rename package to dgo

Author: James Dunham

DESCRIPTION

@@ -1,5 +1,5 @@
-Package: dgirt
-Title: Dynamic Group-Level IRT and Small Area Estimation
+Package: dgo
+Title: Dynamic Estimation of Group-level Opinion
 Version: 0.2.7
 Date: 2016-10-12
 Description: Fit dynamic group-level IRT models from individual or aggregated
@@ -13,8 +13,8 @@ Authors@R: c(
     person("Christopher", "Warshaw", email = "cwarshaw@mit.edu", role = c("aut"))
     )
 License: GPL-3
-URL: https://github.com/jamesdunham/dgirt
-BugReports: https://github.com/jamesdunham/dgirt/issues
+URL: https://github.com/jamesdunham/dgo
+BugReports: https://github.com/jamesdunham/dgo/issues
 Depends:
     R (>= 3.2.2),
     Rcpp (>= 0.11.0),
@@ -35,7 +35,8 @@ Suggests:
     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
+RcppModules: stan_fit42016_09_14_mod, stan_fit42016_04_20_mod,
+    stan_fit42015_12_16_mod
 NeedsCompilation: yes
 Collate:
     'RcppExports.R'
@@ -61,6 +62,7 @@ Collate:
     'methods-dgirtfit.r'
     'methods-dgirtin.r'
     'name_helpers.r'
+    'package.R'
     'rake_partial.r'
     'restrict_input_data.r'
     'reweight_item_responses.r'

Makefile

@@ -1,7 +1,7 @@
 # Makefile for development use
 
 VERSION := $(shell sed -n 3p DESCRIPTION | sed 's/Version: //' | cat)
-BINARY := dgirt_$(VERSION).tar.gz
+BINARY := dgo_$(VERSION).tar.gz
 
 all: build check install readme doc
 
@@ -11,29 +11,29 @@ build:
 	  --no-resave-data --no-manual
 
 check: 
-	R CMD CHECK dgirt_$(VERSION).tar.gz
+	R CMD CHECK dgo_$(VERSION).tar.gz
 
 check-cran: 
-	R CMD CHECK --as-cran dgirt_$(VERSION).tar.gz
+	R CMD CHECK --as-cran dgo_$(VERSION).tar.gz
 
-install: dgirt_$(VERSION).tar.gz
-	R CMD INSTALL --no-multiarch --with-keep.source dgirt_$(VERSION).tar.gz
+install: dgo_$(VERSION).tar.gz
+	R CMD INSTALL --no-multiarch --with-keep.source dgo_$(VERSION).tar.gz
 
 install-code:
 	R CMD INSTALL --no-multiarch --with-keep.source --no-docs .
 
-readme: dgirt_$(VERSION).tar.gz
+readme: dgo_$(VERSION).tar.gz
 	R --vanilla --slave -e "rmarkdown::render('README.Rmd')"
 
-doc: dgirt_$(VERSION).tar.gz
-	R CMD CHECK --no-install --no-tests --no-examples dgirt_$(VERSION).tar.gz
+doc: dgo_$(VERSION).tar.gz
+	R CMD CHECK --no-install --no-tests --no-examples dgo_$(VERSION).tar.gz
 
 quick-install:
 	R CMD INSTALL --no-multiarch --no-docs --no-html \
 	  --with-keep.source .
 
-quick-check dgirt_$(VERSION).tar.gz:
+quick-check dgo_$(VERSION).tar.gz:
 	R --no-site-file --no-environ  \
 	  --no-save --no-restore --quiet CMD build .  \
 	  --no-resave-data --no-manual
-	R CMD CHECK dgirt_$(VERSION).tar.gz
+	R CMD CHECK dgo_$(VERSION).tar.gz

NAMESPACE

@@ -1,31 +1,47 @@
-useDynLib(dgirt)
-export(shape)
+# Generated by roxygen2: do not edit by hand
+
+S3method(as.data.frame,dgirtfit)
 export(dgirt)
-export(dgirt_plot)
-export(get_item_names)
-S3method(as.data.frame, dgirtfit)
-exportMethods(poststratify)
-exportMethods(extract)
+export(expand_rownames)
+export(plot_rhats)
+export(shape)
+export(summarize)
+exportMethods(dgirt_plot)
 exportMethods(get_item_n)
 exportMethods(get_item_names)
 exportMethods(get_n)
 exportMethods(get_posterior_mean)
-exportMethods(show)
-exportMethods(rhats)
+exportMethods(plot)
 exportMethods(plot_rhats)
+exportMethods(poststratify)
+exportMethods(rhats)
+exportMethods(show)
 exportMethods(summarize)
-exportMethods(print)
-exportMethods(plot)
 exportMethods(summary)
-import(data.table)
-import(rstan)
-importFrom("concatenate", "cc", "cc_and", "cc_or", "cn", "cn_and") 
 import(R6)
-importFrom(lubridate, "seconds_to_period")
-import(methods)
 import(Rcpp)
+import(data.table)
 import(ggplot2)
-importFrom("stats", "as.formula", "formula", "model.frame",
-    "model.matrix", "na.fail", "na.omit", "quantile", "sd",
-    "setNames", "weighted.mean", "weights")
-importFrom("utils", "capture.output", "type.convert", "packageVersion")
+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)
+importFrom(stats,model.frame)
+importFrom(stats,model.matrix)
+importFrom(stats,na.fail)
+importFrom(stats,na.omit)
+importFrom(stats,quantile)
+importFrom(stats,sd)
+importFrom(stats,setNames)
+importFrom(stats,weighted.mean)
+importFrom(stats,weights)
+importFrom(utils,capture.output)
+importFrom(utils,packageVersion)
+importFrom(utils,type.convert)
+useDynLib(dgo)

