tests/testthat/test_NMcreateDoses.R

In NMsim: Seamless 'Nonmem' Simulation Platform

library(data.table)
data.table::setDTthreads(1)
library(NMdata)

NMdataConf(reset=TRUE)

context("NMcreateDoses")

test_that("Basic",{
    fileRef <- "testReference/NMcreateDoses_01.rds"

    ## simple - ok
    res <- NMcreateDoses(TIME=0,AMT=10)
    expect_equal_to_reference(res,fileRef)

})


test_that("custom CMT value",{
    res1 <- NMcreateDoses(TIME=0,AMT=10)
    res2 <- NMcreateDoses(TIME=0,AMT=10,CMT=2)

    res1$CMT <- 2
    expect_equal(res1,res2)
})

test_that("Expand columns",{
    fileRef <- "testReference/NMcreateDoses_02.rds"
    res <- NMcreateDoses(TIME=c(0,12),AMT=10,CMT=2)

    expect_equal_to_reference(res,fileRef)

})

test_that("makes no sense to expand TIME",{
    expect_error(
        NMcreateDoses(TIME=c(0),AMT=c(0,10),CMT=2)
    )
})


test_that("non-unique AMT",{
    ## this is due to a bug that once was where AMT would get shortened because it's non-unique
    fileRef <- "testReference/NMcreateDoses_03.rds"
    res <- NMcreateDoses(TIME=c(0,1,4,5),AMT=c(2,1,4,2),CMT=c(1,1,2))
    expect_equal_to_reference(res,fileRef)
})

## II/ADDL simple example missing


## II/ADDL should only be applied to last event. addl.lastonly
## argument?
test_that("II/ADDL",{
    fileRef <- "testReference/NMcreateDoses_04.rds"
    res <- NMcreateDoses(TIME=c(0,12),AMT=10,addl=list(II=12,ADDL=3),CMT=2)

    expect_equal_to_reference(res,fileRef)

})


## II/ADDL should only be applied to last event. addl.lastonly
## argument?
test_that("ADDL and II one by one",{
    fileRef <- "testReference/NMcreateDoses_04b.rds"
    res1 <- NMcreateDoses(TIME=c(0,12),AMT=10,II=12,ADDL=3,CMT=2)
    res2 <- NMcreateDoses(TIME=c(0,12),AMT=10,addl=list(II=12,ADDL=3),CMT=2)

    res <- list(
        res1
       ,
        res2
    )
    expect_equal_to_reference(res,fileRef)

    ## this should be an error
    expect_error( NMcreateDoses(TIME=c(0,12),AMT=10,II=12,ADDL=2,addl=list(II=12,ADDL=3),CMT=2))

})


test_that("II and ADDL must be of equal length",{
    fileRef <- "testReference/NMcreateDoses_04c.rds"
    ## one longer than the other
    expect_error(NMcreateDoses(TIME=c(0,12),AMT=10,II=c(0,12),ADDL=3,CMT=2))
    expect_error(NMcreateDoses(TIME=c(0,12),AMT=10,addl=list(II=c(0,12),ADDL=3),CMT=2))
    ##  leaving out II
    expect_error(
        NMcreateDoses(TIME=c(0,12),AMT=10,ADDL=3,CMT=2)
    )

})

## II/ADDL should only be applied to last event. addl.lastonly
## argument?
test_that("II and ADDL of length=1",{
    fileRef <- "testReference/NMcreateDoses_04d.rds"
    ##NMcreateDoses(TIME=c(0,12),AMT=data.table(dos=1:2,AMT=c(10,20)),CMT=2)
    res <- NMcreateDoses(TIME=c(0,12),AMT=data.table(dos=1:2,AMT=c(10,20)),II=12,ADDL=3,CMT=2)

    res
    expect_equal_to_reference(res,fileRef)

    readRDS(fileRef)
})

test_that("NA columns",{

    ## options(warn=2)
    fileRef <- "testReference/NMcreateDoses_04e.rds"
    res <- NMcreateDoses(TIME=c(0,12),AMT=data.table(dos=1:2,AMT=c(10,20)),CMT=NA)

    expect_equal_to_reference(res,fileRef)

})




### covariates
test_that("covariates basics",{
    fileRef <- "testReference/NMcreateDoses_05.rds"

    res <- NMcreateDoses(TIME=c(0),AMT=data.table(DOSE=c(10,50),AMT=c(10,50)))
    expect_equal_to_reference(res,fileRef)
})


test_that("covariates basics 2",{
    fileRef <- "testReference/NMcreateDoses_06.rds"
    res <- NMcreateDoses(TIME=data.table(regimen=c("SD","MD","MD"),TIME=c(0,0,12)),AMT=10,CMT=1)

    expect_equal_to_reference(res,fileRef)
})


