Merge pull request #240 from stan-dev/fix-r-cmd-check-issues

Avoid R cmd check NOTEs about some internal functions

NAMESPACE

@@ -14,6 +14,8 @@ 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(compute_point_estimate,default)
+S3method(compute_point_estimate,matrix)
 S3method(crps,matrix)
 S3method(crps,numeric)
 S3method(dim,importance_sampling)
@@ -33,12 +35,15 @@ S3method(loo_approximate_posterior,"function")
 S3method(loo_approximate_posterior,array)
 S3method(loo_approximate_posterior,matrix)
 S3method(loo_compare,default)
+S3method(loo_compare,psis_loo_ss_list)
 S3method(loo_crps,matrix)
 S3method(loo_model_weights,default)
 S3method(loo_moment_match,default)
 S3method(loo_predictive_metric,matrix)
 S3method(loo_scrps,matrix)
 S3method(loo_subsample,"function")
+S3method(n_draws,default)
+S3method(n_draws,matrix)
 S3method(nobs,psis_loo_ss)
 S3method(plot,loo)
 S3method(plot,psis)
@@ -78,6 +83,9 @@ S3method(scrps,numeric)
 S3method(sis,array)
 S3method(sis,default)
 S3method(sis,matrix)
+S3method(thin_draws,default)
+S3method(thin_draws,matrix)
+S3method(thin_draws,numeric)
 S3method(tis,array)
 S3method(tis,default)
 S3method(tis,matrix)
@@ -86,9 +94,6 @@ S3method(waic,"function")
 S3method(waic,array)
 S3method(waic,matrix)
 S3method(weights,importance_sampling)
-export(.compute_point_estimate)
-export(.ndraws)
-export(.thin_draws)
 export(E_loo)
 export(compare)
 export(crps)

R/loo_compare.psis_loo_ss_list.R

@@ -4,6 +4,7 @@
 #' @param ... Currently ignored.
 #' @return A `compare.loo_ss` object.
 #' @author Mans Magnusson
+#' @export
 loo_compare.psis_loo_ss_list <- function(x, ...) {
 
   checkmate::assert_list(x, any.missing = FALSE, min.len = 1)

R/loo_subsample.R

@@ -138,7 +138,7 @@ loo_subsample.function <-
     cores <- loo_cores(cores)
 
     checkmate::assert_choice(loo_approximation, choices = loo_approximation_choices(), null.ok = FALSE)
-    checkmate::assert_int(loo_approximation_draws, lower = 1, upper = .ndraws(draws), null.ok = TRUE)
+    checkmate::assert_int(loo_approximation_draws, lower = 1, upper = n_draws(draws), null.ok = TRUE)
     checkmate::assert_choice(estimator, choices = estimator_choices())
 
     .llgrad <- .llhess <- NULL
@@ -234,7 +234,7 @@ loo_subsample.function <-
                                  .llgrad = .llgrad,
                                  .llhess = .llhess,
                                  data_dim = dim(data),
-                                 ndraws = .ndraws(draws))
+                                 ndraws = n_draws(draws))
     loo_ss
   }
 
@@ -379,13 +379,13 @@ update.psis_loo_ss <- function(object, ...,
 
     if (length(observations) == 1) {
       # Add new samples pointwise and diagnostic
-      object <- rbind.psis_loo_ss(object, x = loo_obj)
+      object <- rbind_psis_loo_ss(object, x = loo_obj)
 
       # Update m_i for current pointwise (diagnostic stay the same)
       object$pointwise <- update_m_i_in_pointwise(object$pointwise, cidxs$add, type = "add")
     } else {
       # Add new samples pointwise and diagnostic
-      object <- rbind.psis_loo_ss(object, loo_obj)
+      object <- rbind_psis_loo_ss(object, loo_obj)
 
       # Replace m_i current pointwise and diagnostics
       object$pointwise <- update_m_i_in_pointwise(object$pointwise, cidxs$add, type = "replace")
@@ -537,20 +537,20 @@ elpd_loo_approximation <- function(.llfun, data, draws, cores, loo_approximation
   if (loo_approximation == "none") return(rep(1L,N))
 
   if (loo_approximation %in% c("tis", "sis")) {
-    draws <- .thin_draws(draws, loo_approximation_draws)
+    draws <- thin_draws(draws, loo_approximation_draws)
     is_values <- suppressWarnings(loo.function(.llfun, data = data, draws = draws, is_method = loo_approximation))
     return(is_values$pointwise[, "elpd_loo"])
   }
 
   if (loo_approximation == "waic") {
-    draws <- .thin_draws(draws, loo_approximation_draws)
+    draws <- thin_draws(draws, loo_approximation_draws)
     waic_full_obj <- waic.function(.llfun, data = data, draws = draws)
     return(waic_full_obj$pointwise[,"elpd_waic"])
   }
 
   # Compute the lpd or log p(y_i|y_{-i})
   if (loo_approximation == "lpd") {
-    draws <- .thin_draws(draws, loo_approximation_draws)
+    draws <- thin_draws(draws, loo_approximation_draws)
     lpds <- compute_lpds(N, data, draws, .llfun, cores)
     return(lpds) # Use only the lpd
   }
@@ -561,8 +561,8 @@ elpd_loo_approximation <- function(.llfun, data, draws, cores, loo_approximation
       loo_approximation == "waic_grad_marginal" |
       loo_approximation == "waic_hess") {
 
