inst/unittests/runit.importMethodBlock.R
In MangoTheCat/RNMImport: Tools for importing and manipulating NONMEM data.
# $LastChangedDate: 2010-01-12 15:55:59 +0000 (Tue, 12 Jan 2010) $
# $LastChangedBy: fgochez $
# $Rev: 14609 $
#
# Author: fgochez
###############################################################################
# tests the low-level function .importMethodBlock (in importNmLstNM7)
test.importMethodBlock <- function()
{
# sample method block
testBlock <- c(" #METH: Iterative Two Stage", " EM/BAYES SETUP", " THETAS THAT ARE MU MODELED:",
" 1 2 3 4", " THETAS THAT ARE SIGMA-LIKE:", " ", " ",
" MONITORING OF SEARCH:", "", " iteration 0 OBJ= -439.445868533902 ",
" iteration 5 OBJ= -1119.48137768895 ", " iteration 10 OBJ= -1120.19191233229 ",
" iteration 15 OBJ= -1120.26385480453 ", " iteration 20 OBJ= -1120.28483467697 ",
" iteration 25 OBJ= -1120.29421562205 ", " iteration 30 OBJ= -1120.29934078386 ",
" iteration 35 OBJ= -1120.30236183088 ", " iteration 40 OBJ= -1120.30417175997 ",
" iteration 45 OBJ= -1120.30528535008 ", " iteration 50 OBJ= -1120.30595982428 ",
" iteration 55 OBJ= -1120.30637009744 ", " iteration 60 OBJ= -1120.30662747964 ",
" iteration 65 OBJ= -1120.30677846680 ", " iteration 70 OBJ= -1120.30687589562 ",
" iteration 75 OBJ= -1120.30693225876 ", " iteration 80 OBJ= -1120.30696556872 ",
" iteration 85 OBJ= -1120.30699553335 ", " iteration 90 OBJ= -1120.30701400145 ",
" iteration 95 OBJ= -1120.30702142508 ", " iteration 100 OBJ= -1120.30702424494 ",
" iteration 105 OBJ= -1120.30702412937 ", " iteration 110 OBJ= -1120.30702950237 ",
" Convergence achieved", " Elapsed estimation time in seconds: 9.99",
" ", " #TERM:", " OPTIMIZATION COMPLETED", " ", "", " ETABAR IS THE ARITHMETIC MEAN OF THE ETA-ESTIMATES,",
" AND THE P-VALUE IS GIVEN FOR THE NULL HYPOTHESIS THAT THE TRUE MEAN IS 0.",
"", " ETABAR: 4.1783E-08 2.5281E-08 2.2517E-08 1.3946E-08",
" SE: 3.9054E-02 2.9143E-02 3.5180E-02 3.4116E-02",
"", " P VAL.: 1.0000E+00 1.0000E+00 1.0000E+00 1.0000E+00",
" ", " ETAshrink(%): 3.3135E+00 1.9596E+01 2.2806E+01 1.4537E+01",
" EPSshrink(%): 3.1694E+01", " ", " #TERE:", " Elapsed covariance time in seconds: 0.05",
"1", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ",
" ", " ", " ", " ", " ", " ", " ", " ", " ************************************************************************************************************************",
" ******************** ********************",
" ******************** ITERATIVE TWO STAGE ********************",
" #OBJT:************** FINAL VALUE OF OBJECTIVE FUNCTION ********************",
" ******************** ********************",
" ************************************************************************************************************************",
" ", "", "", "", "", "", " #OBJV:******************************************** -1120.307 **************************************************",
"1", " ************************************************************************************************************************",
" ******************** ********************",
" ******************** ITERATIVE TWO STAGE ********************",
" ******************** FINAL PARAMETER ESTIMATE ********************",
" ******************** ********************",
" ************************************************************************************************************************",
