Merge pull request #239 from stan-dev/register-internal-methods

Register internal S3 methods

DESCRIPTION

@@ -53,5 +53,5 @@ Suggests:
 VignetteBuilder: knitr
 Encoding: UTF-8
 SystemRequirements: pandoc (>= 1.12.3), pandoc-citeproc
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -5,9 +5,15 @@ S3method("[",loo)
 S3method("[[",loo)
 S3method(E_loo,default)
 S3method(E_loo,matrix)
+S3method(E_loo_khat,default)
+S3method(E_loo_khat,matrix)
 S3method(ap_psis,array)
 S3method(ap_psis,default)
 S3method(ap_psis,matrix)
+S3method(as.psis_loo,psis_loo)
+S3method(as.psis_loo,psis_loo_ss)
+S3method(as.psis_loo_ss,psis_loo)
+S3method(as.psis_loo_ss,psis_loo_ss)
 S3method(crps,matrix)
 S3method(crps,numeric)
 S3method(dim,importance_sampling)
@@ -50,6 +56,7 @@ S3method(print,psis_loo)
 S3method(print,psis_loo_ap)
 S3method(print,stacking_weights)
 S3method(print,waic)
+S3method(print_dims,elpd_generic)
 S3method(print_dims,importance_sampling)
 S3method(print_dims,importance_sampling_loo)
 S3method(print_dims,kfold)
@@ -59,6 +66,8 @@ S3method(print_dims,waic)
 S3method(psis,array)
 S3method(psis,default)
 S3method(psis,matrix)
+S3method(psis_n_eff,default)
+S3method(psis_n_eff,matrix)
 S3method(relative_eff,"function")
 S3method(relative_eff,array)
 S3method(relative_eff,default)

R/E_loo.R

@@ -240,11 +240,11 @@ E_loo.matrix <-
 E_loo_khat <- function(x, psis_object, log_ratios, ...) {
   UseMethod("E_loo_khat")
 }
-
+#' @export
 E_loo_khat.default <- function(x, psis_object, log_ratios, ...) {
   .E_loo_khat_i(x, log_ratios, attr(psis_object, "tail_len"))
 }
-
+#' @export
 E_loo_khat.matrix <- function(x, psis_object, log_ratios, ...) {
   tail_lengths <- attr(psis_object, "tail_len")
   sapply(seq_len(ncol(x)), function(i) {

R/effective_sample_sizes.R

@@ -170,6 +170,8 @@ relative_eff.importance_sampling <- function(x, ...) {
 psis_n_eff <- function(w, ...) {
   UseMethod("psis_n_eff")
 }
+
+#' @export
 psis_n_eff.default <- function(w, r_eff = NULL, ...) {
   ss <- sum(w^2)
   if (is.null(r_eff)) {
@@ -179,6 +181,8 @@ psis_n_eff.default <- function(w, r_eff = NULL, ...) {
   stopifnot(length(r_eff) == 1)
   1 / ss * r_eff
 }
+
+#' @export
 psis_n_eff.matrix <- function(w, r_eff = NULL, ...) {
   ss <- colSums(w^2)
   if (is.null(r_eff)) {

R/elpd.R

@@ -65,7 +65,7 @@ elpd_object <- function(pointwise, dims) {
     class = c("elpd_generic", "loo")
   )
 }
-
+#' @export
 print_dims.elpd_generic <- function(x, ...) {
   cat(
     "Computed from",

R/loo_subsample.R

@@ -884,11 +884,11 @@ psis_loo_ss_object <- function(x,
 as.psis_loo_ss <- function(x) {
   UseMethod("as.psis_loo_ss")
 }
-
+#' @export
 as.psis_loo_ss.psis_loo_ss <- function(x) {
   x
 }
-
+#' @export
 as.psis_loo_ss.psis_loo <- function(x) {
   class(x) <- c("psis_loo_ss", class(x))
   x$estimates <- cbind(x$estimates, matrix(0, nrow = nrow(x$estimates)))
@@ -913,10 +913,11 @@ as.psis_loo <- function(x) {
   UseMethod("as.psis_loo")
 }
 
+#' @export
 as.psis_loo.psis_loo <- function(x) {
   x
 }
-
+#' @export
 as.psis_loo.psis_loo_ss <- function(x) {
   if (x$loo_subsampling$data_dim[1] == nrow(x$pointwise)) {
     x$estimates <- x$estimates[, 1:2]