Move non-essential packages from Imports to Suggests

DESCRIPTION

@@ -36,29 +36,29 @@ Depends: R (>= 4.0)
 Imports: 
   ape (>= 5.6),
   cli (>= 3.0),
-  cluster,
   fastmap,
   fastmatch (>= 1.1.3),
-  fs,
-  future,
   PlotTools,
-  promises,
-  protoclust,
   Rcpp,
   Rdpack (>= 0.7),
   Rogue (> 2.0.0),
-  shiny (>= 1.6.0),
-  shinyjs,
   stats,
   stringi,
   TreeDist (>= 2.6.3),
   TreeTools (>= 1.16),
 Suggests:
+  cluster,
+  fs,
+  future,
   knitr,
   phangorn (>= 2.2.1),
+  promises,
+  protoclust,
   Quartet,
   readxl,
   rmarkdown,
+  shiny (>= 1.6.0),
+  shinyjs,
   shinytest,
   spelling,
   testthat,

NAMESPACE

@@ -205,18 +205,10 @@ importFrom(cli,cli_h1)
 importFrom(cli,cli_progress_bar)
 importFrom(cli,cli_progress_done)
 importFrom(cli,cli_progress_update)
-importFrom(cluster,pam)
-importFrom(cluster,silhouette)
 importFrom(fastmap,fastmap)
 importFrom(fastmatch,"%fin%")
 importFrom(fastmatch,fmatch)
-importFrom(fs,path_sanitize)
-importFrom(future,future)
 importFrom(graphics,par)
-importFrom(promises,future_promise)
-importFrom(protoclust,protoclust)
-importFrom(shiny,runApp)
-importFrom(shinyjs,useShinyjs)
 importFrom(stats,as.dist)
 importFrom(stats,cutree)
 importFrom(stats,median)

R/ClusterStrings.R

@@ -18,8 +18,6 @@
 #'                  paste0("AnotherCluster_", letters[1:6])))
 #' @template MRS
 #' @importFrom utils adist
-#' @importFrom cluster pam silhouette
-#' @importFrom protoclust protoclust
 #' @importFrom stats as.dist cutree
 #' @family utility functions
 #' @export
@@ -28,6 +26,9 @@ ClusterStrings <- function (x, maxCluster = 12) {
     stop("`maxCluster` must be at least two.")
   }
 
+  .InstallSuggestedPackage("cluster")
+  .InstallSuggestedPackage("protoclust")
+
   if (length(unique(x)) < maxCluster) {
     nom <- unique(x)
     structure(match(x, nom), "med" = nom)
@@ -42,19 +43,19 @@ ClusterStrings <- function (x, maxCluster = 12) {
     kInc <- 1 / (nMethodsChecked * nK)
 
     pamClusters <- lapply(possibleClusters, function (k) {
-      pam(dists, k = k)
+      cluster::pam(dists, k = k)
     })
     pamSils <- vapply(pamClusters, function (pamCluster) {
-      mean(silhouette(pamCluster)[, 3])
+      mean(cluster::silhouette(pamCluster)[, 3])
     }, double(1))
     bestPam <- which.max(pamSils)
     pamSil <- pamSils[bestPam]
     pamCluster <- pamClusters[[bestPam]][["clustering"]]
 
-    hTree <- protoclust(as.dist(dists))
+    hTree <- protoclust::protoclust(as.dist(dists))
     hClusters <- lapply(possibleClusters, function (k) cutree(hTree, k = k))
     hSils <- vapply(hClusters, function (hCluster) {
-      mean(silhouette(hCluster, dists)[, 3])
+      mean(cluster::silhouette(hCluster, dists)[, 3])
     }, double(1))
     bestH <- which.max(hSils)
     hSil <- hSils[bestH]