-    draws <- .thin_draws(draws, loo_approximation_draws)
-    point_est <- .compute_point_estimate(draws)
+    draws <- thin_draws(draws, loo_approximation_draws)
+    point_est <- compute_point_estimate(draws)
     lpds <- compute_lpds(N, data, point_est, .llfun, cores)
     if (loo_approximation == "plpd") return(lpds) # Use only the lpd
   }
@@ -572,7 +572,7 @@ elpd_loo_approximation <- function(.llfun, data, draws, cores, loo_approximation
       loo_approximation == "waic_hess") {
     checkmate::assert_true(!is.null(.llgrad))
 
-    point_est <- .compute_point_estimate(draws)
+    point_est <- compute_point_estimate(draws)
     # Compute the lpds
     lpds <- compute_lpds(N, data, point_est, .llfun, cores)
 
@@ -620,79 +620,77 @@ elpd_loo_approximation <- function(.llfun, data, draws, cores, loo_approximation
 
 #' Compute a point estimate from a draws object
 #'
-#' @details This is a generic function to thin draws from arbitrary draws
+#' @noRd
+#' @details This is a generic function to compute point estimates from draws
 #'   objects. The function is internal and should only be used by developers to
 #'   enable [loo_subsample()] for arbitrary draws objects.
 #'
 #' @param draws A draws object with draws from the posterior.
 #' @return A 1 by P matrix with point estimates from a draws object.
-#' @keywords internal
-#' @export
-.compute_point_estimate <- function(draws) {
-  UseMethod(".compute_point_estimate")
+compute_point_estimate <- function(draws) {
+  UseMethod("compute_point_estimate")
 }
-
-.compute_point_estimate.matrix <- function(draws) {
+#' @export
+compute_point_estimate.matrix <- function(draws) {
   t(as.matrix(colMeans(draws)))
 }
-
-.compute_point_estimate.default <- function(draws) {
-  stop(".compute_point_estimate() has not been implemented for objects of class '", class(draws), "'")
+#' @export
+compute_point_estimate.default <- function(draws) {
+  stop("compute_point_estimate() has not been implemented for objects of class '", class(draws), "'")
 }
 
 #' Thin a draws object
 #'
+#' @noRd
 #' @details This is a generic function to thin draws from arbitrary draws
 #'   objects. The function is internal and should only be used by developers to
 #'   enable [loo_subsample()] for arbitrary draws objects.
 #'
 #' @param draws A draws object with posterior draws.
 #' @param loo_approximation_draws The number of posterior draws to return (ie after thinning).
-#' @keywords internal
-#' @export
 #' @return A thinned draws object.
-.thin_draws <- function(draws, loo_approximation_draws) {
-  UseMethod(".thin_draws")
+thin_draws <- function(draws, loo_approximation_draws) {
+  UseMethod("thin_draws")
 }
 
-.thin_draws.matrix <- function(draws, loo_approximation_draws) {
+#' @export
+thin_draws.matrix <- function(draws, loo_approximation_draws) {
   if (is.null(loo_approximation_draws)) return(draws)
-  checkmate::assert_int(loo_approximation_draws, lower = 1, upper = .ndraws(draws), null.ok = TRUE)
-  S <- .ndraws(draws)
+  checkmate::assert_int(loo_approximation_draws, lower = 1, upper = n_draws(draws), null.ok = TRUE)
+  S <- n_draws(draws)
   idx <- 1:loo_approximation_draws * S %/% loo_approximation_draws
   draws <- draws[idx, , drop = FALSE]
   draws
 }
-
-.thin_draws.numeric <- function(draws, loo_approximation_draws) {
-  .thin_draws.matrix(as.matrix(draws), loo_approximation_draws)
+#' @export
+thin_draws.numeric <- function(draws, loo_approximation_draws) {
+  thin_draws.matrix(as.matrix(draws), loo_approximation_draws)
 }
-
-.thin_draws.default <- function(draws, loo_approximation_draws) {
-  stop(".thin_draws() has not been implemented for objects of class '", class(draws), "'")
+#' @export
+thin_draws.default <- function(draws, loo_approximation_draws) {
+  stop("thin_draws() has not been implemented for objects of class '", class(draws), "'")
 }
 
 
 #' The number of posterior draws in a draws object.
 #'
+#' @noRd
 #' @details This is a generic function to return the total number of draws from
 #'   an arbitrary draws objects. The function is internal and should only be
 #'   used by developers to enable [loo_subsample()] for arbitrary draws objects.
 #'
 #' @param x A draws object with posterior draws.
 #' @return An integer with the number of draws.
-#' @keywords internal
-#' @export
-.ndraws <- function(x) {
-  UseMethod(".ndraws")
+n_draws <- function(x) {
+  UseMethod("n_draws")
 }
-
-.ndraws.matrix <- function(x) {
+#' @export
+n_draws.matrix <- function(x) {
   nrow(x)
 }
-
-.ndraws.default <- function(x) {
-  stop(".ndraws() has not been implemented for objects of class '", class(x), "'")
+#' @export
+n_draws.default <- function(x) {
+  stop("n_draws() has not been implemented for objects of class '", class(x), "'")
 }
 
 ## Subsampling -----
@@ -969,7 +967,7 @@ add_subsampling_vars_to_pointwise <- function(pointwise, idxs, elpd_loo_approx)
 #' @param object A `psis_loo_ss` object.
 #' @param x A `psis_loo` object.
 #' @return An updated `psis_loo_ss` object.
-rbind.psis_loo_ss <- function(object, x) {
+rbind_psis_loo_ss <- function(object, x) {
   checkmate::assert_class(object, "psis_loo_ss")
   if (is.null(x)) return(object) # Fallback
   checkmate::assert_class(x, "psis_loo")