unittests/runit.importModelData.R
In MarioGS/NMImport: Tools for importing and manipulating NONMEM data.
# SVN revision: $Rev: 115297 $
# Date of last change: $LastChangedDate: 2014-07-22 09:21:30 +0100 (Tue, 22 Jul 2014) $
# Last changed by: $LastChangedBy: jli@MANGO.LOCAL $
#
# Original author: fgochez
# Copyright Mango Solutions, Chippenham, UK
###############################################################################
# test the importModelData function
test.importModelData <- function()
{
.importNmModData <- RNMImport:::.importNmModData
importModelData <- RNMImport:::importModelData
# first test: checks that multiple IGNORE= are handled correctly
unitTestPath <- get("TestPath", envir = .RNMImportTestEnv)
testDir <- file.path(unitTestPath, "testdata")
# x <- readNmData(file.path(testDir, "data3"))
dataStatement <- RNMImport:::.importNmModData("$DATA data3.dat IGNORE=I IGNORE=(TIME.EQ.1)")
inputStatement <- RNMImport:::.importNmModInput("$INPUT AMT TIME DV")
testInput1 <- as.matrix(RNMImport:::importModelData(dataStatement, inputStatement, path = testDir))
rownames(testInput1) <- NULL
# checkEquals(testInput$TIME, 0, .27)
checkEquals(testInput1, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE=c and IGNORE=list work correctly at the same time")
# second test:
dataStatement2 <- RNMImport:::.importNmModData("$DATA data4.dat")
inputStatement2 <- RNMImport:::.importNmModInput("$INPUT AMT TIME DV")
testInput2 <- as.matrix(RNMImport:::importModelData(dataStatement2, inputStatement2, path = testDir))
rownames(testInput2) <- NULL
checkEquals( testInput2, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE=# by default!" )
# third tests: IGNORE=list used alone
dataStatement3 <- RNMImport:::.importNmModData("$DATA data3 IGNORE=(TIME.LT.1)")
inputStatement3 <- RNMImport:::.importNmModInput("$INPUT AMT TIME DV")
testInput3 <- as.matrix( RNMImport:::importModelData(dataStatement3, inputStatement3, path = testDir) )
rownames(testInput3) <- NULL
checkEquals( testInput3,
cbind(AMT = rep(NA, 8),
TIME = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
DV = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9)),
msg = " |IGNORE=code alone works as expected" )
# test IGNORE = 'C'
dataStatement4 <- RNMImport:::.importNmModData("$DATA data3.dat IGNORE='I'")
testInput4 <- as.matrix( RNMImport:::importModelData(dataStatement4, inputStatement, path = testDir) )
rownames(testInput4) <- NULL
checkEquals( testInput4, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE='I' same as IGNORE=I " )
dataStatement5 <- RNMImport:::.importNmModData("$DATA data3.dat IGNORE=\"I\"")
testInput5 <- as.matrix( RNMImport:::importModelData(dataStatement5, inputStatement, path = testDir) )
rownames(testInput5) <- NULL
checkEquals( testInput5, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE=\"I\" same as IGNORE=I " )
# check that LABEL=X is allowed
dataStatement6 <- .importNmModData("$DATA data3.dat IGNORE=I IGNORE=(TIME=1)")
testInput6 <- as.matrix(importModelData(dataStatement6, inputStatement, path = testDir))
rownames(testInput6) <- NULL
checkEquals(testInput6, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE=(LABEL=X) works")
dataStatement7 <- .importNmModData("$DATA data3.dat IGNORE=I IGNORE=(TIME.EQ.1,DV.LT.2.01)")
testInput7 <- as.matrix(importModelData(dataStatement7, inputStatement, path = testDir))
rownames(testInput7) <- NULL
checkEquals(testInput7, cbind(AMT = c(320, NA,NA,NA,NA,NA,NA),
TIME = c(0,0.52,1.92,3.5,5.02,9,12),
DV = c(NA, 7.91,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE=(LABEL1.OP.X,LABEL2.OP.Y) works")
# check that mixed IGNORE/IGN statements are allowed
# related to issue
dataStatement8 <- .importNmModData("$DATA data3.dat IGN=I IGNORE=(TIME=1)")
testInput8 <- as.matrix(importModelData(dataStatement8, inputStatement, path = testDir))
rownames(testInput8) <- NULL
checkEquals(testInput8, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE=(LABEL=X) works")
}
# test aliasing of columns
# function (dataStatement, inputStatement, dropCols = TRUE, trim = FALSE,
# path = NULL, duplicateAliased = TRUE)
test.importModelDataAliasDrop <- function()