" ", "", "", " THETA - VECTOR OF FIXED EFFECTS PARAMETERS *********",
"", "", " TH 1 TH 2 TH 3 TH 4 ", " ",
" 1.68E+00 1.59E+00 8.13E-01 2.37E+00", " ", "", "",
" OMEGA - COV MATRIX FOR RANDOM EFFECTS - ETAS ********", "",
"", " ETA1 ETA2 ETA3 ETA4", " ", " ETA1",
"+ 1.65E-01", " ", " ETA2", "+ 4.13E-03 1.33E-01",
" ", " ETA3", "+ 5.38E-03 1.72E-02 2.10E-01", " ", " ETA4",
"+ -1.61E-02 1.23E-02 5.08E-02 1.61E-01", " ", "", "",
" SIGMA - COV MATRIX FOR RANDOM EFFECTS - EPSILONS ****", "",
"", " EPS1", " ", " EPS1", "+ 5.53E-02", " ",
"1", " ************************************************************************************************************************",
" ******************** ********************",
" ******************** ITERATIVE TWO STAGE ********************",
" ******************** STANDARD ERROR OF ESTIMATE (S) ********************",
" ******************** ********************",
" ************************************************************************************************************************",
" ", "", "", " THETA - VECTOR OF FIXED EFFECTS PARAMETERS *********",
"", "", " TH 1 TH 2 TH 3 TH 4 ", " ",
" 4.61E-02 4.90E-02 6.52E-02 5.39E-02", " ", "", "",
" OMEGA - COV MATRIX FOR RANDOM EFFECTS - ETAS ********", "",
"", " ETA1 ETA2 ETA3 ETA4", " ", " ETA1",
"+ 2.89E-02", " ", " ETA2", "+ 2.31E-02 3.48E-02",
" ", " ETA3", "+ 3.24E-02 3.82E-02 6.49E-02", " ", " ETA4",
"+ 2.76E-02 2.73E-02 4.51E-02 4.05E-02", " ", "", "",
" SIGMA - COV MATRIX FOR RANDOM EFFECTS - EPSILONS ****", "",
"", " EPS1", " ", " EPS1", "+ 7.72E-03", " ",
"1", " ************************************************************************************************************************",
" ******************** ********************",
" ******************** ITERATIVE TWO STAGE ********************",
" ******************** COVARIANCE MATRIX OF ESTIMATE (S) ********************",
" ******************** ********************",
" ************************************************************************************************************************",
" ", "", " TH 1 TH 2 TH 3 TH 4 OM11 OM12 OM13 OM14 OM22 OM23 OM24 OM33",
" OM34 OM44 SG11", " ", " TH 1", "+ 2.13E-03",
" ", " TH 2", "+ 3.66E-04 2.40E-03", " ", " TH 3", "+ 3.64E-04 2.18E-04 4.25E-03",
" ", " TH 4", "+ -2.55E-05 1.60E-04 1.61E-03 2.91E-03",
" ", " OM11", "+ -2.46E-04 9.76E-05 7.27E-05 -8.56E-05 8.37E-04",
" ", " OM12", "+ 1.38E-05 1.77E-04 3.65E-05 -1.34E-04 3.11E-04 5.33E-04",
" ", " OM13", "+ -1.66E-04 -1.41E-06 -2.52E-04 2.27E-04 1.41E-04 2.40E-04 1.05E-03",
" ", " OM14", "+ -1.79E-04 -2.14E-04 1.49E-04 1.76E-04 2.22E-04 1.82E-04 5.45E-04 7.64E-04",
" ", " OM22", "+ -3.84E-05 -1.99E-05 -2.09E-04 -1.13E-04 1.40E-04 2.37E-04 8.43E-05 1.39E-04 1.21E-03",
" ", " OM23", "+ -7.76E-05 -8.97E-05 6.47E-05 1.26E-04 1.88E-04 3.92E-05 -6.21E-05 -3.03E-05 2.81E-04 1.46E-03",
" ", " OM24", "+ -2.59E-04 -1.03E-04 1.42E-04 1.55E-04 1.15E-04 8.62E-05 2.30E-05 9.12E-05 3.79E-04 5.84E-04 7.47E-04",
" ", " OM33", "+ -3.25E-04 -3.28E-04 -1.99E-04 5.31E-04 2.23E-04 1.48E-04 8.08E-04 3.88E-04 5.47E-04 4.35E-04 4.05E-04 4.21E-03",
" ", " OM34", "+ -2.06E-05 -9.04E-05 2.63E-04 2.74E-04 2.52E-04 1.17E-04 2.93E-04 2.20E-04 3.80E-04 3.73E-04 3.34E-04 2.20E-03",
" 2.04E-03", " ", " OM44", "+ 3.13E-05 -1.72E-05 1.96E-04 -2.92E-04 2.72E-04 1.27E-04 6.60E-05 1.56E-04 3.27E-04 1.96E-04 2.28E-04 1.11E-03",