NEWS.md

@@ -1,4 +1,18 @@
-# dgirt 0.2.5
+# 0.2.7
+
+* Package renamed dgo: Dynamic Estimation of Group-level Opinion
+* Tweaks to pass CRAN checks: clean up examples and docs
+* Use roxygen2 for classes, methods, and `NAMESPACE`
+* Fix checks on `P`, `S` related to `group_names` change in 0.2.5
+* Fix Rcpp module issue from 0.2.6 (`Error in .doLoadActions(where, attach)`)
+* Export `expand_rownames()`
+ 
+# 0.2.6
+
+* Fix error in `dgirt_plot`
+* Fix path in `tools/make_cpp.R`
+
+# 0.2.5
 
 * `group_names` is no longer required. If omitted, the geographic variable given
   by `geo_name` will define groups.

R/RcppExports.R

@@ -1,8 +1,7 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-#' @export
 dichotomize_cpp <- function(response) {
-    .Call('dgirt_dichotomize_cpp', PACKAGE = 'dgirt', response)
+    .Call('dgo_dichotomize_cpp', PACKAGE = 'dgo', response)
 }
 

R/class-dgirtfit.r

@@ -1,21 +1,21 @@
-#' Class \code{dgirtfit}: fitted DGIRT model
+#' Class \code{dgirtfit}: a class for fitted DGIRT modelsf
 #'
-#' All \code{\link{rstan}} methods for superclass
-#' \code{\link[rstan]{stanfit-class}} are available. Descriptive labels for
-#' parameters on time periods, local geographic areas, and grouping variables
-#' will be added to most output.
+#' Fitting a dgirt model results in a \code{dgirtfit} object that inherits from
+#' \code{\link{rstan}}'s \code{\link[rstan]{stanfit-class}}. \code{rstan}
+#' methods will be dispatched (only) if a \code{dgirtfit} method does
+#' not exist.
 #'
 #' @slot dgirt_in \code{\link{dgirtin-class}} data used to fit the model.
 #'
-#' @aliases dgirtfit dgirtfit-class 
+#' @aliases dgirtfit dgirtfit-class
 #' @seealso \code{\link{stanfit-class}} \code{\link{dgirtin-class}}
 #' @rdname dgirtfit-class
 #' @name dgirtfit-class
 #' @examples
 #' data(toy_dgirtfit)
 #' # summarize the fitted results
 #' summary(toy_dgirtfit, pars = 'xi')
-#' 
+#'
 #' # get posterior means with a convenience function
 #' get_posterior_mean(toy_dgirtfit, pars = 'theta_bar')
 #'
@@ -29,6 +29,6 @@
 #' as.data.frame(toy_dgirtfit, pars = 'theta_bar')
 #' extract(toy_dgirtfit, pars = 'theta_bar')
 dgirtfit <- setClass("dgirtfit",
-                     contains = "stanfit",
-                     slots = list(dgirt_in = "ANY",
-                                  call = "language"))
+  contains = "stanfit",
+  slots = list(dgirt_in = "ANY",
+    call = "language"))

R/class-dgirtin.r

@@ -1,13 +1,27 @@
 #' Class \code{dgirtIn}: data prepared for modeling with \code{dgirt}
+#'
+#' \code{shape} generates objects of class \code{dgirtIn} for modeling with
+#' \code{dgirt}.
+#'
+#' @aliases dgirtin-class, get_item_n, get_item_names, get_n, dgirtIn-method,
+#'   print.dgirtIn,
 #' @name dgirtin-class
 #' @include constants.r
+#' @import R6
+#' @examples
+#' get_item_names(toy_dgirt_in)
+#' get_n(toy_dgirt_in)
+#' get_n(toy_dgirt_in, by = "year")
+#' get_n(toy_dgirt_in, by = "source")
+#' get_item_n(toy_dgirt_in)
+#' get_item_n(toy_dgirt_in, by = "year")
 NULL
 
