pull all code out of rdev; makescripts in ./inst/maintenance metrumre…

…searchgroup#154
marianklose · Dec 16, 2016 · 4a905b4 · 4a905b4
1 parent 7fa98d4
commit 4a905b4
Show file tree

Hide file tree

Showing 273 changed files with 27 additions and 15 deletions.
diff --git a/rdev/.Rbuildignore → .Rbuildignore b/rdev/.Rbuildignore → .Rbuildignore
@@ -1,3 +1,4 @@
+
 ^.*\.Rproj$
 ^\.Rproj\.user$
 vignettes/.*[.]toc$
@@ -16,4 +17,15 @@ inst/project/.*[.]so$
 inst/models/.*[.]o$
 inst/models/.*[.]so$
 inst/models/.*[.]check$
+inst/maintenance
 src/.*[.]tar.gz$
+.*[.]tar.gz$
+img
+README.Rmd
+README.md
+NEWS.md
+.git
+.gitignore
+.travis.yml
+.Rinstignore
+Makefile
diff --git a/rdev/.Rinstignore → .Rinstignore b/rdev/.Rinstignore → .Rinstignore
diff --git a/rdev/DESCRIPTION → DESCRIPTION b/rdev/DESCRIPTION → DESCRIPTION
diff --git a/Makefile b/Makefile
@@ -1,9 +1,9 @@
 SHELL := /bin/bash
 #LIBDIR=${HOME}/Rlibs/lib
 PACKAGE=mrgsolve
-VERSION=$(shell grep Version rdev/DESCRIPTION |awk '{print $$2}')
+VERSION=$(shell grep Version DESCRIPTION |awk '{print $$2}')
 TARBALL=${PACKAGE}_${VERSION}.tar.gz
-PKGDIR=rdev/
+PKGDIR=.
 CHKDIR=Rchecks
 
 ## Set libPaths:
@@ -25,11 +25,11 @@ all:
 
 .PHONY: doc
 doc:
-	Rscript makescripts/doc_mrgsolve.R
+	Rscript inst/maintenance/doc_mrgsolve.R
 
 .PHONY: staticdoc
 staticdoc:
-	Rscript makescripts/staticdocs.R
+	Rscript inst/maintenance/staticdocs.R
 
 build:
 	R CMD build --md5 $(PKGDIR)
@@ -58,16 +58,16 @@ check-cran:
 
 test:
 	R CMD INSTALL ${PKGDIR}
-	Rscript -e 'library(testthat)' -e 'test_dir("rdev/tests/testthat")'
+	Rscript -e 'library(testthat)' -e 'test_dir("tests/testthat")'
 
 .PHONY: tests
 tests:
-	Rscript makescripts/tests.R
+	Rscript inst/maintenance/tests.R
 
 clean:
 	if test -d ${CHKDIR}/mrgsolve.Rcheck; then rm -rf ${CHKDIR}/mrgsolve.Rcheck;fi
 
