doc tweaks

jamesdunham · Oct 29, 2017 · 25dd83f · 25dd83f
2 parents 367ade3 + a07effe
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diff --git a/R/class-dgirt_fit.r b/R/class-dgirt_fit.r
@@ -1,4 +1,4 @@
-#' Class \code{dgirt_fit}: a class for fitted models
+#' A class for fitted dynamic group IRT models
 #'
 #' \code{\link{dgirt}} returns a fitted model object of class \code{dgirt_fit},
 #' which inherits from \code{\link{dgo_fit}}.
@@ -29,7 +29,7 @@
 #' 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
+#' A class for fitted dynamic group IRT models
 #'
 #' dgo 0.2.8 deprecated the \code{dgirtfit} class and replaced it with the
 #' \code{\link{dgirt_fit}} class. 

diff --git a/R/class-dgirtin.r b/R/class-dgirtin.r
@@ -1,7 +1,7 @@
-#' Class \code{dgirtIn}: data prepared for modeling with \code{dgirt}
+#' A class for data ready to model
 #'
-#' \code{shape} generates objects of class \code{dgirtIn} for modeling with
-#' \code{dgirt} and \code{dgmrp}.
+#' \code{shape()} generates objects of class \code{dgirtIn} for modeling with
+#' \code{dgirt()} and \code{dgmrp()}.
 #'
 #' @aliases dgirtin-class, get_item_n, get_item_names, get_n, dgirtIn-method,
 #'   print.dgirtIn,

diff --git a/R/class-dgmrp_fit.r b/R/class-dgmrp_fit.r
@@ -1,4 +1,4 @@
-#' Class \code{dgmrp_fit}: a class for fitted models
+#' A class for fitted dynamic group MRP models
 #'
 #' \code{\link{dgmrp}} returns a fitted model object of class \code{dgmrp_fit},
 #' which inherits from \code{\link{dgo_fit}}.

diff --git a/R/class-dgo_fit.r b/R/class-dgo_fit.r
@@ -1,4 +1,4 @@
-#' Class \code{dgo_fit}: a class for fitted models
+#' A class for fitted models
 #'
 #' \code{dgo_fit} is a superclass for \code{\link{dgirt_fit}} and
 #' \code{\link{dgmrp_fit}} that inherits from the

diff --git a/R/dgirt.r b/R/dgirt.r
@@ -1,4 +1,4 @@
-#' \code{dgirt} and \code{dgmrp}: fit a DGIRT or single-issue MRP model
+#' Fit a dynamic group IRT or single-issue MRP model
 #'
 #' \code{dgirt} and \code{dgmrp} make calls to \code{\link[rstan]{stan}} with
 #' the Stan code and data for their respective models.
@@ -34,7 +34,7 @@
 #' @param hierarchical_model Whether a hierarchical model should be used to
 #' smooth the group IRT estimates. If set to FALSE, the model will return raw
 #' group-IRT model estimates for each group. Default \code{TRUE}.
-#' @param model A Stan model object of class `stanmodel` to be used in
+#' @param model A Stan model object of class \code{stanmodel} to be used in
 #' estimation. Specifying this argument avoids repeated model compilation. Note
 #' that the Stan model object for a model fitted with \code{dgirt()} or
 #' \code{dgmrp()} can be found in the the \code{stanmodel} slot of the resulting

diff --git a/R/methods-dgirtfit-plot.r b/R/methods-dgirtfit-plot.r
@@ -4,7 +4,10 @@ utils::globalVariables(c("facet_vars"))
 setGeneric("dgirt_plot", signature = "x", function(x, ...)
            standardGeneric("dgirt_plot"))
 
-#' \code{dgirt_plot}: plot \code{dgo_fit}-class objects
+#' Plot estimates and diagnostic statistics
+#'
+#' \code{dgirt_plot} plots estimates from a dgo model. \code{plot_rhats} plots
+#' split R-hats.
 #'
 #' @param x A \code{dgo_fit-class} object.
 #' @param y_fun Summary function to be plotted as \code{y}.
@@ -37,15 +40,13 @@ setMethod("dgirt_plot", signature(x = "dgo_fit"),
                 y_min, y_max)
 })
 
-#' \code{dgirt_plot}: plot \code{data.frame} objects
-#'
+#' @rdname plot-method
 #' @param group_names Discrete grouping variables, if any, which will be used as
 #' the \code{color} argument in \code{aes}.
 #' @param time_name A time variable with numeric values that will be plotted on
 #' the x axis.
 #' @param geo_name A variable representing local areas that will be used in
 #' faceting.
-#' @rdname plot-method
 #' @export
 #' @examples
 #' \dontrun{
@@ -103,12 +104,10 @@ plot_internal <- function(samples, group_names, time_name, geo_name, y_fun,
   p
 }
 