R/MaximizeParsimony.R

@@ -999,17 +999,9 @@ Resample <- function(dataset, tree, method = "jack", proportion = 2 / 3,
 #' Launch tree search graphical user interface
 #' 
 #' @rdname MaximizeParsimony
-#' @importFrom cluster pam silhouette
-#' @importFrom future future
-#' @importFrom PlotTools SpectrumLegend
-#' @importFrom promises future_promise
-#' @importFrom protoclust protoclust
-#' @importFrom Rogue ColByStability
-#' @importFrom shiny runApp
-#' @importFrom shinyjs useShinyjs
-#' @importFrom TreeDist ClusteringInfoDistance
 #' @export
 EasyTrees <- function () {#nocov start
+  .InstallSuggestedPackage("shinyjs")
   shiny::runApp(system.file("Parsimony", package = "TreeSearch"))
 }
 

R/TaxonInfluence.R

@@ -106,7 +106,6 @@
 #' @family tree scoring
 #' @importFrom ape read.nexus write.nexus
 #' @importFrom cli cli_alert_info cli_h1
-#' @importFrom fs path_sanitize
 #' @importFrom stats weighted.mean
 #' @importFrom TreeDist ClusteringInfoDistance
 #' @encoding UTF-8
@@ -122,6 +121,7 @@ TaxonInfluence <- function(
     ...
   ) {
   if (!is.null(savePath)) {
+    .InstallSuggestedPackage("fs")
     saveDir <- dirname(paste0(savePath, "taxon_name"))
     if (!dir.exists(saveDir)) {
       dir.create(saveDir, recursive = TRUE)
@@ -153,9 +153,13 @@ TaxonInfluence <- function(
   # Return:
   vapply(names(dataset), function(leaf) {
 
-    leafFile <- paste0(savePath, path_sanitize(leaf), ".nex")
+    leafFile <- if (!is.null(savePath)) {
+      paste0(savePath, fs::path_sanitize(leaf), ".nex")
+    } else {
+      NULL
+    }
 
-    result <- if (useCache && file.exists(leafFile)) {
+    result <- if (useCache && !is.null(leafFile) && file.exists(leafFile)) {
       if (verbosity > 1) {
         cli_alert_info(paste("Seeking cache: ", leafFile))
       }

R/TreeSearch_utilities.R

@@ -11,3 +11,28 @@ EmptyPhyDat <- function(tree) {
 #' @rdname TreeSearch
 #' @export
 DoNothing <- function(x = NULL) {x}
+
+# Helper function to install suggested packages with user prompt
+.InstallSuggestedPackage <- function(package) {
+  if (!requireNamespace(package, quietly = TRUE)) {
+    if (interactive()) {
+      message("Package '", package, "' is required but not installed.")
+      response <- readline(prompt = paste0("Install ", package, "? (y/n): "))
+      if (tolower(trimws(response)) == "y") {
+        install.packages(package)
+        if (!requireNamespace(package, quietly = TRUE)) {
+          stop("Failed to install package '", package, "'", call. = FALSE)
+        }
+      } else {
+        stop("Package '", package, "' is required. ",
+             "Install it with: install.packages('", package, "')",
+             call. = FALSE)
+      }
+    } else {
+      stop("Package '", package, "' is required. ",
+           "Install it with: install.packages('", package, "')",
+           call. = FALSE)
+    }
+  }
+}
+

tests/testthat/test-ClusterStrings.R

@@ -1,4 +1,7 @@
 test_that("ClusterStrings() works", {
+  skip_if_not_installed("cluster")
+  skip_if_not_installed("protoclust")
+
   x <- rep(letters[1:6], 1:6)
   expect_equal(ClusterStrings(x),
                structure(rep(1:6, 1:6), "med" = letters[1:6]))

tests/testthat/test-TaxonInfluence.R

@@ -23,6 +23,8 @@ test_that("TaxonInfluence() works", {
 })
 
 test_that("TaxonInfluence() saves intermediate trees", {
+  skip_if_not_installed("fs")
+
   library("TreeTools") # for phyDat manipulation
   data("congreveLamsdellMatrices", package = "TreeSearch")
   set.seed(0)