{
.importNmModData <- RNMImport:::.importNmModData
importModelData <- RNMImport:::importModelData
.importNmModInput <- RNMImport:::.importNmModInput
# first test: checks that multiple IGNORE= are handled correctly
unitTestPath <- get("TestPath", envir = .RNMImportTestEnv)
testDir <- file.path(unitTestPath, "testdata")
# x <- readNmData(file.path(testDir, "data3"))
dataStatement1 <- .importNmModData("$DATA data4.dat IGNORE=#")
inputStatement <- .importNmModInput("$INPUT AMT TIME=TIM DV=FOO")
testInput1 <- as.matrix(importModelData( dataStatement1, inputStatement, path = testDir ))
rownames(testInput1) <- NULL
checkEquals(testInput1, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01),
TIM = c(0,.27,0.52,1,1.92,3.5,5.02,9,12), FOO = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01) ) ,
" | aliasing works as expected")
inputStatement2 <- .importNmModInput( "$INPUT AMT=DROP TIME=TIM DV=FOO")
testInput2 <- as.matrix( importModelData( dataStatement1, inputStatement2, path = testDir, dropCols = TRUE ) )
rownames(testInput2) <- NULL
checkEquals(testInput2, cbind( TIME = c(0,.27,0.52,1,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01),
TIM = c(0,.27,0.52,1,1.92,3.5,5.02,9,12), FOO = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01) ),
msg = " |drop = TRUE works as expected")
## now check that IGNORE= can be applied with aliased columns
dataStatement3 <- .importNmModData("$DATA data3 IGNORE=(TIME.LT.1)")
dataStatement4 <- .importNmModData("$DATA data3 IGNORE=(TIM.LT.1)")
testInput3 <- as.matrix( importModelData(dataStatement3, inputStatement, path = testDir) )
rownames(testInput3) <- NULL
checkEquals( testInput3,
cbind(AMT = rep(NA, 8),
TIME = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
DV = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9),
TIM = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
FOO = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9)),
msg = " | IGNORE = works with one name for TIME" )
testInput4 <- as.matrix( importModelData( dataStatement4, inputStatement, path = testDir ) )
rownames(testInput4) <- NULL
checkEquals( testInput4, testInput3, msg = " |IGNORE = works for other alias of TIME" )
# another test: aliasing with extra columns
inputStatement2 <- .importNmModInput("$INPUT MDV AMT EVID=DROP TIME CONC=DV")
dataStatement5 <- .importNmModData("$DATA data5.csv IGNORE=(CONC=2,AMT.GT.10)")
testInput5 <- as.matrix( importModelData( dataStatement5, inputStatement2, path = testDir ) )
checkEquals( testInput5, structure(c(1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 10L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 0L, 9L, 8L, 7L,
6L, 5L, 4L, 3L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 10L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 2L, 3L,
4L, 5L, 6L, 7L, 8L, 0L, 9L, 8L, 7L, 6L, 5L, 4L, 3L, 0L, 9L, 8L,
7L, 6L, 5L, 4L, 3L), .Dim = c(8L, 10L), .Dimnames = list(c("1",
"2", "3", "4", "5", "6", "7", "8"), c("MDV", "AMT", "TIME", "CONC",
"ExtraCol1", "ExtraCol2", "ExtraCol3", "ExtraCol4", "ExtraCol5",
"DV"))), msg = " |dropping columns with extra columns in data set works correctly" )
}
# tests model importing with ACCEPT=(list) statement
test.importModelData.accept <- function()
{
unitTestPath <- get("TestPath", envir = .RNMImportTestEnv)
testDir <- file.path(unitTestPath, "testdata")
.importNmModData <- RNMImport:::.importNmModData
importModelData <- RNMImport:::importModelData
.importNmModInput <- RNMImport:::.importNmModInput
dataStatement1 <- .importNmModData("$DATA data3 ACCEPT=(TIME.GE.1)")
inputStatement <- .importNmModInput("$INPUT AMT TIME=TIM DV=FOO")
testInput1 <- as.matrix( importModelData(dataStatement1, inputStatement, path = testDir) )
rownames(testInput1) <- NULL
checkEquals( testInput1,
cbind(AMT = rep(NA, 8),
TIME = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
DV = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9),
TIM = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
FOO = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9)),
msg = " | ACCEPT = works with one name for TIME" )