 datasets:
-	Rscript makescripts/datasets.R
+	Rscript inst/maintenance/datasets.R
 
 
diff --git a/rdev/NAMESPACE → NAMESPACE b/rdev/NAMESPACE → NAMESPACE
diff --git a/rdev/R/Aaaa.R → R/Aaaa.R b/rdev/R/Aaaa.R → R/Aaaa.R
diff --git a/rdev/R/RcppExports.R → R/RcppExports.R b/rdev/R/RcppExports.R → R/RcppExports.R
diff --git a/rdev/R/altname.R → R/altname.R b/rdev/R/altname.R → R/altname.R
diff --git a/rdev/R/annot.R → R/annot.R b/rdev/R/annot.R → R/annot.R
diff --git a/rdev/R/chain.R → R/chain.R b/rdev/R/chain.R → R/chain.R
diff --git a/rdev/R/class_build.R → R/class_build.R b/rdev/R/class_build.R → R/class_build.R
diff --git a/rdev/R/class_derived.R → R/class_derived.R b/rdev/R/class_derived.R → R/class_derived.R
diff --git a/rdev/R/class_ev.R → R/class_ev.R b/rdev/R/class_ev.R → R/class_ev.R
diff --git a/rdev/R/class_matlist.R → R/class_matlist.R b/rdev/R/class_matlist.R → R/class_matlist.R
diff --git a/rdev/R/class_modlist.R → R/class_modlist.R b/rdev/R/class_modlist.R → R/class_modlist.R
diff --git a/rdev/R/class_mrgmod.R → R/class_mrgmod.R b/rdev/R/class_mrgmod.R → R/class_mrgmod.R
diff --git a/rdev/R/class_mrgsims.R → R/class_mrgsims.R b/rdev/R/class_mrgsims.R → R/class_mrgsims.R
diff --git a/rdev/R/class_numericlist.R → R/class_numericlist.R b/rdev/R/class_numericlist.R → R/class_numericlist.R
diff --git a/rdev/R/class_tgrid.R → R/class_tgrid.R b/rdev/R/class_tgrid.R → R/class_tgrid.R
diff --git a/rdev/R/compile.R → R/compile.R b/rdev/R/compile.R → R/compile.R
diff --git a/rdev/R/complog.R → R/complog.R b/rdev/R/complog.R → R/complog.R
diff --git a/rdev/R/data_set.R → R/data_set.R b/rdev/R/data_set.R → R/data_set.R
diff --git a/rdev/R/datasets.R → R/datasets.R b/rdev/R/datasets.R → R/datasets.R
diff --git a/rdev/R/events.R → R/events.R b/rdev/R/events.R → R/events.R
diff --git a/rdev/R/example.R → R/example.R b/rdev/R/example.R → R/example.R
diff --git a/rdev/R/funset.R → R/funset.R b/rdev/R/funset.R → R/funset.R
diff --git a/rdev/R/generics.R → R/generics.R b/rdev/R/generics.R → R/generics.R
diff --git a/rdev/R/idata_set.R → R/idata_set.R b/rdev/R/idata_set.R → R/idata_set.R
diff --git a/rdev/R/init.R → R/init.R b/rdev/R/init.R → R/init.R
diff --git a/rdev/R/knobs.R → R/knobs.R b/rdev/R/knobs.R → R/knobs.R
diff --git a/rdev/R/library.R → R/library.R b/rdev/R/library.R → R/library.R
diff --git a/rdev/R/matlist.R → R/matlist.R b/rdev/R/matlist.R → R/matlist.R
diff --git a/rdev/R/matrix.R → R/matrix.R b/rdev/R/matrix.R → R/matrix.R
diff --git a/rdev/R/mcache.R → R/mcache.R b/rdev/R/mcache.R → R/mcache.R
diff --git a/rdev/R/model_include.R → R/model_include.R b/rdev/R/model_include.R → R/model_include.R
diff --git a/rdev/R/modlib.R → R/modlib.R b/rdev/R/modlib.R → R/modlib.R
diff --git a/rdev/R/modspec.R → R/modspec.R b/rdev/R/modspec.R → R/modspec.R
diff --git a/rdev/R/mread.R → R/mread.R b/rdev/R/mread.R → R/mread.R
diff --git a/rdev/R/mrgindata.R → R/mrgindata.R b/rdev/R/mrgindata.R → R/mrgindata.R
diff --git a/rdev/R/mrgsims.R → R/mrgsims.R b/rdev/R/mrgsims.R → R/mrgsims.R
diff --git a/rdev/R/mrgsolve.R → R/mrgsolve.R b/rdev/R/mrgsolve.R → R/mrgsolve.R
diff --git a/rdev/R/nmxml.R → R/nmxml.R b/rdev/R/nmxml.R → R/nmxml.R
diff --git a/rdev/R/package.R → R/package.R b/rdev/R/package.R → R/package.R
diff --git a/rdev/R/param.R → R/param.R b/rdev/R/param.R → R/param.R
diff --git a/rdev/R/print.R → R/print.R b/rdev/R/print.R → R/print.R
diff --git a/rdev/R/qsim.R → R/qsim.R b/rdev/R/qsim.R → R/qsim.R
diff --git a/rdev/R/render.R → R/render.R b/rdev/R/render.R → R/render.R
diff --git a/rdev/R/simtime.R → R/simtime.R b/rdev/R/simtime.R → R/simtime.R
diff --git a/rdev/R/update.R → R/update.R b/rdev/R/update.R → R/update.R
diff --git a/rdev/R/utils.R → R/utils.R b/rdev/R/utils.R → R/utils.R
diff --git a/rdev/data/exBoot.RData → data/exBoot.RData b/rdev/data/exBoot.RData → data/exBoot.RData
diff --git a/rdev/data/exTheoph.RData → data/exTheoph.RData b/rdev/data/exTheoph.RData → data/exTheoph.RData
diff --git a/rdev/data/exidata.RData → data/exidata.RData b/rdev/data/exidata.RData → data/exidata.RData
diff --git a/rdev/data/extran1.RData → data/extran1.RData b/rdev/data/extran1.RData → data/extran1.RData
diff --git a/rdev/data/extran2.RData → data/extran2.RData b/rdev/data/extran2.RData → data/extran2.RData
diff --git a/rdev/data/extran3.RData → data/extran3.RData b/rdev/data/extran3.RData → data/extran3.RData
diff --git a/rdev/inst/Rmd/mrgsolve_render_template.Rmd → inst/Rmd/mrgsolve_render_template.Rmd b/rdev/inst/Rmd/mrgsolve_render_template.Rmd → inst/Rmd/mrgsolve_render_template.Rmd
diff --git a/rdev/inst/base/modelheader.h → inst/base/modelheader.h b/rdev/inst/base/modelheader.h → inst/base/modelheader.h
diff --git a/rdev/inst/base/mrgsolv.h → inst/base/mrgsolv.h b/rdev/inst/base/mrgsolv.h → inst/base/mrgsolv.h
diff --git a/rdev/inst/include/RcppInclude.h → inst/include/RcppInclude.h b/rdev/inst/include/RcppInclude.h → inst/include/RcppInclude.h
diff --git a/rdev/inst/include/dataobject.h → inst/include/dataobject.h b/rdev/inst/include/dataobject.h → inst/include/dataobject.h
diff --git a/rdev/inst/include/datarecord.h → inst/include/datarecord.h b/rdev/inst/include/datarecord.h → inst/include/datarecord.h
diff --git a/rdev/inst/include/modelheader.h → inst/include/modelheader.h b/rdev/inst/include/modelheader.h → inst/include/modelheader.h
diff --git a/rdev/inst/include/mrgsolv.h → inst/include/mrgsolv.h b/rdev/inst/include/mrgsolv.h → inst/include/mrgsolv.h
diff --git a/rdev/inst/include/mrgsolve.h → inst/include/mrgsolve.h b/rdev/inst/include/mrgsolve.h → inst/include/mrgsolve.h
diff --git a/rdev/inst/include/odepack_dlsoda.h → inst/include/odepack_dlsoda.h b/rdev/inst/include/odepack_dlsoda.h → inst/include/odepack_dlsoda.h
diff --git a/rdev/inst/include/odeproblem.h → inst/include/odeproblem.h b/rdev/inst/include/odeproblem.h → inst/include/odeproblem.h
diff --git a/rdev/inst/include/tofunptr.h → inst/include/tofunptr.h b/rdev/inst/include/tofunptr.h → inst/include/tofunptr.h
diff --git a/makescripts/datasets.R → inst/maintenance/datasets.R b/makescripts/datasets.R → inst/maintenance/datasets.R
@@ -68,16 +68,16 @@ data2 <- merge(data,idata[,c("ID","CL", "VC", "KA")], by="ID", sort=FALSE, all.x
 #head(data2)
 
 exidata <- idata
-save(exidata,file="rdev/data/exidata.RData")
+save(exidata,file="data/exidata.RData")
 
 extran1 <- doses
-save(extran1, file="rdev/data/extran1.RData")
+save(extran1, file="data/extran1.RData")
 
