Merge pull request #813 from metrumresearchgroup/cran/0.11.0

Cran/0.11.0

.Rbuildignore

@@ -11,16 +11,11 @@ inst/validation
 cran-comments.md
 Rchecks
 mrgsolve\.Rcheck
-.github
-inst/doc
+\.github
 Doxyfile
 doxydoc
 ^.*\.Rproj$
 ^\.Rproj\.user$
-vignettes/.*[.]toc$
-vignettes/.*[.]log$
-vignettes/.*[.]o$
-vignettes/.*[.]so$
 tests/.*[.]o$
 tests/.*[.]so$
 tests/testthat/.*[.]o$
@@ -48,7 +43,16 @@ _config.yml
 Makefile
 docs
 ^DOCS$
-^build$
+^./build$
 ^_pkgdown\.yml$
 ^\.drone\.yml$
 ^\.drone\.jsonnet$
+^doc$
+^Meta$
+vignettes
+vignettes/extra
+vignettes/build
+vignettes/mrgsolve-builds
+vignettes/extra/mrgsolve-builds/
+
+

.gitignore

@@ -15,3 +15,8 @@ Rchecks
 !package/*.tar.gz
 *00_pkg_src
 inst/maintenance/unit/tests.md
+doc
+Meta
+inst/maintenance/unit/mrgsolve-so*
+vignettes/mrgsolve-builds
+vignettes/extra/mrgsolve-builds/

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: mrgsolve
 Title: Simulate from ODE-Based Models
-Version: 0.10.9
+Version: 0.11.0
 Authors@R: 
     c(person(given = "Kyle T", family = "Baron",
              role = c("aut", "cre"),
@@ -21,6 +21,9 @@ Authors@R:
       person(given = "Felicien", family = "Le Louedec",
              comment = c(ORCID = "0000-0003-3699-2729"),
              role = "ctb"),
+      person(given = "Timothy", family = "Waterhouse",
+             comment = c(ORCID = "0000-0002-0954-9660"),
+             role = "ctb"),
       person(given = "Metrum Research Group",
              role = "cph"))
 Maintainer: Kyle T Baron <[email protected]>

Makefile

@@ -1,5 +1,4 @@
 SHELL := /bin/bash
-LIBDIR=${HOME}/Rlibs/lib
 PACKAGE=mrgsolve
 VERSION=$(shell grep Version DESCRIPTION |awk '{print $$2}')
 TARBALL=${PACKAGE}_${VERSION}.tar.gz
@@ -13,12 +12,36 @@ all:
 	make build
 	make install
 
-drone:
+bump-dev:
+	Rscript -e 'usethis::use_version("dev")'
+
+tag-version:
+	git tag $(VERSION)
+	git push origin $(VERSION)
+
+package:
 	make house
-	R CMD build --md5 $(PKGDIR) 
-	R CMD check --as-cran ${TARBALL}
+	make doc
+	make build
+	make install
+	make pkgdown
+
+check:
+	make house
+	make doc
+	make build
+	R CMD check ${TARBALL} --no-manual
+	make unit
+
+check-only:
+	R CMD check --as-cran ${TARBALL} 
+
+cran:
+	make house
+	make doc
+	make build
 	export _MRGSOLVE_SKIP_MODLIB_BUILD_=false
-	Rscript -e '$(LOAD_CANDIDATE); $(TEST_UNIT)'
+	R CMD CHECK --as-cran ${TARBALL}
 
 spelling:
 	Rscript -e 'spelling::spell_check_package(".")'
@@ -36,33 +59,21 @@ no-test:
 	make build
 	R CMD check ${TARBALL} --no-tests --no-manual
 
-everything:
-	make all
-	make pkgdown
-
 pkgdown:
 	Rscript "inst/maintenance/pkgdown.R"
-	cp -r DOCS/ ../../mrgsolve/docs/
-	touch ../../mrgsolve/docs/.nojekyll
+	#cp -r DOCS/ ../mrgsolve/docs/
+	#touch ../mrgsolve/docs/.nojekyll
 
 unit:
 	Rscript -e 'testthat::test_dir("inst/maintenance/unit")'
 