-#' \code{plot}: plot method for \code{dgo_fit}-class objects
-#'
+#' @rdname plot-method
 #' @param y Ignored.
 #' @param ... Further arguments to \code{\link{dgirt_plot}}.
 #'
-#' @rdname plot-method
 #' @export
 #' @examples
 #' \dontrun{
@@ -125,15 +124,11 @@ setMethod("plot", signature(x = "dgo_fit", y = "missing"),
 setGeneric("plot_rhats", signature = "x", function(x, ...)
            standardGeneric("plot_rhats"))
 
-#' \code{plot_rhats}: plot split R-hats from \code{dgo_fit}-class objects
-#'
-#' This function plots R-hats from a dgirt model.
-#'
+#' @rdname plot-method
 #' @param facet_vars Optionally, one or more variables passed to \code{facet_wrap}
 #' @param shape_var,color_var,x_var Optionally, a variable passed to the
 #' \code{shape}, \code{color}, or \code{x} arguments of \code{aes_string},
 #' respectively.
-#' @rdname plot-method
 #' @export
 #' @examples
 #' \dontrun{

diff --git a/R/methods-dgirtfit-poststratify.r b/R/methods-dgirtfit-poststratify.r
@@ -1,6 +1,6 @@
 utils::globalVariables(c("value", "scaled_prop"))
 
-#' \code{poststratify}: reweight and aggregate estimates
+#' Reweight and aggregate estimates
 #'
 #' This function reweights and aggregates estimates from \code{dgirt} for strata
 #' defined by modeled variables. The names of each of the model's time,

diff --git a/R/methods-dgirtin.r b/R/methods-dgirtin.r
@@ -1,13 +1,11 @@
 #' @rdname dgirtin-class
 setGeneric("summary")
 
-#' Summarize DGIRT Data
-#'
+#' @rdname dgirtin-class
 #' @param x An object of class \code{dgirtIn} as returned by \code{shape}.
 #' @param ... Unused.
 #' @param object An object of class \code{dgirtIn} as returned by \code{shape}.
 #'
-#' @rdname dgirtin-class
 #' @include class-dgirtin.r
 #' @export
 setMethod("summary", c(object = "dgirtIn"),
@@ -48,14 +46,12 @@ setMethod("print", c("x" = "dgirtIn"),
 setGeneric("get_item_names", signature = "x",
   function(x) standardGeneric("get_item_names"))
 
-#' Get Items Names in DGIRT Data.
-#'
+#' @rdname dgirtin-class
 #' @return A list of item names.
 #' @examples
 #' data(toy_dgirt_in)
 #' get_item_names(toy_dgirt_in)
 #' @include class-dgirtin.r
-#' @rdname dgirtin-class
 #' @aliases get_item_names
 #' @export
 setMethod("get_item_names", c("x" = "dgirtIn"),
@@ -69,12 +65,11 @@ setGeneric("get_n", signature = c("x", "by", "aggregate_name"),
            function(x, by = NULL, aggregate_name = NULL)
              standardGeneric("get_n"))
 
-#' Count Respondents in DGIRT Data.
-#'
+#' @rdname dgirtin-class
 #' @param by The name of a grouping variable.
-#' @param aggregate_name If specified `get_n` will operate on the table passed
-#' to `shape` as `aggregate_data` instead of on the individual data and count
-#' nonmissingness in the given variable.
+#' @param aggregate_name If specified \code{get_n} will operate on the table
+#' passed to \code{shape} as \code{aggregate_data} instead of on the individual
+#' data and count nonmissingness in the given variable.
 #'
 #' @examples
 #' # respondent count
@@ -87,10 +82,8 @@ setGeneric("get_n", signature = c("x", "by", "aggregate_name"),
 #' # respondent count by year and survey identifier
 #' get_n(toy_dgirt_in, by = c("year", "source"))
 #'
-#' @seealso `\link{get_item_n}, \link{get_item_names}`
 #' @include class-dgirtin.r
 #' @aliases get_n
-#' @rdname dgirtin-class
 #' @export
 setMethod("get_n", c("x" = "dgirtIn"),
   function(x, by = NULL, aggregate_name = NULL) {
@@ -117,17 +110,15 @@ stop_if_no_aggregates <- function(x) {
 setGeneric("get_item_n", signature = c("x", "by", "aggregate_data"),
            function(x, by = NULL, aggregate_data = FALSE) standardGeneric("get_item_n"))
 