" 1.34E-03 1.64E-03", " ", " SG11", "+ 4.53E-05 6.21E-05 -4.89E-06 2.71E-05 -6.00E-05 -4.28E-05 -5.80E-05 -7.91E-05 -8.04E-05 8.12E-06 -4.10E-05 -1.00E-04",
" -1.11E-04 -1.19E-04 5.96E-05", " ", "1", " ************************************************************************************************************************",
" ******************** ********************",
" ******************** ITERATIVE TWO STAGE ********************",
" ******************** CORRELATION MATRIX OF ESTIMATE (S) ********************",
" ******************** ********************",
" ************************************************************************************************************************",
" ", "", " TH 1 TH 2 TH 3 TH 4 OM11 OM12 OM13 OM14 OM22 OM23 OM24 OM33",
" OM34 OM44 SG11", " ", " TH 1", "+ 1.00E+00",
" ", " TH 2", "+ 1.62E-01 1.00E+00", " ", " TH 3", "+ 1.21E-01 6.83E-02 1.00E+00",
" ", " TH 4", "+ -1.02E-02 6.06E-02 4.58E-01 1.00E+00",
" ", " OM11", "+ -1.84E-01 6.89E-02 3.86E-02 -5.49E-02 1.00E+00",
" ", " OM12", "+ 1.29E-02 1.56E-01 2.43E-02 -1.07E-01 4.66E-01 1.00E+00",
" ", " OM13", "+ -1.11E-01 -8.87E-04 -1.19E-01 1.30E-01 1.51E-01 3.21E-01 1.00E+00",
" ", " OM14", "+ -1.40E-01 -1.58E-01 8.29E-02 1.18E-01 2.78E-01 2.85E-01 6.09E-01 1.00E+00",
" ", " OM22", "+ -2.39E-02 -1.16E-02 -9.22E-02 -6.00E-02 1.38E-01 2.94E-01 7.48E-02 1.45E-01 1.00E+00",
" ", " OM23", "+ -4.41E-02 -4.80E-02 2.60E-02 6.12E-02 1.70E-01 4.45E-02 -5.03E-02 -2.88E-02 2.11E-01 1.00E+00",
" ", " OM24", "+ -2.06E-01 -7.68E-02 7.98E-02 1.05E-01 1.46E-01 1.37E-01 2.60E-02 1.21E-01 3.98E-01 5.60E-01 1.00E+00",
" ", " OM33", "+ -1.09E-01 -1.03E-01 -4.71E-02 1.52E-01 1.19E-01 9.90E-02 3.85E-01 2.17E-01 2.42E-01 1.76E-01 2.29E-01 1.00E+00",
" ", " OM34", "+ -9.92E-03 -4.09E-02 8.96E-02 1.12E-01 1.93E-01 1.12E-01 2.01E-01 1.76E-01 2.42E-01 2.16E-01 2.71E-01 7.50E-01",
" 1.00E+00", " ", " OM44", "+ 1.67E-02 -8.64E-03 7.43E-02 -1.34E-01 2.31E-01 1.35E-01 5.03E-02 1.39E-01 2.31E-01 1.26E-01 2.06E-01 4.22E-01",
" 7.32E-01 1.00E+00", " ", " SG11", "+ 1.27E-01 1.64E-01 -9.73E-03 6.50E-02 -2.69E-01 -2.40E-01 -2.32E-01 -3.71E-01 -2.99E-01 2.76E-02 -1.94E-01 -2.01E-01",
" -3.19E-01 -3.80E-01 1.00E+00", " ", "1", " ************************************************************************************************************************",
" ******************** ********************",
" ******************** ITERATIVE TWO STAGE ********************",
" ******************** INVERSE COVARIANCE MATRIX OF ESTIMATE (S) ********************",
" ******************** ********************",
" ************************************************************************************************************************",
" ", "", " TH 1 TH 2 TH 3 TH 4 OM11 OM12 OM13 OM14 OM22 OM23 OM24 OM33",
" OM34 OM44 SG11", " ", " TH 1", "+ 5.64E+02",
" ", " TH 2", "+ -5.81E+01 4.92E+02", " ", " TH 3", "+ -5.58E+01 -1.06E+01 3.58E+02",
" ", " TH 4", "+ 1.88E+01 -4.99E+01 -2.19E+02 5.51E+02",
" ", " OM11", "+ 2.21E+02 -9.34E+01 1.15E+00 9.51E+00 1.82E+03",
" ", " OM12", "+ -1.55E+02 -1.74E+02 -1.34E+02 2.30E+02 -9.71E+02 3.08E+03",
" ", " OM13", "+ 2.25E+01 -1.41E+02 2.11E+02 -1.51E+02 2.36E+02 -6.70E+02 2.11E+03",
" ", " OM14", "+ 3.31E+01 2.38E+02 -1.60E+02 -3.63E+01 -3.83E+02 7.84E+00 -1.33E+03 2.61E+03",
" ", " OM22", "+ -6.43E+01 -3.31E+01 9.65E+01 -5.95E+00 1.16E+02 -4.50E+02 2.16E+02 -1.22E+02 1.18E+03",