-cran:
-	make house
-	make doc
-	make build
-	export _MRGSOLVE_SKIP_MODLIB_BUILD_=false
-	R CMD CHECK --as-cran ${TARBALL}
-
 readme:
 	Rscript -e 'rmarkdown::render("README.Rmd")'
 
 .PHONY: doc
 doc:
 	Rscript -e "roxygen2::roxygenize()"
 
-.PHONY: build
 build:
 	R CMD build --md5 $(PKGDIR) --no-manual
 
@@ -72,24 +83,6 @@ install:
 install-build:
 	R CMD INSTALL --build --install-tests ${TARBALL}
 
-check:
-	make house
-	make doc
-	make build
-	R CMD check ${TARBALL} --no-manual
-	make unit
-
-qcheck: 
-	make doc
-	make build 
-	R CMD check ${TARBALL} --no-manual --no-codoc
-
-check-cran:
-	make house
-	make doc
-	make build
-	R CMD check --as-cran ${TARBALL}
-
 test:
 	R CMD INSTALL ${PKGDIR}
 	make test-all
@@ -126,15 +119,10 @@ check-winhub:
 doxygen: 
 	doxygen doxyfile
 
-bump-dev:
-	Rscript -e 'usethis::use_version("dev")'
-
-tag-version:
-	git tag $(VERSION)
-	git push origin $(VERSION)
-
-testing:
-	cp ${TARBALL} ${MRGSOLVE_TEST_LOC}
-	touch ${MRGSOLVE_TEST_LOC}/${TARBALL}
-	cp -r inst/maintenance/unit ${MRGSOLVE_TEST_LOC}
-	cd ${MRGSOLVE_TEST_LOC} && git commit -am "testing release" && git push -u origin master
+# possibly no longer in use
+drone:
+	make house
+	R CMD build --md5 $(PKGDIR) 
+	R CMD check --as-cran ${TARBALL}
+	export _MRGSOLVE_SKIP_MODLIB_BUILD_=false
+	Rscript -e '$(LOAD_CANDIDATE); $(TEST_UNIT)'

NEWS.md

@@ -1,3 +1,16 @@
+# mrgsolve 0.11.0
+
+- The absolute paths to nonmem output files (`root.xml` or `root.ext`) are now 
+  saved in the model object when nonmem results are imported via `$NMEXT` or 
+  `$NMXML`; paths are accessible by coercing the model object with `as.list()`
+  and looking at the `nm_import` item (#802)
+- Add Tim Waterhouse as contributor (#809)
+- Add `root` argument to `$NMEXT` and `$NMXML` so that the nonmem output files
+  are located relative to the `working` directory (default, previous behavior)
+  or the directory where the `cppfile` is stored; `cppfile` will eventually 
+  replace `working` as the default (#803)
+- Models based on `$PRED` now respect the `obsonly` option (#811)
+
 # mrgsolve 0.10.9
 
 - Dosing into a compartment that is off at the time of the dose turns the 

R/class_mrgmod.R

@@ -467,6 +467,8 @@ setMethod("names", "mrgmod", function(x) {
 #' - `random`: names and labels of `$OMEGA` and `$SIGMA`
 #' - `code`: model source code from `cfile`
 #' - `details`: model details data frame
+#' - `nm_import`: a character vector listing the names of nonmem output files
+#'   that were read to import estimates from a completed nonmem run
 #' - `cpp_variables`: a data frame listing variables internal to the model 
 #'   cpp file
 #' - `atol`: see [solversettings]
@@ -513,7 +515,8 @@ setMethod("as.list", "mrgmod", function(x, deep = FALSE, ...) {
       advan <- x@advan
       functions <- funset(x)
     }
-    cpp_variables <- x@shlib[["cpp_variables"]]
+    cpp_variables <- shlib(x)[["cpp_variables"]]
+    nm_import <- shlib(x)[["nm_import"]]
     details <- x@annot
     code <- x@code
     random <- names(x)[c("omega", "sigma", "omega_labels", "sigma_labels")]
@@ -537,15 +540,13 @@ setMethod("as.list", "mrgmod", function(x, deep = FALSE, ...) {
     init <- as.list(init(x))
     param <- as.list(param(x))
     cmt <- cmt(x)
-
-    covariates <- as.character(x@shlib$covariates)
+    covariates <- as.character(shlib(x)[["covariates"]])
     pars <- pars(x)
     neq <- neq(x)
     npar <- npar(x)
   })
 })
 