 extran2 <- data
-save(extran2, file="rdev/data/extran2.RData")
+save(extran2, file="data/extran2.RData")
 
 extran3 <- data2
-save(extran3,file="rdev/data/extran3.RData")
+save(extran3,file="data/extran3.RData")
 
 data(Theoph)
 dd <- as.data.frame(Theoph)
@@ -90,7 +90,7 @@ dd$cmt[dd$evid==1] <- 1
 dd$conc[dd$time==0] <- 0
 
 exTheoph <- dd
-save(exTheoph, file="rdev/data/exTheoph.RData")
+save(exTheoph, file="data/exTheoph.RData")
 
 
 library(MASS)
@@ -113,7 +113,7 @@ names(pars) <- gsub("SG", "SIGMA", names(pars))
 pars$run <- 1:nrow(pars)
 pars <- shuffle(pars, "run")
 exBoot <- pars
-save(exBoot, file="rdev/data/exBoot.RData")
+save(exBoot, file="data/exBoot.RData")
 
 
 

diff --git a/makescripts/doc_mrgsolve.R → inst/maintenance/doc_mrgsolve.R b/makescripts/doc_mrgsolve.R → inst/maintenance/doc_mrgsolve.R
@@ -3,7 +3,7 @@ message("\n\nwriting documentation ... \n")
 library(methods)
 library(devtools)
 
-pkg <- file.path("rdev")
+pkg <- file.path(".")
 ## message("\nwriting header files for nullmodel and housemodel\n")
 r <- file.path(pkg,"R")
 src <- file.path(pkg,"src")
@@ -16,7 +16,7 @@ x2 <- file.copy(file.path(inc,"mrgsolv.h"),file.path(inst,"base", "mrgsolv.h"),o
 stopifnot(all(c(x1,x2)))
 
 
-document(pkg)
+document()
 