# now check aliased version
dataStatement2 <- .importNmModData("$DATA data3 ACCEPT=(TIM.GE.1)")
testInput2 <- as.matrix( importModelData(dataStatement1, inputStatement, path = testDir) )
rownames(testInput2) <- NULL
checkEquals( testInput2,
cbind(AMT = rep(NA, 8),
TIME = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
DV = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9),
TIM = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
FOO = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9)),
msg = " | ACCEPT = works with another name for TIME" )
}
# tests model importing with RECORDS=n statement
test.importModelData.records <- function()
{
.importNmModData <- RNMImport:::.importNmModData
importModelData <- RNMImport:::importModelData
.importNmModInput <- RNMImport:::.importNmModInput
# first test: checks that RECORDS=n is handled correctly
unitTestPath <- get("TestPath", envir = .RNMImportTestEnv)
testDir <- file.path(unitTestPath, "testdata")
dataStatement1 <- .importNmModData("$DATA data4.dat RECORDS=5")
inputStatement <- .importNmModInput("$INPUT AMT TIME=TIM DV=FOO")
testInput1 <- as.matrix(importModelData( dataStatement1, inputStatement, path = testDir ))
rownames(testInput1) <- NULL
checkEquals(testInput1, cbind(AMT = c(320,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1,1.92), DV = c(NA,1.71,7.91,8.31,8.33),
TIM = c(0,.27,0.52,1,1.92), FOO = c(NA,1.71,7.91,8.31,8.33) ) ,
" | Only first 5 records used")
# second test: checks RECORD=label
inputStatement2 <- .importNmModInput("$INPUT MDV AMT ID TIME CONC=DV")
dataStatement2 <- .importNmModData("$DATA data5.csv RECORDS=ID")
testInput2 <- as.matrix(importModelData( dataStatement2, inputStatement2, path = testDir ))
rownames(testInput2) <- NULL
# test that only the first two rows were imported
expectedData2 <- rbind( c(1,10,1,1,0), c(0,0,1,2,9) )
colnames(expectedData2) <- c("MDV", "AMT", "ID", "TIME", "CONC")
checkEquals( testInput2[,1:5], expectedData2, msg = " |only first two rows imported" )
}
MarioGS/NMImport documentation built on May 7, 2019, 2:52 p.m.
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# SVN revision: $Rev: 115297 $
# Date of last change: $LastChangedDate: 2014-07-22 09:21:30 +0100 (Tue, 22 Jul 2014) $
# Last changed by: $LastChangedBy: jli@MANGO.LOCAL $
#
# Original author: fgochez
# Copyright Mango Solutions, Chippenham, UK
###############################################################################
# test the importModelData function
test.importModelData <- function()
{
.importNmModData <- RNMImport:::.importNmModData
importModelData <- RNMImport:::importModelData
# first test: checks that multiple IGNORE= are handled correctly
unitTestPath <- get("TestPath", envir = .RNMImportTestEnv)
testDir <- file.path(unitTestPath, "testdata")
# x <- readNmData(file.path(testDir, "data3"))
dataStatement <- RNMImport:::.importNmModData("$DATA data3.dat IGNORE=I IGNORE=(TIME.EQ.1)")
inputStatement <- RNMImport:::.importNmModInput("$INPUT AMT TIME DV")
testInput1 <- as.matrix(RNMImport:::importModelData(dataStatement, inputStatement, path = testDir))
rownames(testInput1) <- NULL
# checkEquals(testInput$TIME, 0, .27)
checkEquals(testInput1, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE=c and IGNORE=list work correctly at the same time")
# second test:
dataStatement2 <- RNMImport:::.importNmModData("$DATA data4.dat")
inputStatement2 <- RNMImport:::.importNmModInput("$INPUT AMT TIME DV")
testInput2 <- as.matrix(RNMImport:::importModelData(dataStatement2, inputStatement2, path = testDir))
rownames(testInput2) <- NULL
checkEquals( testInput2, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE=# by default!" )
# third tests: IGNORE=list used alone
dataStatement3 <- RNMImport:::.importNmModData("$DATA data3 IGNORE=(TIME.LT.1)")
inputStatement3 <- RNMImport:::.importNmModInput("$INPUT AMT TIME DV")
testInput3 <- as.matrix( RNMImport:::importModelData(dataStatement3, inputStatement3, path = testDir) )
rownames(testInput3) <- NULL
checkEquals( testInput3,
cbind(AMT = rep(NA, 8),
TIME = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
DV = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9)),
