rebuild docs with new roxygen; add doxyfile

marianklose · Dec 14, 2019 · 6575805 · 6575805
1 parent ee637ed
commit 6575805
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Showing 59 changed files with 267 additions and 133 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,4 @@
+Doxygen
 DOCS
 mrgsolve.Rcheck
 .DS_store

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -92,4 +92,4 @@ Collate:
     'render.R'
     'update.R'
     'workflows.R'
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
diff --git a/Makefile b/Makefile
@@ -134,4 +134,7 @@ check-win:
 check-winhub:
 	Rscript -e 'rhub::check_on_windows()'
 
+.PHONY: doxygen
+doxygen: 
+	doxygen doxyfile
 
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(.DollarNames,mrgmod)
+S3method(.DollarNames,mrgsims)
 S3method(Req,mrgmod)
 S3method(all,equal.mrgmod)
 S3method(as.data.frame,ev)
@@ -250,6 +252,7 @@ importFrom(stats,setNames)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
 importFrom(tidyselect,vars_select)
+importFrom(utils,.DollarNames)
 importFrom(utils,assignInMyNamespace)
 importFrom(utils,capture.output)
 importFrom(utils,example)

diff --git a/R/Aaaa.R b/R/Aaaa.R
@@ -19,6 +19,7 @@
 ##' 
 ##' @importFrom utils capture.output example str type.convert 
 ##' @importFrom utils packageVersion assignInMyNamespace read.table
+##' @importFrom utils .DollarNames
 ##' @importFrom stats as.formula setNames rnorm
 ##' @importFrom dplyr filter 
 ##' @importFrom dplyr mutate slice as.tbl pull

diff --git a/R/class_mrgmod.R b/R/class_mrgmod.R
@@ -726,3 +726,8 @@ all.equal.mrgmod <- function(target, current,...) {
   t2 <- identical(target.env, current.env)
   all(t1,t2)
 }
+
+#' @export
+.DollarNames.mrgmod <- function(x, pattern){
+  grep(pattern, names(param(x)), value=TRUE)
+}
diff --git a/R/class_mrgsims.R b/R/class_mrgsims.R
@@ -69,4 +69,7 @@ setMethod("as.list", "mrgsims", function(x, ...) {
   structure(out, class = "mrgsims_list")
 })
 
-
+#' @export
+.DollarNames.mrgsims <- function(x, pattern){
+  grep(pattern, names(x), value=TRUE)
+}
diff --git a/doxyfile b/doxyfile
@@ -0,0 +1,11 @@
+PROJECT_NAME = mrgsolve
+DOXYFILE_ENCODING      = UTF-8
+OUTPUT_DIRECTORY = Doxygen
+INPUT =  src/ inst/include inst/base
+FILE_PATTERNS = *.c *.cpp *.h
+FULL_PATH_NAMES = YES
+TAB_SIZE = 8
+EXTRACT_ALL = YES
+EXTRACT_PRIVATE = YES
+WARN_IF_UNDOCUMENTED = YES
+INPUT_ENCODING = UTF-8
diff --git a/man/BLOCK_PARSE.Rd b/man/BLOCK_PARSE.Rd
diff --git a/man/PKMODEL.Rd b/man/PKMODEL.Rd
diff --git a/man/as.ev.Rd b/man/as.ev.Rd
diff --git a/man/as.list-mrgmod-method.Rd b/man/as.list-mrgmod-method.Rd
diff --git a/man/as.list-mrgsims-method.Rd b/man/as.list-mrgsims-method.Rd
diff --git a/man/as_data_set.Rd b/man/as_data_set.Rd
diff --git a/man/blocks.Rd b/man/blocks.Rd
diff --git a/man/cmtn.Rd b/man/cmtn.Rd
diff --git a/man/data_set.Rd b/man/data_set.Rd
diff --git a/man/ev.Rd b/man/ev.Rd
diff --git a/man/ev_days.Rd b/man/ev_days.Rd
diff --git a/man/ev_extract.Rd b/man/ev_extract.Rd
diff --git a/man/ev_methods.Rd b/man/ev_methods.Rd
diff --git a/man/ev_rx.Rd b/man/ev_rx.Rd
diff --git a/man/idata_set.Rd b/man/idata_set.Rd
diff --git a/man/init.Rd b/man/init.Rd
diff --git a/man/knobs.Rd b/man/knobs.Rd
diff --git a/man/matlist.Rd b/man/matlist.Rd
diff --git a/man/matlist_ops.Rd b/man/matlist_ops.Rd
diff --git a/man/matrix_converters.Rd b/man/matrix_converters.Rd
diff --git a/man/mcode.Rd b/man/mcode.Rd
diff --git a/man/merge.Rd b/man/merge.Rd