",{
### ROW is used to recover firstonly data.
## NMdataConf(as.fun="data.table")
## NMdataConf(as.fun=NULL)
NMdataConf(reset=TRUE)
fileRef <- "testReference/NMscanData_15b.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr011.lst")
file.lst <- "testData/nonmem/xgxr011.lst"
NMreadSection(file.lst,section="DATA")
NMreadSection(file.lst,section="TABLE")
### notice that DV PRED RES WRES are returned in firstonly. This is horrible.
## tabs <- NMscanTables(file.lst)
## tabs
res1 <- expect_warning(
NMscanData(file=file.lst,col.row="ROW",merge.by.row=TRUE,check.time = FALSE, quiet=T)
)
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
})
### recoverRows without a row identifier
test_that("recoverRows without a row identifier",{
fileRef <- "testReference/NMscanData_16.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr004.lst")
file.lst <- "testData/nonmem/xgxr004.lst"
NMreadSection(file.lst,section="DATA")
NMreadSection(file.lst,section="TABLE")
### notice that DV PRED RES WRES are returned in firstonly.
## tabs <- NMscanTables(file.lst)
## tabs
res1 <- NMscanData(file=file.lst,merge.by.row=FALSE,recover.rows = T,as.fun="data.table",check.time = FALSE, quiet=T)
dim(res1)
res1[,table(nmout,DOSE)]
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
})
### get a data.frame
test_that("use as.fun to get a data.frame",{
### cbind.by.filters is TRUE, so ROW is used to recover firstonly data.
fileRef <- "testReference/NMscanData_17.rds"
file.lst <- "testData/nonmem/xgxr004.lst"
NMreadSection(file.lst,section="DATA")
NMreadSection(file.lst,section="TABLE")
res1 <- NMscanData(file=file.lst,merge.by.row=FALSE,recover.rows = T,as.fun=as.data.frame,check.time = FALSE, quiet=T)
dim(res1)
class(res1)
with(res1,table(nmout,DOSE))
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
#### explore
## ref <- readRDS(fileRef)
## compareCols(res1,ref)
## setorder(ref,ROW)
## expect_equal(
## res1,ref
## )
## ref <- readRDS(fileRef)
## names(attributes(res1))
## names(attributes(ref))
})
### get a tibble
test_that("use as.fun to get a tibble",{
### cbind.by.filters is TRUE, so ROW is used to recover firstonly data.
fileRef <- "testReference/NMscanData_18.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr004.lst")
file.lst <- "testData/nonmem/xgxr004.lst"
NMreadSection(file.lst,section="DATA")
NMreadSection(file.lst,section="TABLE")
### notice that DV PRED RES WRES are returned in firstonly.
## tabs <- NMscanTables(file.lst)
## tabs
res1 <- NMscanData(file=file.lst,merge.by.row=FALSE,recover.rows = T,as.fun=tibble::as_tibble,check.time = FALSE, quiet=T)
dim(res1)
class(res1)
## fix.time(res1)
## expect_equal_to_reference(
## res1,fileRef,version=2
## )
expect_true(tibble::is_tibble(res1))
expect_equal(dim(res1),c(1502,35))
###### explore diffs
## ref <- readRDS(fileRef)
## compareCols(res1,ref)
## setorder(ref,ROW)
## expect_equal(
## unNMdata(res1),unNMdata(ref)
## )
## ref <- readRDS(fileRef)
## names(attributes(res1))
## names(attributes(ref))
## class(res1)
## class(ref)
})
## test the dir structure with input.txt/output.txt
test_that("dir structure with input.txt/output.txt",{
## options(NMdata.as.fun="none")
## options(NMdata.file.mod=function(file) file.path(dirname(file),"input.txt"))
## options(NMdata.modelname=function(file) basename(dirname(normalizePath(file))))
NMdataConf(reset=TRUE)
NMdataConf(as.fun="data.table")
## NMdataConf(file.mod=function(file) file.path(dirname(file),"input.txt"))
NMdataConf(file.mod=identity)
NMdataConf(modelname=function(file) basename(dirname(normalizePath(file))))
## filedir.lst <- file.nm("xgxr001dir/output.txt")
filedir.lst <- "testData/nonmem/xgxr001dir/output.txt"
res1dir <- NMscanData(filedir.lst,check.time = FALSE,merge.by.row=F, quiet=T)
## test model names from NMinfo and in result data
expect_equal(NMinfo(res1dir,"details")$model,"xgxr001dir")
umod <- unique(res1dir[,model])
expect_equal(length(umod),1)
expect_equal(umod,"xgxr001dir")
})