 ## I think mrgsolve functions available after doc
 foo <- mrgsolve:::as_pack_mod("housemodel",proj, "mrgsolve")

diff --git a/makescripts/staticdocs.R → inst/maintenance/staticdocs.R b/makescripts/staticdocs.R → inst/maintenance/staticdocs.R
diff --git a/makescripts/tests.R → inst/maintenance/tests.R b/makescripts/tests.R → inst/maintenance/tests.R
diff --git a/rdev/inst/models/MODLIST → inst/models/MODLIST b/rdev/inst/models/MODLIST → inst/models/MODLIST
diff --git a/rdev/inst/models/effect.cpp → inst/models/effect.cpp b/rdev/inst/models/effect.cpp → inst/models/effect.cpp
diff --git a/rdev/inst/models/emax.cpp → inst/models/emax.cpp b/rdev/inst/models/emax.cpp → inst/models/emax.cpp
diff --git a/rdev/inst/models/firstmodel.cpp → inst/models/firstmodel.cpp b/rdev/inst/models/firstmodel.cpp → inst/models/firstmodel.cpp
diff --git a/rdev/inst/models/firstmodelExample.cpp → inst/models/firstmodelExample.cpp b/rdev/inst/models/firstmodelExample.cpp → inst/models/firstmodelExample.cpp
diff --git a/rdev/inst/models/irm1.cpp → inst/models/irm1.cpp b/rdev/inst/models/irm1.cpp → inst/models/irm1.cpp
diff --git a/rdev/inst/models/irm2.cpp → inst/models/irm2.cpp b/rdev/inst/models/irm2.cpp → inst/models/irm2.cpp
diff --git a/rdev/inst/models/irm3.cpp → inst/models/irm3.cpp b/rdev/inst/models/irm3.cpp → inst/models/irm3.cpp
diff --git a/rdev/inst/models/irm4.cpp → inst/models/irm4.cpp b/rdev/inst/models/irm4.cpp → inst/models/irm4.cpp
diff --git a/rdev/inst/models/modpk1.cpp → inst/models/modpk1.cpp b/rdev/inst/models/modpk1.cpp → inst/models/modpk1.cpp
diff --git a/rdev/inst/models/modpk1po.cpp → inst/models/modpk1po.cpp b/rdev/inst/models/modpk1po.cpp → inst/models/modpk1po.cpp
diff --git a/rdev/inst/models/modpk2.cpp → inst/models/modpk2.cpp b/rdev/inst/models/modpk2.cpp → inst/models/modpk2.cpp
diff --git a/rdev/inst/models/modpk2po.cpp → inst/models/modpk2po.cpp b/rdev/inst/models/modpk2po.cpp → inst/models/modpk2po.cpp
diff --git a/rdev/inst/models/pk1.cpp → inst/models/pk1.cpp b/rdev/inst/models/pk1.cpp → inst/models/pk1.cpp
diff --git a/rdev/inst/models/pk1cmt.cpp → inst/models/pk1cmt.cpp b/rdev/inst/models/pk1cmt.cpp → inst/models/pk1cmt.cpp
diff --git a/rdev/inst/models/pk1cmt_pop.cpp → inst/models/pk1cmt_pop.cpp b/rdev/inst/models/pk1cmt_pop.cpp → inst/models/pk1cmt_pop.cpp
diff --git a/rdev/inst/models/pk2.cpp → inst/models/pk2.cpp b/rdev/inst/models/pk2.cpp → inst/models/pk2.cpp
diff --git a/rdev/inst/models/pk2cmt.cpp → inst/models/pk2cmt.cpp b/rdev/inst/models/pk2cmt.cpp → inst/models/pk2cmt.cpp
diff --git a/rdev/inst/models/pk3cmt.cpp → inst/models/pk3cmt.cpp b/rdev/inst/models/pk3cmt.cpp → inst/models/pk3cmt.cpp
diff --git a/rdev/inst/models/pkExample.cpp → inst/models/pkExample.cpp b/rdev/inst/models/pkExample.cpp → inst/models/pkExample.cpp
diff --git a/rdev/inst/models/pkpdExample.cpp → inst/models/pkpdExample.cpp b/rdev/inst/models/pkpdExample.cpp → inst/models/pkpdExample.cpp
diff --git a/rdev/inst/models/popExample.cpp → inst/models/popExample.cpp b/rdev/inst/models/popExample.cpp → inst/models/popExample.cpp
diff --git a/rdev/inst/models/tmdd.cpp → inst/models/tmdd.cpp b/rdev/inst/models/tmdd.cpp → inst/models/tmdd.cpp
diff --git a/rdev/inst/models/viral1.cpp → inst/models/viral1.cpp b/rdev/inst/models/viral1.cpp → inst/models/viral1.cpp
diff --git a/rdev/inst/models/viral2.cpp → inst/models/viral2.cpp b/rdev/inst/models/viral2.cpp → inst/models/viral2.cpp
diff --git a/rdev/inst/models/viralExample.cpp → inst/models/viralExample.cpp b/rdev/inst/models/viralExample.cpp → inst/models/viralExample.cpp
diff --git a/rdev/inst/mrgx/mrgx.h → inst/mrgx/mrgx.h b/rdev/inst/mrgx/mrgx.h → inst/mrgx/mrgx.h
diff --git a/rdev/inst/mrgx/simeta.h → inst/mrgx/simeta.h b/rdev/inst/mrgx/simeta.h → inst/mrgx/simeta.h
diff --git a/rdev/inst/nonmem/1005/1005.cat → inst/nonmem/1005/1005.cat b/rdev/inst/nonmem/1005/1005.cat → inst/nonmem/1005/1005.cat
diff --git a/rdev/inst/nonmem/1005/1005.coi → inst/nonmem/1005/1005.coi b/rdev/inst/nonmem/1005/1005.coi → inst/nonmem/1005/1005.coi
diff --git a/rdev/inst/nonmem/1005/1005.cor → inst/nonmem/1005/1005.cor b/rdev/inst/nonmem/1005/1005.cor → inst/nonmem/1005/1005.cor
diff --git a/rdev/inst/nonmem/1005/1005.cov → inst/nonmem/1005/1005.cov b/rdev/inst/nonmem/1005/1005.cov → inst/nonmem/1005/1005.cov
diff --git a/rdev/inst/nonmem/1005/1005.cpu → inst/nonmem/1005/1005.cpu b/rdev/inst/nonmem/1005/1005.cpu → inst/nonmem/1005/1005.cpu
diff --git a/rdev/inst/nonmem/1005/1005.ctl → inst/nonmem/1005/1005.ctl b/rdev/inst/nonmem/1005/1005.ctl → inst/nonmem/1005/1005.ctl
