Nothing
# $Rev: 115297 $
# $LastChangedDate: 2014-07-22 09:21:30 +0100 (Tue, 22 Jul 2014) $
# $LastChangedBy: jli@MANGO.LOCAL $
# Tests the show methods
# Author: fgochez
###############################################################################
# ** NOTE:**
# These tests only appear to work if executed from inside the Rgui using runRNMImportTests(...)
# they DO NOT work when run from ant test (thus Hudson), because the output dumped by the show methods
# there can have a different number of lines.
# TODO: Find some way around this.
# this is currently disabled
.test.show.NMRun <- function()
{
run1 <- importNm( "TestData1.ctl", path = file.path(unitTestPath, "testdata/TestRun" ))
# TODO: check the initial chunk of text!
# check the last 3 lines
test1 <- capture.output(show(run1))
expectedOut <- c("Number of problems: 1 ", "Problem statements:", "1 System Test 1 ")
checkEquals(tail(test1, 3), expectedOut)
}
.test.show.NMBasicModel <- function()
{
run1 <- importNm( "TestData1.ctl", path = file.path(unitTestPath, "testdata/TestRun" ))
prob1 <- getProblem(run1)
test1 <- capture.output(show(prob1))
expectedOut <-
c("Standard NONMEM problem:", "###############", "Problem statement: System Test 1 ",
"Data file: Data1 ", "Input table dimensions:", "1061 19 ", "Input table columns:",
"SID SEX AGE RACE HT SMOK HCTZ PROP CON AMT WT TIME SECR DV EVID SS II ID OCC ",
"PK: ", "[1] \"TVCL=THETA(1) \" \"TVV=THETA(2) \" \"TVKA=THETA(3) \" \"CL=TVCL*EXP(ETA(1) ) \" \"V =TVV *EXP(ETA(2) ) \" \"KA=TVKA*EXP(ETA(3) ) \"",
"[7] \"S2=V\" ", "", "Error:", "[1] \"IPRED = F\" \"IRES = DV - F\" \"W = F\" \"IF(W.EQ.0) W = 1\" \"IWRES = IRES/W\" ",
"[6] \"Y = IPRED + W*EPS(1) \"", "Parameter estimates:",
"###############", "THETAs:", "THETA1 THETA2 THETA3 ", " 19.60 84.60 1.66 ",
"OMEGAs:", " OMEGA1 OMEGA2 OMEGA3", "OMEGA1 0.164 0.000 0.0",
"OMEGA2 0.000 0.165 0.0", "OMEGA3 0.000 0.000 1.3",
"SIGMAs:", "[1] 0.0202", "Output table files: sdtab1,patab1,cotab1,catab1,mutab1,mytab1 ",
"Output table dimensions:", "1061 24 ", "Output table columns:",
"ID TIME IPRED IWRES DV PRED RES WRES CL V KA AGE HT WT SECR SEX RACE SMOK HCTZ PROP CON OCC SID absWRES "
)
checkEquals(test1, expectedOut, msg = " |show for NMBasicModel correct")
}
.test.show.NMSimModel <- function()
{
run1 <- importNm( "TestData1SIM.con", path = file.path(unitTestPath, "testdata/TestSimRun" ))
prob1 <- getProblem(run1)
test1 <- capture.output(show(prob1))
expected1 <- c("NONMEM data simulation problem:", "###############", "Problem statement: System Test 2 ",
"PK: ", "[1] \"TVCL=THETA(1) \" \"TVV=THETA(2) \" \"TVKA=THETA(3) \" \"CL=TVCL*EXP(ETA(1) ) \" \"V =TVV *EXP(ETA(2) ) \" \"KA=TVKA*EXP(ETA(3) ) \"",
"[7] \"S2=V\" ", "", "Data file: Data1 ", "Input table dimensions:",
"1061 19 ", "Input table columns:", "SID SEX AGE RACE HT SMOK HCTZ PROP CON AMT WT TIME SECR DV EVID SS II ID OCC ",
"Output table files: sdtab1,patab1,cotab1,catab1,mutab1,mytab1 ",
"Output table dimensions:", "5305 24 ", "Output table columns:",
