Merge pull request #635 from metrumresearchgroup/release/0.10.1

Release/0.10.1

.Rbuildignore

@@ -1,3 +1,5 @@
+Doxygen
+doxyfile
 man/figures/README-.*\.png$
 README.html
 DOCS/

.gitignore

@@ -1,3 +1,4 @@
+Doxygen
 DOCS
 mrgsolve.Rcheck
 .DS_store
@@ -11,3 +12,4 @@ Rchecks
 *.tar.gz
 !package/*.tar.gz
 *00_pkg_src
+inst/maintenance/unit/tests.md

DESCRIPTION

@@ -1,22 +1,39 @@
-Package: mrgsolve
 Type: Package
-Version: 0.10.0
+Package: mrgsolve
 Title: Simulate from ODE-Based Models
-Authors@R: c(
-    person("Kyle T", "Baron", email = "kyleb@metrumrg.com", role=c("aut", "cre"), comment=c(ORCID="0000-0001-7252-5656")),
-    person("Bill", "Gillespie", role = "ctb"),
-    person("Charles", "Margossian", role = "ctb"),
-    person("Devin", "Pastoor", role = "ctb"),
-    person("Bill", "Denney", role = "ctb", comment=c(ORCID="0000-0002-5759-428X")),
-    person("Dilawar", "Singh", role = "ctb"), 
-    person("Metrum Research Group", role = "cph")
-    )
-Maintainer: Kyle T Baron  <kyleb@metrumrg.com>
-URL: https://github.com/metrumresearchgroup/mrgsolve
-BugReports: https://github.com/metrumresearchgroup/mrgsolve/issues
-Description: Fast simulation from ordinary differential equation (ODE) based 
-    models typically employed in quantitative pharmacology and systems biology.  
+Version: 0.10.1
+Authors@R: 
+    c(person(given = "Kyle T",
+             family = "Baron",
+             role = c("aut", "cre"),
+             email = "kyleb@metrumrg.com",
+             comment = c(ORCID = "0000-0001-7252-5656")),
+      person(given = "Bill",
+             family = "Gillespie",
+             role = "ctb"),
+      person(given = "Charles",
+             family = "Margossian",
+             role = "ctb"),
+      person(given = "Devin",
+             family = "Pastoor",
+             role = "ctb"),
+      person(given = "Bill",
+             family = "Denney",
+             role = "ctb",
+             comment = c(ORCID = "0000-0002-5759-428X")),
+      person(given = "Dilawar",
+             family = "Singh",
+             role = "ctb"),
+      person(given = "Metrum Research Group",
+             role = "cph"))
+Maintainer: Kyle T Baron <kyleb@metrumrg.com>
+Description: Fast simulation from ordinary differential equation
+    (ODE) based models typically employed in quantitative pharmacology and
+    systems biology.
 License: GPL (>=2)
+URL: https://github.com/metrumresearchgroup/mrgsolve
+BugReports: 
+    https://github.com/metrumresearchgroup/mrgsolve/issues
 Depends:
     R (>= 3.1.2),
     methods
@@ -26,23 +43,28 @@ Imports:
     magrittr (>= 1.5),
     RcppArmadillo (>= 0.7.900.2.0),
     tibble (>= 2.1.1),
-    rlang (>= 0.3.4), 
-    tidyselect (>= 0.2.5)
-LinkingTo: 
-    Rcpp (>= 0.12.12), 
-    RcppArmadillo (>= 0.7.900.2.0), 
-    BH (>= 1.62.0-1)
+    rlang (>= 0.3.4),
+    tidyselect (>= 0.2.5),
+    lifecycle, 
+    glue
 Suggests:
     lattice,
     testthat,
     xml2 (>= 1.2.0),
-    rmarkdown, 
-    yaml, 
+    rmarkdown,
+    yaml,
     knitr
-LazyLoad: yes
-NeedsCompilation: yes
+LinkingTo: 
+    Rcpp (>= 0.12.12),
+    RcppArmadillo (>= 0.7.900.2.0),
+    BH (>= 1.62.0-1)
+RdMacros: 
+    lifecycle
 Encoding: UTF-8
 Language: en-US
+LazyLoad: yes
+NeedsCompilation: yes
+RoxygenNote: 7.0.2
 SystemRequirements: C++11
 Collate: 
     'RcppExports.R'
@@ -92,4 +114,3 @@ Collate:
     'render.R'
     'update.R'
     'workflows.R'
-RoxygenNote: 6.1.1