" ", " OM23", "+ -8.28E+01 4.75E+01 2.11E+01 -8.60E-01 -2.77E+02 1.11E+02 1.08E+01 1.19E+02 -2.09E+01 1.11E+03",
" ", " OM24", "+ 2.76E+02 9.48E+00 -6.66E+01 -8.42E+01 1.89E+02 -1.88E+02 1.39E+02 -1.42E+02 -4.74E+02 -8.76E+02 2.49E+03",
" ", " OM33", "+ 6.55E+01 7.12E+01 4.88E+01 -3.43E+01 1.19E+01 5.27E+01 -3.83E+02 1.08E+02 -1.26E+02 5.83E-01 -5.26E+00 7.25E+02",
" ", " OM34", "+ -1.04E+02 -3.10E+01 -3.23E+01 -1.81E+02 -5.40E+01 1.44E+01 1.26E+02 3.20E+01 7.07E+01 -1.34E+02 -7.42E+01 -8.74E+02",
" 2.36E+03", " ", " OM44", "+ -2.01E+01 -5.44E+01 -8.13E+01 2.87E+02 -1.27E+02 8.51E+01 1.28E+02 -9.18E+01 -6.00E+01 6.08E+01 -4.86E+01 2.03E+02",
" -1.30E+03 1.69E+03", " ", " SG11", "+ -2.14E+02 -5.78E+02 2.10E+01 -1.38E+02 7.71E+02 3.09E+02 4.95E+02 1.31E+03 1.00E+03 -9.24E+02 7.64E+02 -4.59E+02",
" 7.06E+02 1.06E+03 2.55E+04", " ", "1", " ", " ")
# this attribute should be turned into the "method" field of the output list
attr(testBlock, "method.name") <- "Iterative Two Stage"
processedBlock <- RNMImport:::.importMethodBlock(testBlock)
# extract just final estimates
finalEst <- processedBlock$FinalEstimates
# method name obtained correctly
checkEquals(processedBlock$method, "Iterative Two Stage", msg = " |method name passed down correctly." )
# objective function value correct
checkEquals(processedBlock$Objective.Final, -1120.307, msg = " | objective function is correct")
# theta final estimates correct
checkEquals(unname(finalEst$THETA), c(1.680, 1.590, 0.813, 2.370),
msg = " | theta final estimates correct")
# omega finals correct
checkEquals( finalEst$OMEGA,
structure(c(0.165, 0.00413, 0.00538, -0.0161, 0.00413, 0.133,
0.0172, 0.0123, 0.00538, 0.0172, 0.21, 0.0508, -0.0161, 0.0123,
0.0508, 0.161), .Dim = c(4L, 4L), .Dimnames = list(c("ETA1",
"ETA2", "ETA3", "ETA4"), c("ETA1", "ETA2", "ETA3", "ETA4"))),
msg = " |omega finals correct")
# sigma finals correct
checkEquals(finalEst$SIGMA, structure(0.0553, .Dim = c(1L, 1L), .Dimnames = list("EPS1",
"EPS1")), msg = " |sigma finals correct" )
stdErr <- processedBlock$StandardError
# theta standard error correct
checkEquals( stdErr$THETA, structure(c(0.0461, 0.049, 0.0652, 0.0539), .Names = c("TH1",
"TH2", "TH3", "TH4")),
msg = " |theta standard error correct" )
# omega standard error correct
checkEquals( stdErr$OMEGA, structure(c(0.0289, 0.0231, 0.0324, 0.0276, 0.0231, 0.0348, 0.0382,
0.0273, 0.0324, 0.0382, 0.0649, 0.0451, 0.0276, 0.0273, 0.0451,
0.0405), .Dim = c(4L, 4L), .Dimnames = list(c("ETA1", "ETA2",
"ETA3", "ETA4"), c("ETA1", "ETA2", "ETA3", "ETA4"))),
msg = " |omega standard error correct")
checkEquals( stdErr$SIGMA, structure(0.00772, .Dim = c(1L, 1L), .Dimnames = list("EPS1",
"EPS1")),
, msg = " |sigma standard error correct")
# covariance matrices available and of correct dimension
checkTrue(all( c(dim(processedBlock$CovarianceMatrix), dim(processedBlock$InverseCovarianceMatrix), dim(processedBlock$CorrelationMatrix) ) == 15 ),
msg = " |covariance matrices available and of correct dimension" )
# check that shrink values have been imported correctly
checkEquals(processedBlock$ETAshrink, c(3.3135, 19.596, 22.806, 14.537) )
checkEquals(processedBlock$EPSshrink, 31.694 )
# check that first line of objective fun termination value is available
checkEquals(processedBlock$TermStatus, "OPTIMIZATION COMPLETED")
}
