Rfast::Dist -> philentropy::distance

Author: EmilHvitfeldt

R/hier_clust.R

@@ -193,9 +193,11 @@ translate_tidyclust.hier_clust <- function(x, engine = x$engine, ...) {
   num_clusters = NULL,
   cut_height = NULL,
   linkage_method = NULL,
-  dist_fun = Rfast::Dist
+  dist_fun = philentropy::distance
 ) {
-  dmat <- dist_fun(x)
+  suppressMessages(
+    dmat <- dist_fun(x)
+  )
   res <- stats::hclust(stats::as.dist(dmat), method = linkage_method)
   attr(res, "num_clusters") <- num_clusters
   attr(res, "cut_height") <- cut_height

R/metric-helpers.R

@@ -12,7 +12,7 @@ prep_data_dist <- function(
   object,
   new_data = NULL,
   dists = NULL,
-  dist_fun = Rfast::Dist
+  dist_fun = philentropy::distance
 ) {
   # Sihouettes requires a distance matrix
   if (is.null(new_data) && is.null(dists)) {
@@ -46,7 +46,9 @@ prep_data_dist <- function(
 
   # Calculate distances including optionally supplied params
   if (is.null(dists)) {
-    dists <- dist_fun(new_data)
+    suppressMessages(
+      dists <- dist_fun(new_data)
+    )
   }
 
   return(
@@ -69,5 +71,7 @@ get_centroid_dists <- function(new_data, centroids, dist_fun = Rfast::dista) {
     rlang::abort("Centroids must have same columns as data.")
   }
 
-  dist_fun(centroids, new_data)
+  suppressMessages(
+    dist_fun(centroids, new_data)
+  )
 }

R/metric-silhouette.R

@@ -27,7 +27,7 @@ silhouette <- function(
   object,
   new_data = NULL,
   dists = NULL,
-  dist_fun = Rfast::Dist
+  dist_fun = philentropy::distance
 ) {
   if (inherits(object, "cluster_spec")) {
     rlang::abort(
@@ -126,7 +126,7 @@ silhouette_avg.cluster_fit <- function(
   ...
 ) {
   if (is.null(dist_fun)) {
-    dist_fun <- Rfast::Dist
+    dist_fun <- philentropy::distance
   }
 
   res <- silhouette_avg_impl(object, new_data, dists, dist_fun, ...)
@@ -148,7 +148,7 @@ silhouette_avg_vec <- function(
   object,
   new_data = NULL,
   dists = NULL,
-  dist_fun = Rfast::Dist,
+  dist_fun = philentropy::distance,
   ...
 ) {
   silhouette_avg_impl(object, new_data, dists, dist_fun, ...)
@@ -158,7 +158,7 @@ silhouette_avg_impl <- function(
   object,
   new_data = NULL,
   dists = NULL,
-  dist_fun = Rfast::Dist,
+  dist_fun = philentropy::distance,
   ...
 ) {
   mean(silhouette(object, new_data, dists, dist_fun, ...)$sil_width)

R/metric-sse.R

@@ -43,7 +43,9 @@ sse_within <- function(object, new_data = NULL, dist_fun = Rfast::dista) {
       n_members = summ$n_members
     )
   } else {
-    dist_to_centroids <- dist_fun(summ$centroids, new_data)
+    suppressMessages(
+      dist_to_centroids <- dist_fun(summ$centroids, new_data)
+    )
 
     res <- dist_to_centroids %>%
       tibble::as_tibble(.name_repair = "minimal") %>%
@@ -253,7 +255,9 @@ sse_total_impl <- function(
   } else {
     overall_mean <- colSums(summ$centroids * summ$n_members) /
       sum(summ$n_members)
-    tot <- dist_fun(t(as.matrix(overall_mean)), new_data)^2 %>% sum()
+    suppressMessages(
+      tot <- dist_fun(t(as.matrix(overall_mean)), new_data)^2 %>% sum()
+    )
   }
 
   return(tot)

man/dot-hier_clust_fit_stats.Rd

@@ -291,7 +291,7 @@ matrix (i.e., all pairwise distances between observations).
 
 ```{r}
 my_dist_1 <- function(x) {
-  Rfast::Dist(x, method = "manhattan")
+  philentropy::distance(x, method = "manhattan")
 }
 
 my_dist_2 <- function(x, y) {