Makefile

@@ -71,7 +71,7 @@ doc:
 	Rscript inst/maintenance/doc_mrgsolve.R
 
 build:
-	R CMD build --md5 $(PKGDIR)
+	R CMD build --md5 $(PKGDIR) --no-manual
 
 install:
 	R CMD INSTALL --install-tests ${TARBALL} -l ~/Rlibs
@@ -83,7 +83,7 @@ check:
 	make house
 	make doc
 	make build
-	R CMD check ${TARBALL} -o ${CHKDIR}
+	R CMD check ${TARBALL} -o ${CHKDIR} --no-manual
 	make unit
 
 qcheck: 
@@ -134,4 +134,7 @@ check-win:
 check-winhub:
 	Rscript -e 'rhub::check_on_windows()'
 
+.PHONY: doxygen
+doxygen: 
+	doxygen doxyfile
 

NAMESPACE

@@ -1,8 +1,11 @@
 # 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)
+S3method(as.environment,mrgmod)
 S3method(as.matrix,ev)
 S3method(as.tbl,mrgsims)
 S3method(as_tibble,mrgsims)
@@ -59,6 +62,7 @@ S3method(summarise,each)
 S3method(summarise,mrgsims)
 S3method(summary,mrgmod)
 S3method(summary,mrgsims)
+S3method(within,mrgmod)
 export("%>%")
 export("%then%")
 export(Req)
@@ -104,6 +108,7 @@ export(expand_observations)
 export(file_show)
 export(filter)
 export(filter_sims)
+export(house)
 export(idata_set)
 export(init)
 export(inventory)
@@ -137,6 +142,7 @@ export(numerics_only)
 export(obsaug)
 export(obsonly)
 export(omat)
+export(outvars)
 export(parse_rx)
 export(plot_sims)
 export(qsim)
@@ -146,6 +152,7 @@ export(req)
 export(revar)
 export(s_)
 export(see)
+export(select_sims)
 export(simargs)
 export(smat)
 export(soloc)
@@ -235,11 +242,14 @@ importFrom(dplyr,summarise)
 importFrom(dplyr,summarise_at)
 importFrom(dplyr,summarise_each)
 importFrom(dplyr,ungroup)
+importFrom(glue,glue)
+importFrom(lifecycle,deprecate_soft)
 importFrom(magrittr,"%>%")
 importFrom(magrittr,"%T>%")
 importFrom(rlang,"!!!")
 importFrom(rlang,"!!")
 importFrom(rlang,enquo)
+importFrom(rlang,enquos)
 importFrom(rlang,eval_tidy)
 importFrom(rlang,quo_name)
 importFrom(rlang,quos)
@@ -250,6 +260,7 @@ 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)

NEWS.md

@@ -1,3 +1,26 @@
+# mrgsolve 0.10.1
+
+- Add `select_sims` method for selecting columns in `mrgsims` object #585
+- Fix bug where system was improperly advanced on steady state dosing record 
+  with a lag time when the system failed to reach steady state #596
+- Add better compartment level control for advancing system to steady state #598
+- Allow user to set `CXX_FLAGS` in `$ENV` block #603
+- Add `N_CMT` plugin so that the number (index) of every compartment is available
+  by name (e.g. `N_CENT` for the number index of the central compartment) #606
+- Fix bug where `blocks()` failed when the model was defined in `Rmd` file #608
+- Call ODE block every time the system tries to advance so that variables 
+  calculated in ODE are properly calculated in output #613
+- Add `within` method for mrgmod #616
+- Access initial compartment values and other model object items with `$` 
+  operator for `mrgmod` #620
+- Add plot method for signature `c("mrgsims", "character")`; pass in a character
+  vector of outputs to plot #630
+- The house model, previously accessible by `mrgsolve:::house()` is now an 
+  exported function #625
+- Exporting outvars function to extract names of current output variables from
+  the model object
+- Now importing lifecycle and glue packages
+
 # mrgsolve 0.10.0
 
 - Remove `qsim` and all associated functions

R/Aaaa.R

@@ -1,4 +1,4 @@
-# Copyright (C) 2013 - 2019  Metrum Research Group
+# Copyright (C) 2013 - 2020  Metrum Research Group
 #
 # This file is part of mrgsolve.
 #
@@ -15,43 +15,46 @@
 # You should have received a copy of the GNU General Public License
 # along with mrgsolve.  If not, see <http://www.gnu.org/licenses/>.
 