diff --git a/rdev/inst/nonmem/1005/1005.ext → inst/nonmem/1005/1005.ext b/rdev/inst/nonmem/1005/1005.ext → inst/nonmem/1005/1005.ext
diff --git a/rdev/inst/nonmem/1005/1005.grd → inst/nonmem/1005/1005.grd b/rdev/inst/nonmem/1005/1005.grd → inst/nonmem/1005/1005.grd
diff --git a/rdev/inst/nonmem/1005/1005.lst → inst/nonmem/1005/1005.lst b/rdev/inst/nonmem/1005/1005.lst → inst/nonmem/1005/1005.lst
diff --git a/rdev/inst/nonmem/1005/1005.phi → inst/nonmem/1005/1005.phi b/rdev/inst/nonmem/1005/1005.phi → inst/nonmem/1005/1005.phi
diff --git a/rdev/inst/nonmem/1005/1005.shk → inst/nonmem/1005/1005.shk b/rdev/inst/nonmem/1005/1005.shk → inst/nonmem/1005/1005.shk
diff --git a/rdev/inst/nonmem/1005/1005.shm → inst/nonmem/1005/1005.shm b/rdev/inst/nonmem/1005/1005.shm → inst/nonmem/1005/1005.shm
diff --git a/rdev/inst/nonmem/1005/1005.tab → inst/nonmem/1005/1005.tab b/rdev/inst/nonmem/1005/1005.tab → inst/nonmem/1005/1005.tab
diff --git a/rdev/inst/nonmem/1005/1005.xml → inst/nonmem/1005/1005.xml b/rdev/inst/nonmem/1005/1005.xml → inst/nonmem/1005/1005.xml
diff --git a/rdev/inst/nonmem/1005/1005par.tab → inst/nonmem/1005/1005par.tab b/rdev/inst/nonmem/1005/1005par.tab → inst/nonmem/1005/1005par.tab
diff --git a/rdev/inst/nonmem/1005/INTER → inst/nonmem/1005/INTER b/rdev/inst/nonmem/1005/INTER → inst/nonmem/1005/INTER
diff --git a/inst/project/housemodel.RDS b/inst/project/housemodel.RDS
diff --git a/rdev/inst/project/housemodel.cpp → inst/project/housemodel.cpp b/rdev/inst/project/housemodel.cpp → inst/project/housemodel.cpp
diff --git a/rdev/man/CAPTURE.Rd → man/CAPTURE.Rd b/rdev/man/CAPTURE.Rd → man/CAPTURE.Rd
diff --git a/rdev/man/PKMODEL.Rd → man/PKMODEL.Rd b/rdev/man/PKMODEL.Rd → man/PKMODEL.Rd
diff --git a/rdev/man/Req.Rd → man/Req.Rd b/rdev/man/Req.Rd → man/Req.Rd
diff --git a/rdev/man/aboutsolver.Rd → man/aboutsolver.Rd b/rdev/man/aboutsolver.Rd → man/aboutsolver.Rd
diff --git a/rdev/man/as.list_mrgmod.Rd → man/as.list_mrgmod.Rd b/rdev/man/as.list_mrgmod.Rd → man/as.list_mrgmod.Rd
diff --git a/rdev/man/as_bmat.Rd → man/as_bmat.Rd b/rdev/man/as_bmat.Rd → man/as_bmat.Rd
diff --git a/rdev/man/as_data_set.Rd → man/as_data_set.Rd b/rdev/man/as_data_set.Rd → man/as_data_set.Rd
diff --git a/rdev/man/assign_ev.Rd → man/assign_ev.Rd b/rdev/man/assign_ev.Rd → man/assign_ev.Rd
diff --git a/rdev/man/blocks.Rd → man/blocks.Rd b/rdev/man/blocks.Rd → man/blocks.Rd
diff --git a/rdev/man/bmat.Rd → man/bmat.Rd b/rdev/man/bmat.Rd → man/bmat.Rd
diff --git a/rdev/man/carry.out.Rd → man/carry.out.Rd b/rdev/man/carry.out.Rd → man/carry.out.Rd
diff --git a/rdev/man/carry_out.Rd → man/carry_out.Rd b/rdev/man/carry_out.Rd → man/carry_out.Rd
diff --git a/rdev/man/chain.Rd → man/chain.Rd b/rdev/man/chain.Rd → man/chain.Rd
diff --git a/rdev/man/cmt_list-class.Rd → man/cmt_list-class.Rd b/rdev/man/cmt_list-class.Rd → man/cmt_list-class.Rd
diff --git a/rdev/man/cmtn.Rd → man/cmtn.Rd b/rdev/man/cmtn.Rd → man/cmtn.Rd
diff --git a/rdev/man/code.Rd → man/code.Rd b/rdev/man/code.Rd → man/code.Rd
diff --git a/rdev/man/cvec.Rd → man/cvec.Rd b/rdev/man/cvec.Rd → man/cvec.Rd
diff --git a/rdev/man/data_set.Rd → man/data_set.Rd b/rdev/man/data_set.Rd → man/data_set.Rd
diff --git a/rdev/man/design.Rd → man/design.Rd b/rdev/man/design.Rd → man/design.Rd
diff --git a/rdev/man/details.Rd → man/details.Rd b/rdev/man/details.Rd → man/details.Rd
diff --git a/rdev/man/ev-class.Rd → man/ev-class.Rd b/rdev/man/ev-class.Rd → man/ev-class.Rd
diff --git a/rdev/man/ev_ops.Rd → man/ev_ops.Rd b/rdev/man/ev_ops.Rd → man/ev_ops.Rd
diff --git a/rdev/man/events.Rd → man/events.Rd b/rdev/man/events.Rd → man/events.Rd
diff --git a/rdev/man/exdatasets.Rd → man/exdatasets.Rd b/rdev/man/exdatasets.Rd → man/exdatasets.Rd
diff --git a/rdev/man/expand.idata.Rd → man/expand.idata.Rd b/rdev/man/expand.idata.Rd → man/expand.idata.Rd
diff --git a/rdev/man/file_show.Rd → man/file_show.Rd b/rdev/man/file_show.Rd → man/file_show.Rd
diff --git a/rdev/man/handle_CMT.Rd → man/handle_CMT.Rd b/rdev/man/handle_CMT.Rd → man/handle_CMT.Rd
diff --git a/rdev/man/handle_FIXED.Rd → man/handle_FIXED.Rd b/rdev/man/handle_FIXED.Rd → man/handle_FIXED.Rd
diff --git a/rdev/man/handle_INIT.Rd → man/handle_INIT.Rd b/rdev/man/handle_INIT.Rd → man/handle_INIT.Rd
diff --git a/rdev/man/handle_PARAM.Rd → man/handle_PARAM.Rd b/rdev/man/handle_PARAM.Rd → man/handle_PARAM.Rd
diff --git a/rdev/man/handle_THETA.Rd → man/handle_THETA.Rd b/rdev/man/handle_THETA.Rd → man/handle_THETA.Rd
diff --git a/rdev/man/house.Rd → man/house.Rd b/rdev/man/house.Rd → man/house.Rd