MangoTheCat/RNMImport documentation built on May 8, 2019, 4:36 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# $LastChangedDate: 2010-01-12 15:55:59 +0000 (Tue, 12 Jan 2010) $
# $LastChangedBy: fgochez $
# $Rev: 14609 $
#
# Author: fgochez
###############################################################################
# tests the low-level function .importMethodBlock (in importNmLstNM7)
test.importMethodBlock <- function()
{
# sample method block
testBlock <- c(" #METH: Iterative Two Stage", " EM/BAYES SETUP", " THETAS THAT ARE MU MODELED:",
" 1 2 3 4", " THETAS THAT ARE SIGMA-LIKE:", " ", " ",
" MONITORING OF SEARCH:", "", " iteration 0 OBJ= -439.445868533902 ",
" iteration 5 OBJ= -1119.48137768895 ", " iteration 10 OBJ= -1120.19191233229 ",
" iteration 15 OBJ= -1120.26385480453 ", " iteration 20 OBJ= -1120.28483467697 ",
" iteration 25 OBJ= -1120.29421562205 ", " iteration 30 OBJ= -1120.29934078386 ",
" iteration 35 OBJ= -1120.30236183088 ", " iteration 40 OBJ= -1120.30417175997 ",
" iteration 45 OBJ= -1120.30528535008 ", " iteration 50 OBJ= -1120.30595982428 ",
" iteration 55 OBJ= -1120.30637009744 ", " iteration 60 OBJ= -1120.30662747964 ",
" iteration 65 OBJ= -1120.30677846680 ", " iteration 70 OBJ= -1120.30687589562 ",
" iteration 75 OBJ= -1120.30693225876 ", " iteration 80 OBJ= -1120.30696556872 ",
" iteration 85 OBJ= -1120.30699553335 ", " iteration 90 OBJ= -1120.30701400145 ",
" iteration 95 OBJ= -1120.30702142508 ", " iteration 100 OBJ= -1120.30702424494 ",
" iteration 105 OBJ= -1120.30702412937 ", " iteration 110 OBJ= -1120.30702950237 ",
" Convergence achieved", " Elapsed estimation time in seconds: 9.99",
" ", " #TERM:", " OPTIMIZATION COMPLETED", " ", "", " ETABAR IS THE ARITHMETIC MEAN OF THE ETA-ESTIMATES,",
" AND THE P-VALUE IS GIVEN FOR THE NULL HYPOTHESIS THAT THE TRUE MEAN IS 0.",
"", " ETABAR: 4.1783E-08 2.5281E-08 2.2517E-08 1.3946E-08",
" SE: 3.9054E-02 2.9143E-02 3.5180E-02 3.4116E-02",
"", " P VAL.: 1.0000E+00 1.0000E+00 1.0000E+00 1.0000E+00",
" ", " ETAshrink(%): 3.3135E+00 1.9596E+01 2.2806E+01 1.4537E+01",
" EPSshrink(%): 3.1694E+01", " ", " #TERE:", " Elapsed covariance time in seconds: 0.05",
"1", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ", " ",
" ", " ", " ", " ", " ", " ", " ", " ", " ************************************************************************************************************************",
" ******************** ********************",
" ******************** ITERATIVE TWO STAGE ********************",
" #OBJT:************** FINAL VALUE OF OBJECTIVE FUNCTION ********************",
" ******************** ********************",
" ************************************************************************************************************************",
" ", "", "", "", "", "", " #OBJV:******************************************** -1120.307 **************************************************",
"1", " ************************************************************************************************************************",
" ******************** ********************",
" ******************** ITERATIVE TWO STAGE ********************",
" ******************** FINAL PARAMETER ESTIMATE ********************",
" ******************** ********************",
" ************************************************************************************************************************",