#### compare mod/lst vs input/output
## this test isn't ready.
### Todo: Delete components from NMinfo and then test equality
test_that("input.txt/output.txt - unset modelname",{
NMdataConf(reset=TRUE)
NMdataConf(as.fun="data.table")
## NMdataConf(file.mod=function(file) file.path(dirname(file),"input.txt"))
NMdataConf(file.mod=identity)
NMdataConf(modelname=function(file) basename(dirname(normalizePath(file))))
## filedir.lst <- file.nm("xgxr001dir/output.txt")
filedir.lst <- "testData/nonmem/xgxr001dir/output.txt"
res1dir <- NMscanData(filedir.lst,check.time = FALSE,merge.by.row=T, quiet=T)
NMdataConf(file.mod="default")
NMdataConf(modelname=NULL)
## file.lst <- NMdata_filepath("examples/nonmem/xgxr001.lst")
file.lst <- "testData/nonmem/xgxr001.lst"
res1 <- NMscanData(file=file.lst,check.time = FALSE, quiet=T)
## unNMdata(res1)
## unNMdata(res1dir)
## this test isn't ready. How do I execute the input.txt/output.txt model?
els.details <- c("call","model","file.lst","file.mod")
for(elem in els.details){
attributes(res1)$NMdata$details[elem] <- NULL
attributes(res1dir)$NMdata$details[elem] <- NULL
}
attributes(res1)$NMdata$datafile$DATA <- NULL
attributes(res1dir)$NMdata$datafile$DATA <- NULL
attributes(res1)$NMdata$datafile$string <- NULL
attributes(res1dir)$NMdata$datafile$string <- NULL
fix.time(res1)
meta.res1 <- NMinfo(res1)
meta.res1$details$logtime.lst <- NULL
setattr(res1,"NMdata",meta.res1)
fix.time(res1dir)
meta.res1dir <- NMinfo(res1dir)
meta.res1dir$details$logtime.lst <- NULL
setattr(res1dir,"NMdata",meta.res1dir)
## these differ a little in the two estimates
cols.differ <- c("TVKA","TVCL","TVV3","TVQ","KA","CL","V3","Q","V2","IPRED","PRED","RES","WRES")
res1[,(cols.differ):=NULL]
res1dir[,(cols.differ):=NULL]
expect_equal(unNMdata(res1[,!("model")]),unNMdata(res1dir[,!("model")]))
## NMinfo(res1,"tables")
## NMinfo(res1dir,"tables")
NMdataConf(as.fun=NULL)
})
test_that("output.txt, file.mod=identity - NMinfo file.mod=output.txt?",{
NMdataConf(reset=TRUE)
NMdataConf(as.fun="data.table")
NMdataConf(file.mod=identity)
NMdataConf(modelname=function(file) basename(dirname(normalizePath(file))))
## filedir.lst <- file.nm("xgxr001dir/output.txt")
filedir.lst <- "testData/nonmem/xgxr001dir/output.txt"
res1 <- NMscanData(filedir.lst,check.time = FALSE,merge.by.row=F, quiet=T)
expect_equal(basename(NMinfo(res1,"details")$file.lst),"output.txt")
})
##
test_that("Duplicate columns in input data",{
NMdataConf(reset=TRUE)
fileRef <- "testReference/NMscanData_20.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr015.lst")
file.lst <- "testData/nonmem/xgxr015.lst"
## debugonce(NMscanData)
res <- expect_warning(
NMscanData(file=file.lst,merge.by.row=FALSE,check.time = FALSE, quiet=T)
)
fix.time(res)
## names(res$row)
expect_equal_to_reference(res,fileRef,version=2)
})