msg = " |IGNORE=code alone works as expected" )
# test IGNORE = 'C'
dataStatement4 <- RNMImport:::.importNmModData("$DATA data3.dat IGNORE='I'")
testInput4 <- as.matrix( RNMImport:::importModelData(dataStatement4, inputStatement, path = testDir) )
rownames(testInput4) <- NULL
checkEquals( testInput4, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE='I' same as IGNORE=I " )
dataStatement5 <- RNMImport:::.importNmModData("$DATA data3.dat IGNORE=\"I\"")
testInput5 <- as.matrix( RNMImport:::importModelData(dataStatement5, inputStatement, path = testDir) )
rownames(testInput5) <- NULL
checkEquals( testInput5, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE=\"I\" same as IGNORE=I " )
# check that LABEL=X is allowed
dataStatement6 <- .importNmModData("$DATA data3.dat IGNORE=I IGNORE=(TIME=1)")
testInput6 <- as.matrix(importModelData(dataStatement6, inputStatement, path = testDir))
rownames(testInput6) <- NULL
checkEquals(testInput6, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE=(LABEL=X) works")
dataStatement7 <- .importNmModData("$DATA data3.dat IGNORE=I IGNORE=(TIME.EQ.1,DV.LT.2.01)")
testInput7 <- as.matrix(importModelData(dataStatement7, inputStatement, path = testDir))
rownames(testInput7) <- NULL
checkEquals(testInput7, cbind(AMT = c(320, NA,NA,NA,NA,NA,NA),
TIME = c(0,0.52,1.92,3.5,5.02,9,12),
DV = c(NA, 7.91,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE=(LABEL1.OP.X,LABEL2.OP.Y) works")
# check that mixed IGNORE/IGN statements are allowed
# related to issue
dataStatement8 <- .importNmModData("$DATA data3.dat IGN=I IGNORE=(TIME=1)")
testInput8 <- as.matrix(importModelData(dataStatement8, inputStatement, path = testDir))
rownames(testInput8) <- NULL
checkEquals(testInput8, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.33,6.85,6.08,4.55,3.01)), msg = " |IGNORE=(LABEL=X) works")
}
# test aliasing of columns
# function (dataStatement, inputStatement, dropCols = TRUE, trim = FALSE,
# path = NULL, duplicateAliased = TRUE)
test.importModelDataAliasDrop <- function()
{
.importNmModData <- RNMImport:::.importNmModData
importModelData <- RNMImport:::importModelData
.importNmModInput <- RNMImport:::.importNmModInput
# first test: checks that multiple IGNORE= are handled correctly
unitTestPath <- get("TestPath", envir = .RNMImportTestEnv)
testDir <- file.path(unitTestPath, "testdata")
# x <- readNmData(file.path(testDir, "data3"))
dataStatement1 <- .importNmModData("$DATA data4.dat IGNORE=#")
inputStatement <- .importNmModInput("$INPUT AMT TIME=TIM DV=FOO")
testInput1 <- as.matrix(importModelData( dataStatement1, inputStatement, path = testDir ))
rownames(testInput1) <- NULL
checkEquals(testInput1, cbind(AMT = c(320,NA,NA,NA,NA,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01),
TIM = c(0,.27,0.52,1,1.92,3.5,5.02,9,12), FOO = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01) ) ,
" | aliasing works as expected")
inputStatement2 <- .importNmModInput( "$INPUT AMT=DROP TIME=TIM DV=FOO")
testInput2 <- as.matrix( importModelData( dataStatement1, inputStatement2, path = testDir, dropCols = TRUE ) )
rownames(testInput2) <- NULL
checkEquals(testInput2, cbind( TIME = c(0,.27,0.52,1,1.92,3.5,5.02,9,12),
DV = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01),
TIM = c(0,.27,0.52,1,1.92,3.5,5.02,9,12), FOO = c(NA,1.71,7.91,8.31,8.33,6.85,6.08,4.55,3.01) ),
msg = " |drop = TRUE works as expected")
## now check that IGNORE= can be applied with aliased columns
dataStatement3 <- .importNmModData("$DATA data3 IGNORE=(TIME.LT.1)")
dataStatement4 <- .importNmModData("$DATA data3 IGNORE=(TIM.LT.1)")
testInput3 <- as.matrix( importModelData(dataStatement3, inputStatement, path = testDir) )
rownames(testInput3) <- NULL
checkEquals( testInput3,
cbind(AMT = rep(NA, 8),
TIME = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
DV = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9),
TIM = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
FOO = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9)),
msg = " | IGNORE = works with one name for TIME" )
