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@philipdelff
philipdelff committed Oct 18, 2023
1 parent 4d47609 commit 03ae05e
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -58,6 +58,7 @@ inst/examples/nonmem/backup_*
inst/examples/nonmem/*\.ext
inst/examples/nonmem/*\.phi
inst/examples/nonmem/xgxr001dir/backup_*
tests_manual/testthat/testOutput
/doc/
/Meta/
*\.pnm
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2 changes: 1 addition & 1 deletion devel/todo.org
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Expand Up @@ -11,7 +11,7 @@
"default" as an actual param value.
*** DONE Allow for say input.txt/output.txt
**** NMtransInput
*** TODO Support a drop argument
*** TODO [#B] Support a drop argument
It has been initiated in the code. I believe it can be finished after
the translate part. The colnames table is the trickier part to update.
*** DONE Support for return as tibble or whatever
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14 changes: 14 additions & 0 deletions devel/vignettes_compile.R
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### vignettes are too large to be included on CRAN. I think because they are in .Rbuildignore devtools::document does not build them. I don't quite understand that because Roxygen is configured to build them in DESCRIPTION. Anyway, I had to run this to update them.

dir.vignettes <- "~/wdirs/NMdata/vignettes"
setwd(dir.vignettes)

library(NMdata)
library(rmarkdown)

names.vignettes <- cc(DataPrepare,"NMdata-cheat","NMdata-FAQ",NMscanData)

for(fn in names.vignettes){
render(fnExtension(fn,"Rmd"))
}

11 changes: 11 additions & 0 deletions tests/testthat/testData/nonmem/estim_debug.ext
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TABLE NO. 1: Laplacian Conditional Estimation: Goal Function=MINIMUM VALUE OF OBJECTIVE FUNCTION: Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0 Superproblem2=0 Iteration2=0
ITERATION THETA1 THETA2 THETA3 SIGMA(1,1) OMEGA(1,1) OMEGA(2,1) OMEGA(2,2) OBJ
0 7.09000E+00 2.98000E-01 1.15000E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 115.85529154812808
14 7.16625E+00 2.32987E-01 1.65673E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 112.40346696014036
-1000000000 7.16625E+00 2.32987E-01 1.65673E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 112.40346696014036
-1000000001 1.74290E-01 6.07397E-02 3.07520E-03 0.00000E+00 1.00000E+10 1.00000E+10 1.00000E+10 0.0000000000000000
-1000000004 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.0000000000000000
-1000000005 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+10 1.00000E+10 1.00000E+10 1.00000E+10 0.0000000000000000
-1000000006 0.00000E+00 0.00000E+00 0.00000E+00 1.00000E+00 1.00000E+00 1.00000E+00 1.00000E+00 0.0000000000000000
-1000000007 0.00000E+00 3.70000E+01 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.0000000000000000
-1000000008 3.95568E-04 -1.46051E-03 -7.63924E-02 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.0000000000000000
52 changes: 52 additions & 0 deletions tests/testthat/testData/nonmem/estim_debug.phi
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TABLE NO. 1: Laplacian Conditional Estimation: Problem=1 Subproblem=0 Superproblem1=0 Iteration1=0 Superproblem2=0 Iteration2=0
SUBJECT_NO ID ETA(1) ETA(2) ETC(1,1) ETC(2,1) ETC(2,2) OBJ
1 108 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.0000000000000000
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3 142 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.27076418174345984
4 152 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 11.822176871268185
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6 250 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.0000000000000000
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