### this is not a real test. Need to be able to test how the merges were performed.
## test_that("col.row and merge.by.row=TRUE from NMdataConf",{
## NMdataConf(reset=TRUE)
## NMdataConf(col.row="ROW", merge.by.row=TRUE)
## NMdataConf()
## file.lst <- system.file("examples/nonmem/xgxr001.lst" ,package="NMdata")
## res1 <- NMscanData(file=file.lst)
## })
test_that("Modifying row identifier",{
NMdataConf(reset=TRUE)
## file.lst <- NMdata_filepath("examples/nonmem/xgxr016.lst")
file.lst <- "testData/nonmem/xgxr016.lst"
res <-
expect_error(
NMscanData(file=file.lst,merge.by.row=TRUE,check.time = FALSE, quiet=T)
)
})
test_that("merge.by.row=ifAvailable when available",{
NMdataConf(reset=TRUE)
fileRef <- "testReference/NMscanData_21.rds"
file.lst <- system.file("examples/nonmem/xgxr001.lst" ,package="NMdata")
res1 <- NMscanData(file=file.lst,merge.by.row="ifAvailable",check.time=FALSE, quiet=T)
## dim(res1)
### we don't need metadata for this test
unNMdata(res1)
expect_equal_to_reference(res1,fileRef,version=2)
})
test_that("merge.by.row=ifAvailable when not available",{
fileRef <- "testReference/NMscanData_22.rds"
## file.lst <- NMdata_filepath("examples/nonmem/xgxr004.lst")
file.lst <- "testData/nonmem/xgxr004.lst"
res1 <- NMscanData(file=file.lst,merge.by.row="ifAvailable",recover.rows = T,as.fun="data.table",check.time = FALSE, quiet=T)
dim(res1)
res1[,table(nmout,DOSE)]
fix.time(res1)
## compareCols(readRDS(fileRef),res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
##### explore diffs
## ref <- readRDS(fileRef)
## compareCols(res1,ref)
## setorder(ref,ROW)
## expect_equal(
## unNMdata(res1),unNMdata(ref)
## )
})
test_that("col.row does not exist, but merge.by.row==TRUE",{
### col.row does not exist, but merge.by.row==TRUE
fileRef <- "testReference/NMscanData_22b.rds"
NMdataConf(reset=T)
NMdataConf(check.time=F)
file.lst <- system.file("examples/nonmem/xgxr001.lst" ,package="NMdata")
## warning becauses the merge was not possible even though merge.by.row
res1 <-
expect_warning(
NMscanData(file=file.lst,col.row="NONEXIST",merge.by.row=TRUE, quiet=T)
)
fix.time(res1)
expect_equal_to_reference(res1,fileRef)
##### explore diffs
## ref <- readRDS(fileRef)
## indices( attributes(res1)$NMdata$tables)
## indices(attributes(ref)$NMdata$tables)
})
test_that("col.row is NULL, but merge.by.row==TRUE",{
### col.row is NULL, but merge.by.row==TRUE
file.lst <- system.file("examples/nonmem/xgxr001.lst" ,package="NMdata")
## error is that it's not in output. It's not in input either though
expect_error(
res1=NMscanData(file=file.lst,col.row=NULL,merge.by.row=TRUE, quiet=T)
)
})
test_that("A filter without operator",{
fileRef <- "testReference/NMscanData_23.rds"
file.lst <- "testData/nonmem/xgxr010.lst"
res1 <- NMscanData(file=file.lst,merge.by.row="ifAvailable",as.fun="data.table",check.time = FALSE, quiet=T)
res1[,.N,by=.(DOSE)]
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
})
test_that("Including a redundant output table",{
NMdataConf(reset=T)
NMdataConf(as.fun="data.table")
fileRef <- "testReference/NMscanData_24.rds"
## file.lst <- file.nm("xgxr019.lst")
file.lst <- "testData/nonmem/xgxr019.lst"
## notice no cols are taken from the redundant table - correct
res1 <- NMscanData(file=file.lst,merge.by.row="ifAvailable",as.fun="data.table",check.time = FALSE, quiet=T)
## tabs1 <- NMscanTables(file=file.lst,as.fun="data.table",details=T,rep.count=F)
## tabs1$meta
## tabs1$data[[4]]
## NMinfo(res1,"tables")
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
## inp1 <- NMscanInput(file=file.lst)
}
)
## this one has a commented DATA section and an extra DV in output table
test_that("redundant output",{
NMdataConf(reset=T)
NMdataConf(as.fun="data.table")
### ctl file naming is supported by default now
## NMdataConf(file.mod=function(x)sub("\\.lst$",".ctl",x))
NMdataConf(check.time=FALSE)
fileRef <- "testReference/NMscanData_25.rds"
file.lst <- "testData/nonmem/estim_debug.ctl"
## notice no cols are taken from the redundant table - correct
res1 <- expect_message(
NMscanData(file=file.lst, quiet=T)
)
## tabs1 <- NMscanTables(file=file.lst,as.fun="data.table",details=T,rep.count=F)
## tabs1$meta
## tabs1$data[[4]]
## NMinfo(res1,"tables")
fix.time(res1)
expect_equal_to_reference(
res1,fileRef,version=2
)
## inp1 <- NMscanInput(file=file.lst)
}
)