-#' Count Respondents for Items in DGIRT Data
-#'
-#' @include class-dgirtin.r
 #' @rdname dgirtin-class
+#' @include class-dgirtin.r
 #' @examples
 #' data(toy_dgirt_in)
 #' get_item_n(toy_dgirt_in)
 #' get_item_n(toy_dgirt_in, by = "year")
 #' @aliases get_item_n
-#' @param aggregate_data If specified `get_item_n` will operate on the table passed
-#' to `shape` as `aggregate_data` instead of on the individual data.
+#' @param aggregate_data If specified \code{get_item_n} will operate on the table passed
+#' to \code{shape} as \code{aggregate_data} instead of on the individual data.
 #' @export
 setMethod("get_item_n", c("x" = "dgirtIn"),
   function(x, by = NULL, aggregate_data = FALSE) {
@@ -157,8 +148,7 @@ zero_nas <- function(n, by) {
     .SDcols = setdiff(names(n), by)]
 }
 
-#' Show Summary of DGIRT Data
-#' @include class-dgirtin.r
 #' @rdname dgirtin-class
+#' @include class-dgirtin.r
 #' @export
 setMethod("show", c("dgirtIn"), function(object) summary(object))
diff --git a/R/shape.r b/R/shape.r
@@ -1,4 +1,4 @@
-#' \code{shape}: prepare data for modeling with \code{dgirt} or \code{dgmrp}
+#' Prepare data for modeling
 #'
 #' This function shapes data for use in a dgirt or dgmrp model. Most
 #' arguments give the name or names of key variables in the data. These

diff --git a/R/toy_dgirt_in.r b/R/toy_dgirt_in.r
@@ -1,4 +1,4 @@
-#' Class \code{dgirtIn}: a minimal example object
+#' A minimal example of shaped data
 #'
 #' \code{\link[dgo]{shape}} returns a \code{\link[dgo]{dgirtin-class}} object
 #' used with \code{\link[dgo]{dgirt}} for DGIRT modeling. \code{toy_dgirt_in} is

diff --git a/R/toy_dgirtfit.r b/R/toy_dgirtfit.r
@@ -1,4 +1,4 @@
-#' Class \code{dgirtfit}: a minimal example object
+#' A minimal example of a fitted model
 #'
 #' \code{\link[dgo]{dgirt}} returns a \code{\link[dgo]{dgirtfit}}-class object
 #' that extends \code{\link[rstan]{stanfit-class}}. \code{toy_dgirtfit} is a

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -15,11 +15,15 @@ reference:
     contents:
     - shape
     - toy_dgirt_in
+    - dgirtin-class
   - title: Estimation
     contents:
     - dgirt
     - dgmrp
     - toy_dgirtfit
+    - dgirt_fit-class
+    - dgmrp_fit-class
+    - dgo_fit-class
   - title: Postestimation
     contents:
     - poststratify

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,22 +1,11 @@
 ## Test environments
 
-* local Ubuntu 16.04, R 3.4.0
-* Ubuntu 12.04 (on travis-ci), R 3.4.0 (devel, release) and R 3.3.3
-* OS X 10.11 and 10.12 (on travis-ci), R 3.4.0 (devel, release) and R 3.3.3
-* Windows Server 2012 R2 x64 (on appveyor), R 3.4.0 (devel and release) and R
-  3.3.3
+* Ubuntu 14.04.5 LTS (on travis-ci), R 3.4.2 (devel, release) and R 3.3.3
+* macOS 10.12.5 and 10.11.6 (on travis-ci), R 3.4.2 (devel, release) and R 3.3.3
+* Windows Server 2012 R2 x64 (on appveyor), R 3.4.2 (release) i386 and x64
 
 
 ## R CMD check results
 
-There were no ERRORs or WARNINGs. 
+There were no ERRORs, WARNINGs, or NOTEs. 
 
-There was one NOTE:
-
-* "Days since last update: 6": This submission attempts to resolve a build
-  failure (only) on
-  [r-release-osx-x86_64](https://www.r-project.org/nosvn/R.check/r-release-osx-x86_64/dgo-00check.html)
-  resulting from a failing test, which does not occur on travis-ci. This
-  submission avoids using dependency RStan during tests and removes a dependency
-  on Rcpp. The goal of these changes is to render moot variation in build
-  environments.
diff --git a/docs/reference/dgirt.html b/docs/reference/dgirt.html
diff --git a/docs/reference/dgirt_fit-class.html b/docs/reference/dgirt_fit-class.html