register internal s3 methods (doesn't actually export them)

see r-lib/roxygen2#1175

Author: jgabry

NAMESPACE

@@ -2,16 +2,31 @@
 
 S3method("[",neff_ratio)
 S3method("[",rhat)
+S3method(apply_transformations,array)
+S3method(apply_transformations,matrix)
+S3method(diagnostic_factor,neff_ratio)
+S3method(diagnostic_factor,rhat)
 S3method(log_posterior,CmdStanMCMC)
 S3method(log_posterior,stanfit)
 S3method(log_posterior,stanreg)
+S3method(melt_mcmc,matrix)
+S3method(melt_mcmc,mcmc_array)
 S3method(neff_ratio,CmdStanMCMC)
 S3method(neff_ratio,stanfit)
 S3method(neff_ratio,stanreg)
+S3method(num_chains,data.frame)
+S3method(num_chains,mcmc_array)
+S3method(num_iters,data.frame)
+S3method(num_iters,mcmc_array)
+S3method(num_params,data.frame)
+S3method(num_params,mcmc_array)
 S3method(nuts_params,CmdStanMCMC)
 S3method(nuts_params,list)
 S3method(nuts_params,stanfit)
 S3method(nuts_params,stanreg)
+S3method(parameter_names,array)
+S3method(parameter_names,default)
+S3method(parameter_names,matrix)
 S3method(plot,bayesplot_grid)
 S3method(plot,bayesplot_scheme)
 S3method(pp_check,default)

R/helpers-mcmc.R

@@ -124,6 +124,8 @@ select_parameters <-
 #' @return A molten data frame.
 #'
 melt_mcmc <- function(x, ...) UseMethod("melt_mcmc")
+
+#' @export
 melt_mcmc.mcmc_array <- function(x,
                                  varnames =
                                    c("Iteration", "Chain", "Parameter"),
@@ -144,6 +146,7 @@ melt_mcmc.mcmc_array <- function(x,
 }
 
 # If all chains are already merged
+#' @export
 melt_mcmc.matrix <- function(x,
                              varnames = c("Draw", "Parameter"),
                              value.name = "Value",
@@ -305,13 +308,17 @@ chain_list2array <- function(x) {
 
 # Get parameter names from a 3-D array
 parameter_names <- function(x) UseMethod("parameter_names")
+
+#' @export
 parameter_names.array <- function(x) {
   stopifnot(is_3d_array(x))
   dimnames(x)[[3]] %||% abort("No parameter names found.")
 }
+#' @export
 parameter_names.default <- function(x) {
   colnames(x) %||% abort("No parameter names found.")
 }
+#' @export
 parameter_names.matrix <- function(x) {
   colnames(x) %||% abort("No parameter names found.")
 }
@@ -391,6 +398,8 @@ validate_transformations <-
 apply_transformations <- function(x, ...) {
   UseMethod("apply_transformations")
 }
+
+#' @export
 apply_transformations.matrix <- function(x, ..., transformations = list()) {
   pars <- colnames(x)
   x_transforms <- validate_transformations(transformations, pars)
@@ -400,6 +409,8 @@ apply_transformations.matrix <- function(x, ..., transformations = list()) {
 
   x
 }
+
+#' @export
 apply_transformations.array <- function(x, ..., transformations = list()) {
   stopifnot(length(dim(x)) == 3)
   pars <- dimnames(x)[[3]]
@@ -437,17 +448,23 @@ num_chains <- function(x, ...) UseMethod("num_chains")
 num_iters <- function(x, ...) UseMethod("num_iters")
 num_params <- function(x, ...) UseMethod("num_params")
 
+#' @export
 num_params.mcmc_array <- function(x, ...) dim(x)[3]
+#' @export
 num_chains.mcmc_array <- function(x, ...) dim(x)[2]
+#' @export
 num_iters.mcmc_array <- function(x, ...) dim(x)[1]
+#' @export
 num_params.data.frame <- function(x, ...) {
   stopifnot("Parameter" %in% colnames(x))
   length(unique(x$Parameter))
 }
+#' @export
 num_chains.data.frame <- function(x, ...) {
   stopifnot("Chain" %in% colnames(x))
   length(unique(x$Chain))
 }
+#' @export
 num_iters.data.frame <- function(x, ...) {
   cols <- colnames(x)
   stopifnot("Iteration" %in% cols || "Draws" %in% cols)

R/mcmc-diagnostics.R

@@ -364,12 +364,14 @@ diagnostic_factor <- function(x, ...) {
   UseMethod("diagnostic_factor")
 }
 
+#' @export
 diagnostic_factor.rhat <- function(x, ..., breaks = c(1.05, 1.1)) {
   cut(x, breaks = c(-Inf, breaks, Inf),
       labels = c("low", "ok", "high"),
       ordered_result = FALSE)
 }
 
+#' @export
 diagnostic_factor.neff_ratio <- function(x, ..., breaks = c(0.1, 0.5)) {
   cut(x, breaks = c(-Inf, breaks, Inf),
       labels = c("low", "ok", "high"),

R/ppc-discrete.R

@@ -367,7 +367,7 @@ ppc_bars_data <-
 #' @param y,yrep,group User's already validated `y`, `yrep`, and (if applicable)
 #'   `group` arguments.
 #' @param prob,freq User's `prob` and `freq` arguments.
-#' @importFrom dplyr "%>%" ungroup count arrange mutate summarise across full_join rename all_of
+#' @importFrom dplyr %>% ungroup count arrange mutate summarise across full_join rename all_of
 .ppc_bars_data <- function(y, yrep, group = NULL, prob = 0.9, freq = TRUE) {
   alpha <- (1 - prob) / 2
   probs <- sort(c(alpha, 0.5, 1 - alpha))