" ", "", "", " THETA - VECTOR OF FIXED EFFECTS PARAMETERS *********",
"", "", " TH 1 TH 2 TH 3 TH 4 ", " ",
" 1.68E+00 1.59E+00 8.13E-01 2.37E+00", " ", "", "",
" OMEGA - COV MATRIX FOR RANDOM EFFECTS - ETAS ********", "",
"", " ETA1 ETA2 ETA3 ETA4", " ", " ETA1",
"+ 1.65E-01", " ", " ETA2", "+ 4.13E-03 1.33E-01",
" ", " ETA3", "+ 5.38E-03 1.72E-02 2.10E-01", " ", " ETA4",
"+ -1.61E-02 1.23E-02 5.08E-02 1.61E-01", " ", "", "",
" SIGMA - COV MATRIX FOR RANDOM EFFECTS - EPSILONS ****", "",
"", " EPS1", " ", " EPS1", "+ 5.53E-02", " ",
"1", " ************************************************************************************************************************",
" ******************** ********************",
" ******************** ITERATIVE TWO STAGE ********************",
" ******************** STANDARD ERROR OF ESTIMATE (S) ********************",
" ******************** ********************",
" ************************************************************************************************************************",
" ", "", "", " THETA - VECTOR OF FIXED EFFECTS PARAMETERS *********",
"", "", " TH 1 TH 2 TH 3 TH 4 ", " ",
" 4.61E-02 4.90E-02 6.52E-02 5.39E-02", " ", "", "",
" OMEGA - COV MATRIX FOR RANDOM EFFECTS - ETAS ********", "",
"", " ETA1 ETA2 ETA3 ETA4", " ", " ETA1",
"+ 2.89E-02", " ", " ETA2", "+ 2.31E-02 3.48E-02",
" ", " ETA3", "+ 3.24E-02 3.82E-02 6.49E-02", " ", " ETA4",
"+ 2.76E-02 2.73E-02 4.51E-02 4.05E-02", " ", "", "",
" SIGMA - COV MATRIX FOR RANDOM EFFECTS - EPSILONS ****", "",
"", " EPS1", " ", " EPS1", "+ 7.72E-03", " ",
"1", " ************************************************************************************************************************",
" ******************** ********************",
" ******************** ITERATIVE TWO STAGE ********************",
" ******************** COVARIANCE MATRIX OF ESTIMATE (S) ********************",
" ******************** ********************",
" ************************************************************************************************************************",
" ", "", " TH 1 TH 2 TH 3 TH 4 OM11 OM12 OM13 OM14 OM22 OM23 OM24 OM33",
" OM34 OM44 SG11", " ", " TH 1", "+ 2.13E-03",
" ", " TH 2", "+ 3.66E-04 2.40E-03", " ", " TH 3", "+ 3.64E-04 2.18E-04 4.25E-03",
" ", " TH 4", "+ -2.55E-05 1.60E-04 1.61E-03 2.91E-03",
" ", " OM11", "+ -2.46E-04 9.76E-05 7.27E-05 -8.56E-05 8.37E-04",
" ", " OM12", "+ 1.38E-05 1.77E-04 3.65E-05 -1.34E-04 3.11E-04 5.33E-04",
" ", " OM13", "+ -1.66E-04 -1.41E-06 -2.52E-04 2.27E-04 1.41E-04 2.40E-04 1.05E-03",
" ", " OM14", "+ -1.79E-04 -2.14E-04 1.49E-04 1.76E-04 2.22E-04 1.82E-04 5.45E-04 7.64E-04",
" ", " OM22", "+ -3.84E-05 -1.99E-05 -2.09E-04 -1.13E-04 1.40E-04 2.37E-04 8.43E-05 1.39E-04 1.21E-03",
" ", " OM23", "+ -7.76E-05 -8.97E-05 6.47E-05 1.26E-04 1.88E-04 3.92E-05 -6.21E-05 -3.03E-05 2.81E-04 1.46E-03",
" ", " OM24", "+ -2.59E-04 -1.03E-04 1.42E-04 1.55E-04 1.15E-04 8.62E-05 2.30E-05 9.12E-05 3.79E-04 5.84E-04 7.47E-04",
" ", " OM33", "+ -3.25E-04 -3.28E-04 -1.99E-04 5.31E-04 2.23E-04 1.48E-04 8.08E-04 3.88E-04 5.47E-04 4.35E-04 4.05E-04 4.21E-03",
" ", " OM34", "+ -2.06E-05 -9.04E-05 2.63E-04 2.74E-04 2.52E-04 1.17E-04 2.93E-04 2.20E-04 3.80E-04 3.73E-04 3.34E-04 2.20E-03",
" 2.04E-03", " ", " OM44", "+ 3.13E-05 -1.72E-05 1.96E-04 -2.92E-04 2.72E-04 1.27E-04 6.60E-05 1.56E-04 3.27E-04 1.96E-04 2.28E-04 1.11E-03",