### TODO: covariates not spanning same covariate values. Should not be supported for now.
test_that("covariates not spanning same covariate values",{
    fileRef <- "testReference/NMcreateDoses_07.rds"

    res <- NMcreateDoses(TIME=data.table(regimen=c("SD","MD","MD"),TIME=c(0,0,12)),AMT=10,CMT=1,addl=list(II=12,ADDL=3,regimen="MD"))
    ##res
    expect_equal_to_reference(res,fileRef)
    if(F){
        res
        readRDS(fileRef)
    }
})



test_that("covariates spanning same covariate values",{
    ## This looks OK.
    fileRef <- "testReference/NMcreateDoses_08.rds"

    res <- NMcreateDoses(TIME=data.table(regimen=c("SD","MD","MD"),TIME=c(0,0,12)),AMT=data.table(AMT=c(10,5),regimen=c("SD","MD")),CMT=1)
    expect_equal_to_reference(res,fileRef)
})


test_that("covariates spanning same covariate values - addl",{
    ## This looks OK.
    fileRef <- "testReference/NMcreateDoses_09.rds"

    res <- NMcreateDoses(TIME=data.table(regimen=c("SD","MD","MD","MD"),TIME=c(0,0,12,24)),AMT=10,CMT=1,addl=data.table(II=c(0,0,0,12),ADDL=c(0,0,0,3),regimen=c("SD",rep("MD",3))))

    expect_equal_to_reference(res,fileRef)
    if(F){
        res
        readRDS(fileRef)
    }
})



test_that("ID as covariate - not supported",{
    expect_error(
        NMcreateDoses(TIME=c(0),AMT=data.table(ID=c(10,50),AMT=c(10,50)))
    )
})


## not sure what extra this example is showing
## NMcreateDoses(TIME=data.table(ID=c(1,1,2,2,2),TIME=c(0,1,0,1,4)),AMT=data.table(ID=c(1,1,2,2),AMT=c(2,1,4,2)))



test_that("Expanding AMT within a covariate",{
    fileRef <- "testReference/NMcreateDoses_10.rds"

    res <- NMcreateDoses(TIME=c(0,1,4),AMT=data.table(DOSELEVEL=c(1,1,2,2),AMT=c(2,1,4,2)))
    expect_equal_to_reference(res,fileRef)
})




test_that("as.fun",{
    fileRef <- "testReference/NMcreateDoses_11.rds"
    res <- NMcreateDoses(TIME=0,AMT=10)
    expect_equal_to_reference(res,fileRef)

    fileRef <- "testReference/NMcreateDoses_12.rds"
    res <- NMcreateDoses(TIME=0,AMT=10,as.fun=as.data.frame)
    expect_equal_to_reference(res,fileRef)
})





test_that("data.frames accepted",{
    res.df <- NMcreateDoses(TIME=c(0),AMT=data.frame(DOSE=c(10,50),AMT=c(10,50)))
    res.dt <- NMcreateDoses(TIME=c(0),AMT=data.table(DOSE=c(10,50),AMT=c(10,50)))
    expect_equal(res.df,res.dt)
})


test_that("col.id",{
    fileRef <- "testReference/NMcreateDoses_13.rds"
    res <- NMcreateDoses(TIME=0,AMT=10,col.id="NOOOO")
    expect_equal_to_reference(res,fileRef)

    fileRef <- "testReference/NMcreateDoses_14.rds"
    res <- NMcreateDoses(TIME=0,AMT=10,col.id=NA)
    expect_equal_to_reference(res,fileRef)
})

test_that("covs in multiple arguments",{
    fileRef <- "testReference/NMcreateDoses_15.rds"

    dt.amt <- data.table(DOSE1=c(100))[,AMT:=DOSE1*1000]
    dt.time <- data.table(TIME=c(0,288,0,432),trtp=rep(c("Treatment 1","Treatment 2"),each=2))
    ## dt.amt
    ## dt.time
    res <- NMcreateDoses(TIME=dt.time,AMT=dt.amt)
    
    expect_equal_to_reference(res,fileRef)

    if(F){
        res
        readRDS(fileRef)
    }
})

test_that("No AMT",{
    fileRef <- "testReference/NMcreateDoses_16.rds"

    res <- NMcreateDoses(TIME=0)
    expect_equal_to_reference(res,fileRef)

    if(F){
        res
        readRDS(fileRef)
    }
})

test_that("Suppress EVID",{
    fileRef <- "testReference/NMcreateDoses_17.rds"

    res1 <- NMcreateDoses(TIME=0,EVID=NULL)
    res2 <- NMcreateDoses(TIME=0,EVID=NA)
    expect_equal(res1,res2)

})