diff --git a/rdev/man/idata_set.Rd → man/idata_set.Rd b/rdev/man/idata_set.Rd → man/idata_set.Rd
diff --git a/rdev/man/init.Rd → man/init.Rd b/rdev/man/init.Rd → man/init.Rd
diff --git a/rdev/man/is.mrgmod.Rd → man/is.mrgmod.Rd b/rdev/man/is.mrgmod.Rd → man/is.mrgmod.Rd
diff --git a/rdev/man/is.mrgsims.Rd → man/is.mrgsims.Rd b/rdev/man/is.mrgsims.Rd → man/is.mrgsims.Rd
diff --git a/rdev/man/knobs.Rd → man/knobs.Rd b/rdev/man/knobs.Rd → man/knobs.Rd
diff --git a/rdev/man/lctran.Rd → man/lctran.Rd b/rdev/man/lctran.Rd → man/lctran.Rd
diff --git a/rdev/man/loadso.Rd → man/loadso.Rd b/rdev/man/loadso.Rd → man/loadso.Rd
diff --git a/rdev/man/lower2matrix.Rd → man/lower2matrix.Rd b/rdev/man/lower2matrix.Rd → man/lower2matrix.Rd
diff --git a/rdev/man/matlist-class.Rd → man/matlist-class.Rd b/rdev/man/matlist-class.Rd → man/matlist-class.Rd
diff --git a/rdev/man/matlist.Rd → man/matlist.Rd b/rdev/man/matlist.Rd → man/matlist.Rd
diff --git a/rdev/man/matlist_ops.Rd → man/matlist_ops.Rd b/rdev/man/matlist_ops.Rd → man/matlist_ops.Rd
diff --git a/rdev/man/mcRNG.Rd → man/mcRNG.Rd b/rdev/man/mcRNG.Rd → man/mcRNG.Rd
diff --git a/rdev/man/mcode.Rd → man/mcode.Rd b/rdev/man/mcode.Rd → man/mcode.Rd
diff --git a/rdev/man/merge.Rd → man/merge.Rd b/rdev/man/merge.Rd → man/merge.Rd
diff --git a/rdev/man/mod.Rd → man/mod.Rd b/rdev/man/mod.Rd → man/mod.Rd
diff --git a/rdev/man/modMATRIX.Rd → man/modMATRIX.Rd b/rdev/man/modMATRIX.Rd → man/modMATRIX.Rd
diff --git a/rdev/man/modelparse.Rd → man/modelparse.Rd b/rdev/man/modelparse.Rd → man/modelparse.Rd
diff --git a/rdev/man/modlib.Rd → man/modlib.Rd b/rdev/man/modlib.Rd → man/modlib.Rd
diff --git a/rdev/man/modlib_details.Rd → man/modlib_details.Rd b/rdev/man/modlib_details.Rd → man/modlib_details.Rd
diff --git a/rdev/man/modlib_pk.Rd → man/modlib_pk.Rd b/rdev/man/modlib_pk.Rd → man/modlib_pk.Rd
diff --git a/rdev/man/modlib_pkpd.Rd → man/modlib_pkpd.Rd b/rdev/man/modlib_pkpd.Rd → man/modlib_pkpd.Rd
diff --git a/rdev/man/modlib_tmdd.Rd → man/modlib_tmdd.Rd b/rdev/man/modlib_tmdd.Rd → man/modlib_tmdd.Rd
diff --git a/rdev/man/modlib_viral.Rd → man/modlib_viral.Rd b/rdev/man/modlib_viral.Rd → man/modlib_viral.Rd
diff --git a/rdev/man/modlist-class.Rd → man/modlist-class.Rd b/rdev/man/modlist-class.Rd → man/modlist-class.Rd
diff --git a/rdev/man/modlist.Rd → man/modlist.Rd b/rdev/man/modlist.Rd → man/modlist.Rd
diff --git a/rdev/man/mread.Rd → man/mread.Rd b/rdev/man/mread.Rd → man/mread.Rd
diff --git a/rdev/man/mrgindata.Rd → man/mrgindata.Rd b/rdev/man/mrgindata.Rd → man/mrgindata.Rd
diff --git a/rdev/man/mrgmod-class.Rd → man/mrgmod-class.Rd b/rdev/man/mrgmod-class.Rd → man/mrgmod-class.Rd
diff --git a/rdev/man/mrgsim.Rd → man/mrgsim.Rd b/rdev/man/mrgsim.Rd → man/mrgsim.Rd
diff --git a/rdev/man/mrgsims-class.Rd → man/mrgsims-class.Rd b/rdev/man/mrgsims-class.Rd → man/mrgsims-class.Rd
diff --git a/rdev/man/mrgsims.Rd → man/mrgsims.Rd b/rdev/man/mrgsims.Rd → man/mrgsims.Rd
diff --git a/rdev/man/mrgsims_dplyr.Rd → man/mrgsims_dplyr.Rd b/rdev/man/mrgsims_dplyr.Rd → man/mrgsims_dplyr.Rd
diff --git a/rdev/man/mrgsolve_example.Rd → man/mrgsolve_example.Rd b/rdev/man/mrgsolve_example.Rd → man/mrgsolve_example.Rd
diff --git a/rdev/man/mrgsolve_package.Rd → man/mrgsolve_package.Rd b/rdev/man/mrgsolve_package.Rd → man/mrgsolve_package.Rd
diff --git a/rdev/man/mrgsolve_template.Rd → man/mrgsolve_template.Rd b/rdev/man/mrgsolve_template.Rd → man/mrgsolve_template.Rd
diff --git a/rdev/man/mvgauss.Rd → man/mvgauss.Rd b/rdev/man/mvgauss.Rd → man/mvgauss.Rd
diff --git a/rdev/man/nmxml.Rd → man/nmxml.Rd b/rdev/man/nmxml.Rd → man/nmxml.Rd
diff --git a/rdev/man/numeric2diag.Rd → man/numeric2diag.Rd b/rdev/man/numeric2diag.Rd → man/numeric2diag.Rd
diff --git a/rdev/man/numericlist-class.Rd → man/numericlist-class.Rd b/rdev/man/numericlist-class.Rd → man/numericlist-class.Rd
diff --git a/rdev/man/numericlist.Rd → man/numericlist.Rd b/rdev/man/numericlist.Rd → man/numericlist.Rd
diff --git a/rdev/man/obsaug.Rd → man/obsaug.Rd b/rdev/man/obsaug.Rd → man/obsaug.Rd
diff --git a/rdev/man/obsonly.Rd → man/obsonly.Rd b/rdev/man/obsonly.Rd → man/obsonly.Rd
diff --git a/rdev/man/omega.Rd → man/omega.Rd b/rdev/man/omega.Rd → man/omega.Rd
diff --git a/rdev/man/param.Rd → man/param.Rd b/rdev/man/param.Rd → man/param.Rd
diff --git a/rdev/man/parameter_list-class.Rd → man/parameter_list-class.Rd b/rdev/man/parameter_list-class.Rd → man/parameter_list-class.Rd
diff --git a/rdev/man/pk_model.Rd → man/pk_model.Rd b/rdev/man/pk_model.Rd → man/pk_model.Rd
diff --git a/rdev/man/plot_batch_mrgsims.Rd → man/plot_batch_mrgsims.Rd b/rdev/man/plot_batch_mrgsims.Rd → man/plot_batch_mrgsims.Rd