"ID TIME IPRED IWRES DV PRED RES WRES CL V KA AGE HT WT SECR SEX RACE SMOK HCTZ PROP CON OCC SID absWRES ",
"Number of simulations performed: 5 ", "Seeds: 20050213 ",
"Final estimates for each subproblem:", "", "THETAs:", " THETA1 THETA2 THETA3",
"sim1 17.2 117.0 1.24", "sim2 18.3 108.0 1.40", "sim3 18.0 108.0 1.24",
"sim4 19.0 98.9 1.55", "sim5 17.1 109.0 1.38", "OMEGAs:",
", , sim1", "", " OMEGA1 OMEGA2 OMEGA3", "OMEGA1 0.174 0.00 0.00",
"OMEGA2 0.000 0.19 0.00", "OMEGA3 0.000 0.00 1.45",
"", ", , sim2", "", " OMEGA1 OMEGA2 OMEGA3", "OMEGA1 0.167 0.000 0.00",
"OMEGA2 0.000 0.143 0.00", "OMEGA3 0.000 0.000 1.24",
"", ", , sim3", "", " OMEGA1 OMEGA2 OMEGA3", "OMEGA1 0.181 0.000 0.00",
"OMEGA2 0.000 0.142 0.00", "OMEGA3 0.000 0.000 1.57",
"", ", , sim4", "", " OMEGA1 OMEGA2 OMEGA3", "OMEGA1 0.245 0.000 0.000",
"OMEGA2 0.000 0.189 0.000", "OMEGA3 0.000 0.000 0.945",
"", ", , sim5", "", " OMEGA1 OMEGA2 OMEGA3", "OMEGA1 0.174 0.000 0.00",
"OMEGA2 0.000 0.197 0.00", "OMEGA3 0.000 0.000 1.47",
"", "SIGMAs:", ", , sim1", "", " SIGMA1", "SIGMA1 0.0241",
"", ", , sim2", "", " SIGMA1", "SIGMA1 0.026", "", ", , sim3",
"", " SIGMA1", "SIGMA1 0.0262", "", ", , sim4", "", " SIGMA1",
"SIGMA1 0.0295", "", ", , sim5", "", " SIGMA1", "SIGMA1 0.0244",
"", "Objective function(s): ", " sim1 sim2 sim3 sim4 sim5 ",
"3696.247 3575.252 3660.355 3606.526 3701.472 ")
checkEquals(test1, expected1, msg = " | show for sim model correct\n")
}
.test.show.NMBasicNM7 <- function()
{
run1 <- importNm( "TestData1.ctl", path = file.path(unitTestPath, "testdata/TestDataNM7" ))
prob1 <- getProblem(run1)
test1 <- capture.output(show(prob1))
expected1 <- c("Standard NONMEM (7) problem:", "###############", "Problem statement: NM7 test 1 ",
"Data file: Data1 ", "Input table dimensions:", "1061 19 ", "Input table columns:",
"SID SEX AGE RACE HT SMOK HCTZ PROP CON AMT WT TIME SECR DV EVID SS II ID OCC ",
"PK: ", "[1] \"TVCL=THETA(1) \" \"TVV=THETA(2) \" \"TVKA=THETA(3) \" \"CL=TVCL*EXP(ETA(1) ) \" \"V =TVV *EXP(ETA(2) ) \" \"KA=TVKA*EXP(ETA(3) ) \"",
"[7] \"S2=V\" ", "", "Error:", "[1] \"IPRED = F\" \"IRES = DV - F\" \"W = F\" \"IF(W.EQ.0) W = 1\" \"IWRES = IRES/W\" ",
"[6] \"Y = IPRED + W*EPS(1) \"", "Methods used: ", "[1] \"Iterative Two Stage\" \"Stochastic Approximation Expectation-Maximization\"",
"Parameter estimates:", "###############", "THETAs:", "[[1]]",
" TH1 TH2 TH3 ", "20.00 77.30 1.27 ", "", "[[2]]", " TH1 TH2 TH3 ",
"19.10 76.70 1.68 ", "", "OMEGAs:", "[[1]]", " ETA1 ETA2 ETA3",
"ETA1 0.157 0.000 0.000", "ETA2 0.000 0.162 0.000", "ETA3 0.000 0.000 0.737",
"", "[[2]]", " ETA1 ETA2 ETA3", "ETA1 0.145 0.000 0.00",
"ETA2 0.000 0.149 0.00", "ETA3 0.000 0.000 1.42", "", "SIGMAs:",
"[[1]]", " EPS1", "EPS1 0.0259", "", "[[2]]", " EPS1",
"EPS1 0.0266", "", "Output table files: tab1 ", "Output table dimensions:",
"1061 11 ", "Output table columns:", "ID TIME IPRED IWRES WT ETA1 DV PRED RES WRES absWRES "
)
checkEquals(test1, expected1, msg = " | show for NMBasic NM7 correct")
}
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