" 1.34E-03 1.64E-03", " ", " SG11", "+ 4.53E-05 6.21E-05 -4.89E-06 2.71E-05 -6.00E-05 -4.28E-05 -5.80E-05 -7.91E-05 -8.04E-05 8.12E-06 -4.10E-05 -1.00E-04",
" -1.11E-04 -1.19E-04 5.96E-05", " ", "1", " ************************************************************************************************************************",
" ******************** ********************",
" ******************** ITERATIVE TWO STAGE ********************",
" ******************** CORRELATION MATRIX OF ESTIMATE (S) ********************",
" ******************** ********************",
" ************************************************************************************************************************",
" ", "", " TH 1 TH 2 TH 3 TH 4 OM11 OM12 OM13 OM14 OM22 OM23 OM24 OM33",
" OM34 OM44 SG11", " ", " TH 1", "+ 1.00E+00",
" ", " TH 2", "+ 1.62E-01 1.00E+00", " ", " TH 3", "+ 1.21E-01 6.83E-02 1.00E+00",
" ", " TH 4", "+ -1.02E-02 6.06E-02 4.58E-01 1.00E+00",
" ", " OM11", "+ -1.84E-01 6.89E-02 3.86E-02 -5.49E-02 1.00E+00",
" ", " OM12", "+ 1.29E-02 1.56E-01 2.43E-02 -1.07E-01 4.66E-01 1.00E+00",
" ", " OM13", "+ -1.11E-01 -8.87E-04 -1.19E-01 1.30E-01 1.51E-01 3.21E-01 1.00E+00",
" ", " OM14", "+ -1.40E-01 -1.58E-01 8.29E-02 1.18E-01 2.78E-01 2.85E-01 6.09E-01 1.00E+00",
" ", " OM22", "+ -2.39E-02 -1.16E-02 -9.22E-02 -6.00E-02 1.38E-01 2.94E-01 7.48E-02 1.45E-01 1.00E+00",
" ", " OM23", "+ -4.41E-02 -4.80E-02 2.60E-02 6.12E-02 1.70E-01 4.45E-02 -5.03E-02 -2.88E-02 2.11E-01 1.00E+00",
" ", " OM24", "+ -2.06E-01 -7.68E-02 7.98E-02 1.05E-01 1.46E-01 1.37E-01 2.60E-02 1.21E-01 3.98E-01 5.60E-01 1.00E+00",
" ", " OM33", "+ -1.09E-01 -1.03E-01 -4.71E-02 1.52E-01 1.19E-01 9.90E-02 3.85E-01 2.17E-01 2.42E-01 1.76E-01 2.29E-01 1.00E+00",
" ", " OM34", "+ -9.92E-03 -4.09E-02 8.96E-02 1.12E-01 1.93E-01 1.12E-01 2.01E-01 1.76E-01 2.42E-01 2.16E-01 2.71E-01 7.50E-01",
" 1.00E+00", " ", " OM44", "+ 1.67E-02 -8.64E-03 7.43E-02 -1.34E-01 2.31E-01 1.35E-01 5.03E-02 1.39E-01 2.31E-01 1.26E-01 2.06E-01 4.22E-01",
" 7.32E-01 1.00E+00", " ", " SG11", "+ 1.27E-01 1.64E-01 -9.73E-03 6.50E-02 -2.69E-01 -2.40E-01 -2.32E-01 -3.71E-01 -2.99E-01 2.76E-02 -1.94E-01 -2.01E-01",
" -3.19E-01 -3.80E-01 1.00E+00", " ", "1", " ************************************************************************************************************************",
" ******************** ********************",
" ******************** ITERATIVE TWO STAGE ********************",
" ******************** INVERSE COVARIANCE MATRIX OF ESTIMATE (S) ********************",
" ******************** ********************",
" ************************************************************************************************************************",
" ", "", " TH 1 TH 2 TH 3 TH 4 OM11 OM12 OM13 OM14 OM22 OM23 OM24 OM33",
" OM34 OM44 SG11", " ", " TH 1", "+ 5.64E+02",
" ", " TH 2", "+ -5.81E+01 4.92E+02", " ", " TH 3", "+ -5.58E+01 -1.06E+01 3.58E+02",
" ", " TH 4", "+ 1.88E+01 -4.99E+01 -2.19E+02 5.51E+02",
" ", " OM11", "+ 2.21E+02 -9.34E+01 1.15E+00 9.51E+00 1.82E+03",
" ", " OM12", "+ -1.55E+02 -1.74E+02 -1.34E+02 2.30E+02 -9.71E+02 3.08E+03",
" ", " OM13", "+ 2.25E+01 -1.41E+02 2.11E+02 -1.51E+02 2.36E+02 -6.70E+02 2.11E+03",
" ", " OM14", "+ 3.31E+01 2.38E+02 -1.60E+02 -3.63E+01 -3.83E+02 7.84E+00 -1.33E+03 2.61E+03",
" ", " OM22", "+ -6.43E+01 -3.31E+01 9.65E+01 -5.95E+00 1.16E+02 -4.50E+02 2.16E+02 -1.22E+02 1.18E+03",
