Merge pull request #16 from jamesdunham/0.2.9

Release 0.2.9

.Rbuildignore

@@ -1,20 +1,18 @@
-^.*\.Rproj$
 ^.*\.Rdata$
-^.*\.png$
+^.*\.Rproj$
+^.*tar.gz$
+^Makefile$
 ^README.Rmd$
-^README_cache$
-^README/$
+^README/
 ^\.DS_Store$
+^\.Rproj\.user$
 ^\.travis\.yml$
-^packrat/
+^appveyor\.yml$
+^codecov\.yml$
+^cran-comments\.md$
 ^data-ext/
 ^docs/
-^wercker\.yml$
+^packrat/
+^readme-cache/
 ^setup.r$
-^Makefile$
-^.*tar.gz$
-^\.Rproj\.user$
-^codecov\.yml$
-^appveyor\.yml$
-^cran-comments\.md$
-
+^wercker\.yml$

.gitignore

@@ -1,5 +1,6 @@
 .Rproj.user
-README_cache/
+dgo.Rcheck/
+*.tar.gz
+readme-cache
 src/*.o
 src/*.so
-src/include/models.hpp.bak

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: dgo
 Title: Dynamic Estimation of Group-Level Opinion
-Version: 0.2.8
-Date: 2017-01-31
-Description: Fit dynamic group-level IRT models from individual or aggregated
-    item response data. This package handles common preprocessing tasks and extends
-    functions for inspecting results, poststratification, and quick iteration over
-    alternative models. Under active development.
+Version: 0.2.9
+Date: 2017-05-21
+Description: Fit dynamic group-level IRT and MRP models from individual or
+    aggregated item response data. This package handles common preprocessing
+    tasks and extends functions for inspecting results, poststratification, and
+    quick iteration over alternative models.
 Maintainer: James Dunham <[email protected]>
 Authors@R: c(
     person("James", "Dunham", email = "[email protected]", role = c("aut", "cre")),
@@ -18,29 +18,24 @@ BugReports: https://github.com/jamesdunham/dgo/issues
 Depends:
     dgodata,
     R (>= 3.2.2),
-    Rcpp (>= 0.11.0),
-    rstan (>= 2.8.1)
+    rstan (>= 2.15.1)
 LazyData: true
 Imports:
     assertthat,
-    concatenate,
     data.table,
     ggplot2,
     lubridate,
     methods,
     R6,
+    Rcpp (>= 0.12.10),
     survey
 Suggests:
     knitr,
     rmarkdown,
     testthat
-LinkingTo: StanHeaders (>= 2.8.0), rstan (>= 2.8.1), BH (>= 1.58.0), Rcpp (>=
-    0.11.0), RcppEigen
-RcppModules: stan_fit42016_09_14_mod, stan_fit42016_04_20_mod,
-    stan_fit42015_12_16_mod, stan_fit42017_01_04_singleissue_mod,
-    stan_fit42017_01_04_mod
+LinkingTo: Rcpp (>= 0.12.10)
 NeedsCompilation: yes
-Collate:
+Collate: 
     'RcppExports.R'
     'aggregate_item_responses.r'
     'assertions.r'
@@ -51,25 +46,22 @@ Collate:
     'class-dgirtin.r'
     'class-dgmrp_fit.r'
     'dgirt.r'
-    'dgmrp.r'
     'dichotomize_item_responses.r'
     'expand_rownames.r'
     'methods-control.r'
     'methods-dgirtfit-plot.r'
     'methods-dgirtfit-poststratify.r'
     'methods-dgirtfit.r'
-    'require_namespace.r'
     'methods-dgirtin.r'
     'name_helpers.r'
     'package.R'
     'rake_partial.r'
     'restrict_input_data.r'
     'reweight_item_responses.r'
     'shape.r'
-    'stanmodels.R'
+    'shape_hierarchical.r'
     'toy_dgirt_in.r'
     'toy_dgirtfit.r'
     'validate_dgirtIn.r'
     'validate_input_data.r'
-    'zzz.R'
 RoxygenNote: 6.0.1

Makefile

@@ -1,39 +1,53 @@
-# Makefile for development use
-
+PKG := $(shell head -1 DESCRIPTION | sed 's/Package: //' | cat)
 VERSION := $(shell sed -n 3p DESCRIPTION | sed 's/Version: //' | cat)
-BINARY := dgo_$(VERSION).tar.gz
+BINARY := $(PKG)_$(VERSION).tar.gz
+MAKEFILE_PATH := $(abspath $(lastword $(MAKEFILE_LIST)))
+CURRENT_DIR := $(notdir $(patsubst %/,%,$(dir $(MAKEFILE_PATH))))
+R_ARGS := --no-site-file --no-environ --no-save \
+	  --no-restore --no-resave-data --no-manual --quiet
+ifneq (, $(findstring r-devel,$(CURRENT_DIR)))
+  R := R_devel.sh
+else
+  R := R
+endif
+
+all: clean build check install readme 
+
+quick: clean 
 
-all: build check install readme doc
+clean:
+	@rm -rf src/*.so src/*.o *tar.gz *Rcheck*
 
 build: 
-	R --no-site-file --no-environ  \
-	  --no-save --no-restore --quiet CMD build .  \
-	  --no-resave-data --no-manual
+	$(R) $(R_ARGS) CMD build .  
 