diff --git a/rdev/man/plot_mrgsims.Rd → man/plot_mrgsims.Rd b/rdev/man/plot_mrgsims.Rd → man/plot_mrgsims.Rd
diff --git a/rdev/man/psim.Rd → man/psim.Rd b/rdev/man/psim.Rd → man/psim.Rd
diff --git a/rdev/man/qsim.Rd → man/qsim.Rd b/rdev/man/qsim.Rd → man/qsim.Rd
diff --git a/rdev/man/recmatrix.Rd → man/recmatrix.Rd b/rdev/man/recmatrix.Rd → man/recmatrix.Rd
diff --git a/rdev/man/relocate.Rd → man/relocate.Rd b/rdev/man/relocate.Rd → man/relocate.Rd
diff --git a/rdev/man/rename_cols.Rd → man/rename_cols.Rd b/rdev/man/rename_cols.Rd → man/rename_cols.Rd
diff --git a/rdev/man/render.Rd → man/render.Rd b/rdev/man/render.Rd → man/render.Rd
diff --git a/rdev/man/reserved.Rd → man/reserved.Rd b/rdev/man/reserved.Rd → man/reserved.Rd
diff --git a/rdev/man/revar.Rd → man/revar.Rd b/rdev/man/revar.Rd → man/revar.Rd
diff --git a/rdev/man/scrape_and_call.Rd → man/scrape_and_call.Rd b/rdev/man/scrape_and_call.Rd → man/scrape_and_call.Rd
diff --git a/rdev/man/scrape_opts.Rd → man/scrape_opts.Rd b/rdev/man/scrape_opts.Rd → man/scrape_opts.Rd
diff --git a/rdev/man/see.Rd → man/see.Rd b/rdev/man/see.Rd → man/see.Rd
diff --git a/rdev/man/show-modlist-method.Rd → man/show-modlist-method.Rd b/rdev/man/show-modlist-method.Rd → man/show-modlist-method.Rd
diff --git a/rdev/man/show-mrgmod-method.Rd → man/show-mrgmod-method.Rd b/rdev/man/show-mrgmod-method.Rd → man/show-mrgmod-method.Rd
diff --git a/rdev/man/sigma.Rd → man/sigma.Rd b/rdev/man/sigma.Rd → man/sigma.Rd
diff --git a/rdev/man/simargs.Rd → man/simargs.Rd b/rdev/man/simargs.Rd → man/simargs.Rd
diff --git a/rdev/man/soloc.Rd → man/soloc.Rd b/rdev/man/soloc.Rd → man/soloc.Rd
diff --git a/rdev/man/stime.Rd → man/stime.Rd b/rdev/man/stime.Rd → man/stime.Rd
diff --git a/rdev/man/tgrid.Rd → man/tgrid.Rd b/rdev/man/tgrid.Rd → man/tgrid.Rd
diff --git a/rdev/man/tgrid_ops.Rd → man/tgrid_ops.Rd b/rdev/man/tgrid_ops.Rd → man/tgrid_ops.Rd
diff --git a/rdev/man/touch_funs.Rd → man/touch_funs.Rd b/rdev/man/touch_funs.Rd → man/touch_funs.Rd
diff --git a/rdev/man/tscale.Rd → man/tscale.Rd b/rdev/man/tscale.Rd → man/tscale.Rd
diff --git a/rdev/man/update.Rd → man/update.Rd b/rdev/man/update.Rd → man/update.Rd
diff --git a/rdev/man/zchain.Rd → man/zchain.Rd b/rdev/man/zchain.Rd → man/zchain.Rd
diff --git a/rdev/inst/project/housemodel.RDS b/rdev/inst/project/housemodel.RDS
diff --git a/rdev/src/Makevars → src/Makevars b/rdev/src/Makevars → src/Makevars
diff --git a/rdev/src/Makevars.win → src/Makevars.win b/rdev/src/Makevars.win → src/Makevars.win
diff --git a/rdev/src/RcppExports.cpp → src/RcppExports.cpp b/rdev/src/RcppExports.cpp → src/RcppExports.cpp
diff --git a/rdev/src/dataobject.cpp → src/dataobject.cpp b/rdev/src/dataobject.cpp → src/dataobject.cpp
diff --git a/rdev/src/datarecord.cpp → src/datarecord.cpp b/rdev/src/datarecord.cpp → src/datarecord.cpp
diff --git a/rdev/src/devtran.cpp → src/devtran.cpp b/rdev/src/devtran.cpp → src/devtran.cpp
diff --git a/rdev/src/housemodel-mread-source.cpp → src/housemodel-mread-source.cpp b/rdev/src/housemodel-mread-source.cpp → src/housemodel-mread-source.cpp
diff --git a/rdev/src/mrgsolve.cpp → src/mrgsolve.cpp b/rdev/src/mrgsolve.cpp → src/mrgsolve.cpp
diff --git a/rdev/src/odepack_dlsoda.cpp → src/odepack_dlsoda.cpp b/rdev/src/odepack_dlsoda.cpp → src/odepack_dlsoda.cpp
diff --git a/rdev/src/odeproblem.cpp → src/odeproblem.cpp b/rdev/src/odeproblem.cpp → src/odeproblem.cpp
diff --git a/rdev/src/opk_dlsoda_mrg.f → src/opk_dlsoda_mrg.f b/rdev/src/opk_dlsoda_mrg.f → src/opk_dlsoda_mrg.f
diff --git a/rdev/src/opkda1_mrg.f → src/opkda1_mrg.f b/rdev/src/opkda1_mrg.f → src/opkda1_mrg.f
diff --git a/rdev/src/opkda2_mrg.f → src/opkda2_mrg.f b/rdev/src/opkda2_mrg.f → src/opkda2_mrg.f
diff --git a/rdev/src/quick.cpp → src/quick.cpp b/rdev/src/quick.cpp → src/quick.cpp
diff --git a/rdev/src/tofunptr.c → src/tofunptr.c b/rdev/src/tofunptr.c → src/tofunptr.c
diff --git a/rdev/tests/testthat.R → tests/testthat.R b/rdev/tests/testthat.R → tests/testthat.R
diff --git a/rdev/tests/testthat/test-D-R-F.R → tests/testthat/test-D-R-F.R b/rdev/tests/testthat/test-D-R-F.R → tests/testthat/test-D-R-F.R
diff --git a/rdev/tests/testthat/test-alag.R → tests/testthat/test-alag.R b/rdev/tests/testthat/test-alag.R → tests/testthat/test-alag.R
diff --git a/rdev/tests/testthat/test-annot.R → tests/testthat/test-annot.R b/rdev/tests/testthat/test-annot.R → tests/testthat/test-annot.R
diff --git a/rdev/tests/testthat/test-bioav.R → tests/testthat/test-bioav.R b/rdev/tests/testthat/test-bioav.R → tests/testthat/test-bioav.R