" ", " OM23", "+ -8.28E+01 4.75E+01 2.11E+01 -8.60E-01 -2.77E+02 1.11E+02 1.08E+01 1.19E+02 -2.09E+01 1.11E+03",
" ", " OM24", "+ 2.76E+02 9.48E+00 -6.66E+01 -8.42E+01 1.89E+02 -1.88E+02 1.39E+02 -1.42E+02 -4.74E+02 -8.76E+02 2.49E+03",
" ", " OM33", "+ 6.55E+01 7.12E+01 4.88E+01 -3.43E+01 1.19E+01 5.27E+01 -3.83E+02 1.08E+02 -1.26E+02 5.83E-01 -5.26E+00 7.25E+02",
" ", " OM34", "+ -1.04E+02 -3.10E+01 -3.23E+01 -1.81E+02 -5.40E+01 1.44E+01 1.26E+02 3.20E+01 7.07E+01 -1.34E+02 -7.42E+01 -8.74E+02",
" 2.36E+03", " ", " OM44", "+ -2.01E+01 -5.44E+01 -8.13E+01 2.87E+02 -1.27E+02 8.51E+01 1.28E+02 -9.18E+01 -6.00E+01 6.08E+01 -4.86E+01 2.03E+02",
" -1.30E+03 1.69E+03", " ", " SG11", "+ -2.14E+02 -5.78E+02 2.10E+01 -1.38E+02 7.71E+02 3.09E+02 4.95E+02 1.31E+03 1.00E+03 -9.24E+02 7.64E+02 -4.59E+02",
" 7.06E+02 1.06E+03 2.55E+04", " ", "1", " ", " ")
# this attribute should be turned into the "method" field of the output list
attr(testBlock, "method.name") <- "Iterative Two Stage"
processedBlock <- RNMImport:::.importMethodBlock(testBlock)
# extract just final estimates
finalEst <- processedBlock$FinalEstimates
# method name obtained correctly
checkEquals(processedBlock$method, "Iterative Two Stage", msg = " |method name passed down correctly." )
# objective function value correct
checkEquals(processedBlock$Objective.Final, -1120.307, msg = " | objective function is correct")
# theta final estimates correct
checkEquals(unname(finalEst$THETA), c(1.680, 1.590, 0.813, 2.370),
msg = " | theta final estimates correct")
# omega finals correct
checkEquals( finalEst$OMEGA,
structure(c(0.165, 0.00413, 0.00538, -0.0161, 0.00413, 0.133,
0.0172, 0.0123, 0.00538, 0.0172, 0.21, 0.0508, -0.0161, 0.0123,
0.0508, 0.161), .Dim = c(4L, 4L), .Dimnames = list(c("ETA1",
"ETA2", "ETA3", "ETA4"), c("ETA1", "ETA2", "ETA3", "ETA4"))),
msg = " |omega finals correct")
# sigma finals correct
checkEquals(finalEst$SIGMA, structure(0.0553, .Dim = c(1L, 1L), .Dimnames = list("EPS1",
"EPS1")), msg = " |sigma finals correct" )
stdErr <- processedBlock$StandardError
# theta standard error correct
checkEquals( stdErr$THETA, structure(c(0.0461, 0.049, 0.0652, 0.0539), .Names = c("TH1",
"TH2", "TH3", "TH4")),
msg = " |theta standard error correct" )
# omega standard error correct
checkEquals( stdErr$OMEGA, structure(c(0.0289, 0.0231, 0.0324, 0.0276, 0.0231, 0.0348, 0.0382,
0.0273, 0.0324, 0.0382, 0.0649, 0.0451, 0.0276, 0.0273, 0.0451,
0.0405), .Dim = c(4L, 4L), .Dimnames = list(c("ETA1", "ETA2",
"ETA3", "ETA4"), c("ETA1", "ETA2", "ETA3", "ETA4"))),
msg = " |omega standard error correct")
checkEquals( stdErr$SIGMA, structure(0.00772, .Dim = c(1L, 1L), .Dimnames = list("EPS1",
"EPS1")),
, msg = " |sigma standard error correct")
# covariance matrices available and of correct dimension
checkTrue(all( c(dim(processedBlock$CovarianceMatrix), dim(processedBlock$InverseCovarianceMatrix), dim(processedBlock$CorrelationMatrix) ) == 15 ),
msg = " |covariance matrices available and of correct dimension" )
# check that shrink values have been imported correctly
checkEquals(processedBlock$ETAshrink, c(3.3135, 19.596, 22.806, 14.537) )
checkEquals(processedBlock$EPSshrink, 31.694 )
# check that first line of objective fun termination value is available
checkEquals(processedBlock$TermStatus, "OPTIMIZATION COMPLETED")
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.