## check.time (warning)
### I'm afraid this could give warnings when run in check or on CRAN.
if(FALSE){
test_that("check time warning",{
NMdataConf(reset=T)
fileRef <- "testReference/NMscanData26.rds"
## file.lst <- "testData/nonmem/xgxr001.lst"
dir.test <- "testData/nonmem/check.time"
if(dir.exists(dir.test)) unlink(dir.test,recursive=TRUE)
dir.create(dir.test)
file.copy("testData/nonmem/xgxr001.lst",dir.test)
file.copy("testData/nonmem/xgxr001_res.txt",dir.test)
file.copy("testData/nonmem/xgxr001.mod",dir.test)
file.lst <- file.path(dir.test,"xgxr001.lst")
file.mod <- fnExtension(file.lst,".mod")
data.new <- sub("../data","../../data",NMreadSection(file.mod,section="data"))
NMwriteSection(file.mod,section="data",newlines=data.new)
res1 <- expect_warning(
NMscanData(file=file.lst, quiet=F, order.columns = F, merge.by.row=FALSE, quiet=T)
)
## dim(res1)'
## without meta
expect_equal_to_reference(unNMdata(res1),fileRef)
## data.table(attributes(readRDS(fileRef))$meta$variables$variable,attributes(res1)$meta$variables$variable)
})
}
test_that("$INPUT copy",{
NMdataConf(reset=T)
NMdataConf(check.time=FALSE)
file.lst.1 <- "testData/nonmem/xgxr022.lst"
res.1 <- NMscanData(file.lst.1, quiet=T)
## NMinfo(res,"input.colname")
NMinfo(res.1,"input.colnames")
NMinfo(res.1,"columns")
file.lst.2 <- "testData/nonmem/xgxr001.lst"
res.2 <- NMscanData(file.lst.2, quiet=T)
expect_equal(ncol(res.1)-ncol(res.2),1)
expect_equal(setdiff(colnames(res.1),colnames(res.2)),c("COMP","EFF0"))
cols.1 <- NMinfo(res.1,"columns")
cols.2 <- NMinfo(res.2,"columns")
expect_equal(setdiff(cols.1$variable,cols.2$variable),c("COMP","EFF0"))
expect_equal(setdiff(cols.2$variable,cols.1$variable),c("eff0"))
})
test_that("only firstonly. Has col.id, no col.row.",{
###### trickers this
## use.input&&!any(tables$meta$full.length)
NMdataConf(reset=T)
NMdataConf(check.time=FALSE)
fileRef <- "testReference/NMscanData_27.rds"
file.lst <- "testData/nonmem/xgxr023.lst"
res <- NMscanData(file.lst,quiet=TRUE)
res <- fix.time(res)
expect_equal_to_reference(res,fileRef)
})
test_that("Two firstonly, one full-length",{
fileRef <- "testReference/NMscanData_28.rds"
file.lst <- "testData/nonmem/xgxr025.lst"
res <- NMscanData(file=file.lst,check.time=F, quiet=T)
res <- fix.time(res)
## ref <- readRDS(fileRef)
expect_equal_to_reference(res,fileRef,version=2)
})
test_that("Two firstonly, one full-length with col.nmrep",{
NMdataConf(reset=TRUE)
#### NMREP is now added to the number of columns taken from the
#### output table that has NMREP. Is that what we want? Or +1? +1 is
#### very complicated for user. Maybe better: if col.nmrep, it is treated like any other column, but in NMinfo(,"tables") there is a column, hasTABLENO
fileRef <- "testReference/NMscanData_28b.rds"
file.lst <- "testData/nonmem/xgxr025.lst"
res <- NMscanData(file=file.lst,check.time=F,col.nmrep=T, quiet=T)
res <- fix.time(res)
## ref <- readRDS(fileRef)
expect_equal_to_reference(res,fileRef,version=2)
})
test_that("Input data as character",{
fileRef <- "testReference/NMscanData29.rds"
file.lst <- "testData/nonmem/xgxr026.lst"
expect_error(NMscanData(file=file.lst,check.time=F))
res <- NMscanData(file=file.lst,check.time=F,use.rds=F, quiet=T)
sapply(res,class)
res <- NMscanData(file=file.lst,check.time=F,use.rds=T,merge.by.row = F, quiet=T)
sapply(res,class)
## res <- fix.time(res)
## ## ref <- readRDS(fileRef)
## expect_equal_to_reference(res,fileRef,version=2)
})
test_that("Input control stream missing",{
NMdataConf(reset=TRUE)
NMdataConf(file.mod="doesNotExist.mod")
fileRef <- "testReference/NMscanData_30.rds"
file.lst <- "testData/nonmem/xgxr001.lst"
res <- NMscanData(file=file.lst,use.input=F, quiet=T)
## check file.mod wasn't used. Notice, merge.by.row is still "ifAvailable" - this was never needed because use.input=FALSE.