diff --git a/rdev/tests/testthat/test-cache.R → tests/testthat/test-cache.R b/rdev/tests/testthat/test-cache.R → tests/testthat/test-cache.R
diff --git a/rdev/tests/testthat/test-carry-out.R → tests/testthat/test-carry-out.R b/rdev/tests/testthat/test-carry-out.R → tests/testthat/test-carry-out.R
diff --git a/rdev/tests/testthat/test-carry_out.R → tests/testthat/test-carry_out.R b/rdev/tests/testthat/test-carry_out.R → tests/testthat/test-carry_out.R
diff --git a/rdev/tests/testthat/test-data_set.R → tests/testthat/test-data_set.R b/rdev/tests/testthat/test-data_set.R → tests/testthat/test-data_set.R
diff --git a/rdev/tests/testthat/test-dplyr-generics.R → tests/testthat/test-dplyr-generics.R b/rdev/tests/testthat/test-dplyr-generics.R → tests/testthat/test-dplyr-generics.R
diff --git a/rdev/tests/testthat/test-env.R → tests/testthat/test-env.R b/rdev/tests/testthat/test-env.R → tests/testthat/test-env.R
diff --git a/rdev/tests/testthat/test-error.R → tests/testthat/test-error.R b/rdev/tests/testthat/test-error.R → tests/testthat/test-error.R
diff --git a/rdev/tests/testthat/test-fixed-cmtn.R → tests/testthat/test-fixed-cmtn.R b/rdev/tests/testthat/test-fixed-cmtn.R → tests/testthat/test-fixed-cmtn.R
diff --git a/rdev/tests/testthat/test-infusion.R → tests/testthat/test-infusion.R b/rdev/tests/testthat/test-infusion.R → tests/testthat/test-infusion.R
diff --git a/rdev/tests/testthat/test-initials.R → tests/testthat/test-initials.R b/rdev/tests/testthat/test-initials.R → tests/testthat/test-initials.R
diff --git a/rdev/tests/testthat/test-iv-po.R → tests/testthat/test-iv-po.R b/rdev/tests/testthat/test-iv-po.R → tests/testthat/test-iv-po.R
diff --git a/rdev/tests/testthat/test-knobs.R → tests/testthat/test-knobs.R b/rdev/tests/testthat/test-knobs.R → tests/testthat/test-knobs.R
diff --git a/rdev/tests/testthat/test-matlist.R → tests/testthat/test-matlist.R b/rdev/tests/testthat/test-matlist.R → tests/testthat/test-matlist.R
diff --git a/rdev/tests/testthat/test-matrix.R → tests/testthat/test-matrix.R b/rdev/tests/testthat/test-matrix.R → tests/testthat/test-matrix.R
diff --git a/rdev/tests/testthat/test-modlib.R → tests/testthat/test-modlib.R b/rdev/tests/testthat/test-modlib.R → tests/testthat/test-modlib.R
diff --git a/rdev/tests/testthat/test-modspec.R → tests/testthat/test-modspec.R b/rdev/tests/testthat/test-modspec.R → tests/testthat/test-modspec.R
diff --git a/rdev/tests/testthat/test-mread.R → tests/testthat/test-mread.R b/rdev/tests/testthat/test-mread.R → tests/testthat/test-mread.R
diff --git a/rdev/tests/testthat/test-mrgindata.R → tests/testthat/test-mrgindata.R b/rdev/tests/testthat/test-mrgindata.R → tests/testthat/test-mrgindata.R
diff --git a/rdev/tests/testthat/test-nmxml.R → tests/testthat/test-nmxml.R b/rdev/tests/testthat/test-nmxml.R → tests/testthat/test-nmxml.R
diff --git a/rdev/tests/testthat/test-obsonly-obsaug.R → tests/testthat/test-obsonly-obsaug.R b/rdev/tests/testthat/test-obsonly-obsaug.R → tests/testthat/test-obsonly-obsaug.R
diff --git a/rdev/tests/testthat/test-opts.R → tests/testthat/test-opts.R b/rdev/tests/testthat/test-opts.R → tests/testthat/test-opts.R
diff --git a/rdev/tests/testthat/test-pkmodel.R → tests/testthat/test-pkmodel.R b/rdev/tests/testthat/test-pkmodel.R → tests/testthat/test-pkmodel.R
diff --git a/rdev/tests/testthat/test-plot.R → tests/testthat/test-plot.R b/rdev/tests/testthat/test-plot.R → tests/testthat/test-plot.R
diff --git a/rdev/tests/testthat/test-plugin.R → tests/testthat/test-plugin.R b/rdev/tests/testthat/test-plugin.R → tests/testthat/test-plugin.R
diff --git a/rdev/tests/testthat/test-records.R → tests/testthat/test-records.R b/rdev/tests/testthat/test-records.R → tests/testthat/test-records.R
diff --git a/rdev/tests/testthat/test-rename.R → tests/testthat/test-rename.R b/rdev/tests/testthat/test-rename.R → tests/testthat/test-rename.R
diff --git a/rdev/tests/testthat/test-request.R → tests/testthat/test-request.R b/rdev/tests/testthat/test-request.R → tests/testthat/test-request.R
diff --git a/rdev/tests/testthat/test-rng.R → tests/testthat/test-rng.R b/rdev/tests/testthat/test-rng.R → tests/testthat/test-rng.R
diff --git a/rdev/tests/testthat/test-update.R → tests/testthat/test-update.R b/rdev/tests/testthat/test-update.R → tests/testthat/test-update.R
diff --git a/rdev/tests/testthat/test-utils.R → tests/testthat/test-utils.R b/rdev/tests/testthat/test-utils.R → tests/testthat/test-utils.R
diff --git a/rdev/tests/testthat/test-z-alag-f.R → tests/testthat/test-z-alag-f.R b/rdev/tests/testthat/test-z-alag-f.R → tests/testthat/test-z-alag-f.R