testInput4 <- as.matrix( importModelData( dataStatement4, inputStatement, path = testDir ) )
rownames(testInput4) <- NULL
checkEquals( testInput4, testInput3, msg = " |IGNORE = works for other alias of TIME" )
# another test: aliasing with extra columns
inputStatement2 <- .importNmModInput("$INPUT MDV AMT EVID=DROP TIME CONC=DV")
dataStatement5 <- .importNmModData("$DATA data5.csv IGNORE=(CONC=2,AMT.GT.10)")
testInput5 <- as.matrix( importModelData( dataStatement5, inputStatement2, path = testDir ) )
checkEquals( testInput5, structure(c(1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 10L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 0L, 9L, 8L, 7L,
6L, 5L, 4L, 3L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 10L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 1L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 2L, 3L,
4L, 5L, 6L, 7L, 8L, 0L, 9L, 8L, 7L, 6L, 5L, 4L, 3L, 0L, 9L, 8L,
7L, 6L, 5L, 4L, 3L), .Dim = c(8L, 10L), .Dimnames = list(c("1",
"2", "3", "4", "5", "6", "7", "8"), c("MDV", "AMT", "TIME", "CONC",
"ExtraCol1", "ExtraCol2", "ExtraCol3", "ExtraCol4", "ExtraCol5",
"DV"))), msg = " |dropping columns with extra columns in data set works correctly" )
}
# tests model importing with ACCEPT=(list) statement
test.importModelData.accept <- function()
{
unitTestPath <- get("TestPath", envir = .RNMImportTestEnv)
testDir <- file.path(unitTestPath, "testdata")
.importNmModData <- RNMImport:::.importNmModData
importModelData <- RNMImport:::importModelData
.importNmModInput <- RNMImport:::.importNmModInput
dataStatement1 <- .importNmModData("$DATA data3 ACCEPT=(TIME.GE.1)")
inputStatement <- .importNmModInput("$INPUT AMT TIME=TIM DV=FOO")
testInput1 <- as.matrix( importModelData(dataStatement1, inputStatement, path = testDir) )
rownames(testInput1) <- NULL
checkEquals( testInput1,
cbind(AMT = rep(NA, 8),
TIME = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
DV = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9),
TIM = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
FOO = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9)),
msg = " | ACCEPT = works with one name for TIME" )
# now check aliased version
dataStatement2 <- .importNmModData("$DATA data3 ACCEPT=(TIM.GE.1)")
testInput2 <- as.matrix( importModelData(dataStatement1, inputStatement, path = testDir) )
rownames(testInput2) <- NULL
checkEquals( testInput2,
cbind(AMT = rep(NA, 8),
TIME = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
DV = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9),
TIM = c(1,1.92,3.5,5.02,7.03,9,12,24.3),
FOO = c(8.31,8.33,6.85,6.08,5.40,4.55,3.01,0.9)),
msg = " | ACCEPT = works with another name for TIME" )
}
# tests model importing with RECORDS=n statement
test.importModelData.records <- function()
{
.importNmModData <- RNMImport:::.importNmModData
importModelData <- RNMImport:::importModelData
.importNmModInput <- RNMImport:::.importNmModInput
# first test: checks that RECORDS=n is handled correctly
unitTestPath <- get("TestPath", envir = .RNMImportTestEnv)
testDir <- file.path(unitTestPath, "testdata")
dataStatement1 <- .importNmModData("$DATA data4.dat RECORDS=5")
inputStatement <- .importNmModInput("$INPUT AMT TIME=TIM DV=FOO")
testInput1 <- as.matrix(importModelData( dataStatement1, inputStatement, path = testDir ))
rownames(testInput1) <- NULL
checkEquals(testInput1, cbind(AMT = c(320,NA,NA,NA,NA),
TIME = c(0,.27,0.52,1,1.92), DV = c(NA,1.71,7.91,8.31,8.33),
TIM = c(0,.27,0.52,1,1.92), FOO = c(NA,1.71,7.91,8.31,8.33) ) ,
" | Only first 5 records used")
# second test: checks RECORD=label
inputStatement2 <- .importNmModInput("$INPUT MDV AMT ID TIME CONC=DV")
dataStatement2 <- .importNmModData("$DATA data5.csv RECORDS=ID")
testInput2 <- as.matrix(importModelData( dataStatement2, inputStatement2, path = testDir ))
rownames(testInput2) <- NULL
# test that only the first two rows were imported
expectedData2 <- rbind( c(1,10,1,1,0), c(0,0,1,2,9) )
colnames(expectedData2) <- c("MDV", "AMT", "ID", "TIME", "CONC")
checkEquals( testInput2[,1:5], expectedData2, msg = " |only first two rows imported" )
}
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