+build-cran:
+	$(R) CMD build . --no-resave-data --no-manual
+
 check: 
-	R CMD check dgo_$(VERSION).tar.gz
+	$(R) CMD check $(PKG)_$(VERSION).tar.gz
 
 check-cran: 
-	R CMD check --as-cran dgo_$(VERSION).tar.gz
+	$(R) CMD check --as-cran $(PKG)_$(VERSION).tar.gz
 
-install: dgo_$(VERSION).tar.gz
-	R CMD INSTALL --no-multiarch --with-keep.source dgo_$(VERSION).tar.gz
+check-quick $(PKG)_$(VERSION).tar.gz:
+	$(R) $(R_ARGS) CMD build . 
+	$(R) CMD check $(PKG)_$(VERSION).tar.gz
+
+install: $(PKG)_$(VERSION).tar.gz
+	$(R) CMD INSTALL --no-multiarch --with-keep.source \
+	  $(PKG)_$(VERSION).tar.gz
 
 install-code:
-	R CMD INSTALL --no-multiarch --with-keep.source --no-docs .
+	$(R) CMD INSTALL --no-multiarch --with-keep.source --no-docs .
 
-readme: dgo_$(VERSION).tar.gz
-	R --vanilla --slave -e "rmarkdown::render('README.Rmd')"
+install-quick:
+	$(R) CMD INSTALL --no-multiarch --no-docs --no-html \
+	  --with-keep.source .
 
-doc: dgo_$(VERSION).tar.gz
-	R CMD check --no-install --no-tests --no-examples dgo_$(VERSION).tar.gz
+readme: $(PKG)_$(VERSION).tar.gz
+	$(R) --vanilla --slave -e "rmarkdown::render('README.Rmd')"
 
-quick-install:
-	R CMD INSTALL --no-multiarch --no-docs --no-html \
-	  --with-keep.source .
+docs:
+	$(R) --vanilla --slave -e "devtools::document()"
 
-quick-check dgo_$(VERSION).tar.gz:
-	R --no-site-file --no-environ  \
-	  --no-save --no-restore --quiet CMD build .  \
-	  --no-resave-data --no-manual
-	R CMD check dgo_$(VERSION).tar.gz

NAMESPACE

@@ -27,11 +27,6 @@ import(dgodata)
 import(ggplot2)
 import(methods)
 import(rstan)
-importFrom(concatenate,cc)
-importFrom(concatenate,cc_and)
-importFrom(concatenate,cc_or)
-importFrom(concatenate,cn)
-importFrom(concatenate,cn_and)
 importFrom(lubridate,seconds_to_period)
 importFrom(stats,as.formula)
 importFrom(stats,formula)

NEWS.md

@@ -1,3 +1,16 @@
+# 0.2.9
+
+* Switch from compiling Stan models at install time to compiling them at
+  runtime, avoiding an Rcpp module issue.
+* Add `model` argument to `dgirt()` and `dgmrp()` taking for reuse a previously
+  compiled Stan model, as found in the `@stanmodel` slot of a `dgirt_fit`- or
+  `dgmrp_fit`-class object.
+* The `version` argument to `dgirt()` and `dgmrp()` can be used to specify
+  arbitrary `.stan` files on the disk in addition to those included with the
+  package.
+* Argument `by` to `get_n()` and `get_item_n()` methods properly accepts a
+  vector of variable names when combined with `aggregate` arguments.
+
 # 0.2.8
 
 * Improve Stan models for shorter run times

R/class-dgirt_fit.r

@@ -26,9 +26,7 @@
 #' apply(as.array(toy_dgirtfit, pars = 'xi'), 3, mean)
 #'
 #' # access the posterior samples
-#' as.array(toy_dgirtfit, pars = 'theta_bar')
-#' as.data.frame(toy_dgirtfit, pars = 'theta_bar')
-#' extract(toy_dgirtfit, pars = 'theta_bar')
+#' head(as.data.frame(toy_dgirtfit, pars = 'theta_bar'))
 dgirt_fit <- setClass("dgirt_fit", contains = c("dgo_fit"))
 
 #' Class \code{dgirtfit}: a class for fitted models

R/class-dgirtin.r

@@ -9,6 +9,7 @@
 #' @include constants.r
 #' @import R6
 #' @examples
+#' data(toy_dgirt_in)
 #' get_item_names(toy_dgirt_in)
 #' get_n(toy_dgirt_in)
 #' get_n(toy_dgirt_in, by = "year")
@@ -54,4 +55,4 @@ dgirtIn <- R6::R6Class("dgirtIn",
       d_in_list
     }),
   private = list(model_objects = model_objects,
-    shape_objects = shape_objects))
+    shape_objects = shape_objects))

R/constants.r

@@ -4,8 +4,8 @@ model_objects <- c("NNl2", "SSl2", "XX", "ZZ", "ZZ_prior", "G", "Q", "T", "N",
 
 shape_objects <- c("gt_items", "group_grid", "group_grid_t", "group_counts",
                   "item_data", "target_data", "aggregate_data", "modifier_data",
-                  "control", "hier_names", "time_observed", "geo_observed",
-                  "call", "mod_par_names", "unmod_par_names", "pkg_version")
+                  "control", "hier_names", "call", "mod_par_names",
+                  "unmod_par_names", "pkg_version")
 
 dgirt_pars <- c("separate_t", "delta_tbar_prior_mean", "delta_tbar_prior_sd",
                 "innov_sd_delta_scale", "innov_sd_theta_scale", "version",