 setOldClass("dgirtIn", "R6")
 dgirtIn <- R6::R6Class("dgirtIn",
   public = c(
     setNames(lapply(c(model_objects, shape_objects), function(x) NULL),
-             c(model_objects, shape_objects)),
+      c(model_objects, shape_objects)),
     initialize = function(ctrl) {
       if (length(ctrl@constant_item)) {
         self$constant_item <- ctrl@constant_item
@@ -16,7 +30,7 @@ dgirtIn <- R6::R6Class("dgirtIn",
       self$unmod_par_names <- ctrl@group_names
     },
     as_list = function(separate_t, delta_tbar_prior_mean, delta_tbar_prior_sd,
-                       innov_sd_delta_scale, innov_sd_theta_scale) {
+      innov_sd_delta_scale, innov_sd_theta_scale) {
       d_in_list <- Map(function(x) self[[x]], private$model_objects)
       if (!length(separate_t) == 1L && is.logical(separate_t))
         stop("\"separate_t\" should be a single logical value")
@@ -37,4 +51,4 @@ dgirtIn <- R6::R6Class("dgirtIn",
       d_in_list
     }),
   private = list(model_objects = model_objects,
-                 shape_objects = shape_objects))
+    shape_objects = shape_objects))

R/dgirt.r

@@ -1,44 +1,42 @@
 #' \code{dgirt}: fit a DGIRT model
 #'
 #' \code{dgirt} makes a call to \code{\link[rstan]{stan}} with the Stan code and
-#' data for a DGIRT model. By default the call overrides the
-#' \code{\link[rstan]{stan}} defaults for \code{pars} to specify typical DGIRT
-#' parameters of interest and sets \code{iter_r} to \code{1L}.
+#' data for a DGIRT model.
 #'
-#' @param shaped_data Output from \code{\link{shape}}.
+#' The user will typically pass further arguments to \code{\link[rstan]{stan}}
+#' via the \code{...} argument, at a minimum \code{iters} and \code{cores}.
+#'
+#' By default \code{dgirt} overrides the \code{\link[rstan]{stan}} default for its
+#' \code{pars} argument to specify typical DGIRT parameters of interest.
+#' \code{dgirt} also sets \code{iter_r} to \code{1L}.
 #'
+#' @param shaped_data Output from \code{\link{shape}}.
 #' @param separate_t Whether smoothing of estimates over time should be
 #' disabled. Default \code{FALSE}.
-#'
 #' @param delta_tbar_prior_mean Prior mean for \code{delta_tbar}, the normal
 #' weight on \code{theta_bar} in the previous period.  Default \code{0.5}.
-#'
 #' @param delta_tbar_prior_sd Prior standard deviation for \code{delta_bar}.
 #' Default \code{0.5}.
-#'
 #' @param innov_sd_delta_scale Prior scale for \code{sd_innov_delta}, the Cauchy
 #' innovation standard deviation of \code{nu_geo} and \code{delta_gamma}.
 #' Default \code{2.5}.
-#'
 #' @param innov_sd_theta_scale Prior scale for \code{sd_innov_theta}, the Cauchy
 #' innovation standard deviation of \code{gamma}, \code{xi}, and if
 #' \code{constant_item} is \code{FALSE} the item difficulty \code{diff}. Default
 #' \code{2.5}.
-#'
 #' @param version The version of the DGIRT model to use.
-#'
 #' @param ... Further arguments passed to \code{\link[rstan]{stan}}.
 #'
 #' @return A \code{\link{dgirtfit-class}} object that extends
 #' \code{\link[rstan]{stanfit-class}}.
-#'
-#' @seealso \code{\link{dgirtfit-class}} \code{\link{shape}}
+#' @seealso \code{dgirt} expects \code{shaped_data} created by
+#'   \code{\link{shape}} and returns an object of class
+#'   \code{\link{dgirtfit-class}}.
+#' \code{\link{dgirtfit-class}} \code{\link{shape}}
 #'
 #' @import rstan
 #' @export
 #' @include constants.r
-#' @examples
-#' dgirt(toy_dgirt_in, iter = 25, chains = 1)
 dgirt <- function(shaped_data, ..., separate_t = FALSE, delta_tbar_prior_mean = 0.5,
                   delta_tbar_prior_sd = 0.5, innov_sd_delta_scale = 2.5,
                   innov_sd_theta_scale = 2.5, version = "2016_09_14") {

R/expand_rownames.r

@@ -8,7 +8,7 @@
 #' by group and time period, or \code{param[t]} for parameters indexed by time
 #' period. \code{expand_rownames} moves this information to columns whose names
 #' are given by the \code{col_names} argument. The rownames in their original
-#' format will appear in another column called \code{rn}. 
+#' format will appear in another column called \code{rn}.
 #'
 #' @param x A table with rownames in the format \code{param[group1__groupK,t]}
 #' or \code{param[t]}.
@@ -22,6 +22,7 @@
 #' @return \code{x} with additional columns (see details).
 #' @seealso \code{\link{dgirtfit-class}}
 #' @include data-toy_dgirtfit.r
+#' @export
 expand_rownames <- function(x, time_name, geo_name, group_names) {
   if (is.matrix(x)) x <- as.data.frame(x, stringsAsFactors = FALSE,
                                        rownames = rownames(x))