## NMinfo(res1a,"details")
fix.time(res)
expect_equal_to_reference(res,fileRef,version=2)
})
test_that("simulation model with subproblems",{
NMdataConf(reset=TRUE)
fileRef <- "testReference/NMscanData_31.rds"
### sim a model with subproblems
## library(devtools)
## load_all("~/wdirs/NMexec")
## file.mod <- "testData/nonmem/xgxr014.mod"
## ## NMexec(file.mod,sge=FALSE,wait=T)
## doses <- NMcreateDoses(TIME=0,AMT=data.table(AMT=c(10,100),DOSE=c(10,100)))
## simdat <- addEVID2(doses,time.sim=1:24,CMT=2)
## simdat[,DV:=NA][
## ,ROW:=.I]
## NMcheckData(simdat)
## NMdataConf(as.fun="data.table")
## sim1 <- NMsim(file.mod,data=simdat,
## suffix.sim="testsim1",dir.sim="testData/simulations"
## ,seed=343108,subproblems=100,nmquiet=T)
### NMsim saves serialized rds. Resaving as version 2
## res.sim <- readRDS("testData/simulations/NMsimData_xgxr014_testsim1.rds")
## saveRDS(res.sim,"testData/simulations/NMsimData_xgxr014_testsim1.rds",version=2)
##### sim done
res <- NMscanData("testData/simulations/xgxr014_testsim1.lst",check.time=F, quiet=T)
fix.time(res)
meta.x <- attr(res,"NMdata")
meta.x$details$time.ok <- NULL
setattr(res,"NMdata",meta.x)
expect_equal_to_reference(res,fileRef,version=2)
}
)
test_that("csv vs rds vs fst",{
fileRef <- "testReference/NMscanData_32.rds"
file.lst <- "testData/nonmem/xgxr014.lst"
res.csv <- NMscanData(file=file.lst, order.columns = F, merge.by.row=FALSE, check.time = FALSE,formats.read=cc(csv), quiet=T)
res.rds <- NMscanData(file=file.lst, order.columns = F, merge.by.row=FALSE, check.time = FALSE,formats.read=cc(rds,csv), quiet=T)
res.fst <- NMscanData(file=file.lst, order.columns = F, merge.by.row=FALSE, check.time = FALSE,formats.read=cc(fst,csv), quiet=T)
res <- dims(res.csv,res.rds,res.fst)
expect_equal_to_reference(res,fileRef,version=2)
})
test_that("inside lappy",{
### there are issues running NMdata functions in lapply - probably due to getArgs
lsts <- c( "testData/nonmem/xgxr014.lst", "testData/nonmem/xgxr032.lst")
res1 <- NMscanData(lsts[1],as.fun="data.table",check.time=FALSE,quiet=TRUE)
res2 <- NMscanData(lsts[2],as.fun="data.table",check.time=FALSE,quiet=TRUE)
res.all <- rbindlist(lapply(lsts,NMscanData,as.fun="data.table",check.time=FALSE,quiet=TRUE),fill=T )
dims1 <- dims(
rbind(res1,res2,fill=T)
,
res.all
)
expect_equal(dims1[,uniqueN(nrows)],1)
expect_equal(dims1[,uniqueN(ncols)],1)
})
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