-
 #' Select parameter values from a model object
 #' 
 #' The \code{$} and \code{[[} operators get the value 

R/handle_spec_block.R

@@ -509,18 +509,16 @@ handle_spec_block.specTABLE <- function(x, env, ...) {
 
 # NMXML --------------------------------
 #' @export
-handle_spec_block.specNMXML <- function(x, ...) {
-  parseNMXML(dump_opts(x), ...)
-}
-
-## Functions for handling code blocks
-parseNMXML <- function(x, env, ...) {
-  pos <- attr(x,"pos")
+handle_spec_block.specNMXML <- function(x, env, ...) {
+  x <- dump_opts(x)
+  pos <- attr(x, "pos")
   x <- tolist(x, envir = env$ENV)
+  x$env <- env
   xml <- do.call(nmxml, x)
   env[["param"]][[pos]] <- xml$theta
   env[["omega"]][[pos]] <- xml$omega
   env[["sigma"]][[pos]] <- xml$sigma
+  env[["nm_import"]] <- c(env[["nm_import"]], xml[["file"]])
   return(NULL)
 }
 
@@ -530,10 +528,12 @@ handle_spec_block.specNMEXT <- function(x, env, ...) {
   x <- dump_opts(x)
   pos <- attr(x, "pos")
   x <- tolist(x, envir = env$ENV)
+  x$env <- env
   ext <- do.call(nmext, x)
   env[["param"]][[pos]] <- ext$theta
   env[["omega"]][[pos]] <- ext$omega
   env[["sigma"]][[pos]] <- ext$sigma
+  env[["nm_import"]] <- c(env[["nm_import"]], ext[["file"]])
   return(NULL)
 }
 

R/matlist.R

@@ -55,7 +55,7 @@
 ##' $OMEGA
 ##' 1 2 3
 ##'
-##' $OMEGA @block
+##' $OMEGA \@block
 ##' 1 0.1 2
 ##'
 ##' $OMEGA \@cor

R/modspec.R

@@ -589,17 +589,18 @@ parse_env <- function(spec, incoming_names = names(spec),project,ENV=new.env())
   n <- length(spec)
   mread.env <- new.env()
   mread.env$project <- project
-  mread.env$param <- vector("list",n)
-  mread.env$fixed <- vector("list",n)
-  mread.env$init  <- vector("list",n)
-  mread.env$omega <- vector("list",n)
-  mread.env$sigma <- vector("list",n)
-  mread.env$annot <- vector("list",n)
+  mread.env$param <- vector("list", n)
+  mread.env$fixed <- vector("list", n)
+  mread.env$init  <- vector("list", n)
+  mread.env$omega <- vector("list", n)
+  mread.env$sigma <- vector("list", n)
+  mread.env$annot <- vector("list", n)
   mread.env$ode   <- vector("list", n)
   mread.env$namespace <- vector("list", n)
-  mread.env$capture <- vector("list",n)
+  mread.env$capture <- vector("list", n)
   mread.env$error <- character(0)
   mread.env$covariates <- character(0)
+  mread.env$nm_import <- character(0)
   mread.env$ENV <- ENV 
   mread.env$blocks <- names(spec)
   mread.env$incoming_names <- incoming_names

R/mread.R

@@ -411,6 +411,7 @@ mread <- function(model, project = getOption("mrgsolve.project", getwd()),
   inc <- spec[["INCLUDE"]]
   if(is.null(inc)) inc <- character(0)
   x@shlib[["include"]] <- inc
+  x@shlib[["nm_import"]] <- mread.env[["nm_import"]]
   x@shlib[["source"]] <- file.path(build$soloc,build$compfile)
   x@shlib[["md5"]] <- build[["md5"]]