-##' @import methods
-##' 
-##' @importFrom utils capture.output example str type.convert 
-##' @importFrom utils packageVersion assignInMyNamespace read.table
-##' @importFrom stats as.formula setNames rnorm
-##' @importFrom dplyr filter 
-##' @importFrom dplyr mutate slice as.tbl pull
-##' @importFrom dplyr bind_rows arrange summarise summarise_at
-##' @importFrom dplyr intersect select rename slice distinct do
-##' @importFrom dplyr distinct first select_vars_ 
-##' @importFrom dplyr select_vars everything 
-##' @importFrom dplyr if_else mutate_at summarise_each is.tbl select
-##' @importFrom dplyr mutate_all group_by ungroup n
-##' @importFrom dplyr data_frame as_data_frame
-##' @importFrom tidyselect vars_select
-##' @importFrom magrittr %>% %T>%
-##' @importFrom Rcpp evalCpp
-##' @importFrom RcppArmadillo armadillo_version
-##' @importFrom tibble tibble as_tibble
-##' @importFrom rlang quos enquo quo_name syms !!! !! eval_tidy
-##' 
-##' @include Aaaa.R
-##' @include class_mrgsims.R
-##' @include class_mrgmod.R
-##' @include class_derived.R
-##' @include class_ev.R
-##' @include class_matlist.R
-##' @include class_numericlist.R
-##' @include class_tgrid.R  
-##' @include generics.R
-##' @include package.R
-##' @include utils.R 
-##' @include RcppExports.R  
-##' 
+#' @import methods
+#' 
+#' @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
+#' @importFrom dplyr bind_rows arrange summarise summarise_at
+#' @importFrom dplyr intersect select rename slice distinct do
+#' @importFrom dplyr distinct first select_vars_ 
+#' @importFrom dplyr select_vars everything 
+#' @importFrom dplyr if_else mutate_at summarise_each is.tbl select
+#' @importFrom dplyr mutate_all group_by ungroup n
+#' @importFrom dplyr data_frame as_data_frame
+#' @importFrom tidyselect vars_select
+#' @importFrom magrittr %>% %T>%
+#' @importFrom Rcpp evalCpp
+#' @importFrom RcppArmadillo armadillo_version
+#' @importFrom tibble tibble as_tibble
+#' @importFrom rlang quos enquo enquos quo_name syms !!! !! eval_tidy
+#' @importFrom lifecycle deprecate_soft
+#' @importFrom glue glue
+#' 
+#' @include Aaaa.R
+#' @include class_mrgsims.R
+#' @include class_mrgmod.R
+#' @include class_derived.R
+#' @include class_ev.R
+#' @include class_matlist.R
+#' @include class_numericlist.R
+#' @include class_tgrid.R  
+#' @include generics.R
+#' @include package.R
+#' @include utils.R 
+#' @include RcppExports.R  
+#' 
 NULL
 
-##' @export
+#' @export
 dplyr::filter
 
 GLOBALS <- new.env()

R/annot.R

@@ -47,12 +47,16 @@ parse_annot_line <- function(x, novalue=FALSE, noname=FALSE,context="not given")
   x <- mytriml(x)
 
   if(nchar(x)==0) return(NULL)
-
+  
   col <- charcount(x,":")[1]
 
   if(col != (2-noname-novalue)) {
-    stop("improper annotation format ", x,"\n", 
-         "  Context: ", context, call.=FALSE) 
+    stop(
+      "improper annotation format\n",
+      " input: ", x, "\n",
+      " context: ", context, 
+      call.=FALSE
+    ) 
   }
 
   ## Fix up line if not name : value : other
@@ -100,7 +104,7 @@ parse_annot_line <- function(x, novalue=FALSE, noname=FALSE,context="not given")
 ##' with \code{mrgsolve:::details()}. 
 ##' 
 ##' @examples
-##' mod <- mrgsolve:::house()
+##' mod <- mrgsolve::house()
 ##' 
 ##' mrgsolve:::details(mod)
 ##' 

R/chain.R

@@ -39,7 +39,7 @@
 ##' strictly for compartments.
 ##' 
 ##' @examples
-##' mod <- mrgsolve:::house()
+##' mod <- mrgsolve::house()
 ##'
 ##' mod %>% Req(CP,RESP) %>% ev(amt=1000) %>%  mrgsim
 ##'
@@ -108,7 +108,7 @@ carry.out <- function(x,...) {
 ##' 
 ##' @examples
 ##' # The model is in hours:
-##' mod <- mrgsolve:::house()
+##' mod <- mrgsolve::house()
 ##' 
 ##' # The output is in days:
 ##' mod %>% tscale(1/24) %>% mrgsim
@@ -187,7 +187,7 @@ obsaug <- function(x,value=TRUE,...) {
 ##' 
 ##' idata <- data[,c("ID", "amt")]
 ##' 
-##' mod <- mrgsolve:::house()
+##' mod <- mrgsolve::house()
 ##' 
 ##' mod %>%
 ##'   omat(dmat(1,1,1,1)) %>%