From a280d32446235d5291d7bc359235e29fe6a452a7 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 4 Nov 2025 16:17:45 +0000
Subject: [PATCH 1/5] Initial plan


From 321f397c6848932e3a2d8cf3f13297376969acfb Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 4 Nov 2025 16:26:04 +0000
Subject: [PATCH 2/5] Replace fastmap and stringi with base R, move packages to
 Suggests

Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>
---
 DESCRIPTION                          | 16 +++++++---------
 R/ClusterStrings.R                   | 22 ++++++++++++++++------
 R/Consistency.R                      | 12 +++++-------
 R/MaximizeParsimony.R                | 14 +++++---------
 R/TaxonInfluence.R                   | 14 +++++++++++---
 R/mpl_morphy_objects.R               |  3 +--
 tests/testthat/test-ClusterStrings.R |  3 +++
 tests/testthat/test-TaxonInfluence.R |  2 ++
 8 files changed, 50 insertions(+), 36 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 911f634f8..641565691 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -36,29 +36,27 @@ 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,
diff --git a/R/ClusterStrings.R b/R/ClusterStrings.R
index 1ee081e7d..caf8ae952 100644
--- a/R/ClusterStrings.R
+++ b/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 +26,18 @@ ClusterStrings <- function (x, maxCluster = 12) {
     stop("`maxCluster` must be at least two.")
   }
   
+  if (!requireNamespace("cluster", quietly = TRUE)) {
+    stop("Package 'cluster' is required for ClusterStrings(). ",
+         "Install it with: install.packages('cluster')",
+         call. = FALSE)
+  }
+  
+  if (!requireNamespace("protoclust", quietly = TRUE)) {
+    stop("Package 'protoclust' is required for ClusterStrings(). ",
+         "Install it with: install.packages('protoclust')",
+         call. = FALSE)
+  }
+  
   if (length(unique(x)) < maxCluster) {
     nom <- unique(x)
     structure(match(x, nom), "med" = nom)
@@ -42,19 +52,19 @@ 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]
diff --git a/R/Consistency.R b/R/Consistency.R
index bd695f758..717412fcf 100644
--- a/R/Consistency.R
+++ b/R/Consistency.R
@@ -109,8 +109,7 @@ Consistency <- function (dataset, tree, nRelabel = 0, compress = FALSE) {
 }
 
 
-#' @importFrom fastmap fastmap
-.CharLengthCache <- fastmap()
+.CharLengthCache <- new.env(parent = emptyenv())
 
 #' Expected length
 #' 
@@ -127,7 +126,6 @@ Consistency <- function (dataset, tree, nRelabel = 0, compress = FALSE) {
 #' 
 #' @export
 #' @importFrom stats median
-#' @importFrom stringi stri_paste
 #' @family tree scoring
 #' @template MRS
 ExpectedLength <- function(dataset, tree, nRelabel = 1000, compress = FALSE) {
@@ -151,9 +149,9 @@ ExpectedLength <- function(dataset, tree, nRelabel = 1000, compress = FALSE) {
   }, integer(nLevels)))
   
   .LengthForChar <- function(x) {
-    key <- stri_paste(c(nRelabel, x), collapse = ",")
-    if (.CharLengthCache$has(key)) {
-      .CharLengthCache$get(key)
+    key <- paste(c(nRelabel, x), collapse = ",")
+    if (exists(key, envir = .CharLengthCache, inherits = FALSE)) {
+      get(key, envir = .CharLengthCache)
     } else {
       patterns <- apply(unname(unique(t(
         as.data.frame(replicate(nRelabel, sample(rep(seq_along(x), x))))))),
@@ -170,7 +168,7 @@ ExpectedLength <- function(dataset, tree, nRelabel = 1000, compress = FALSE) {
         contrast = rwContrast,
         class = "phyDat")
       ret <- median(FastCharacterLength(tree, phy))
-      .CharLengthCache$set(key, ret)
+      assign(key, ret, envir = .CharLengthCache)
       ret
     }
   }
diff --git a/R/MaximizeParsimony.R b/R/MaximizeParsimony.R
index ef6d237cc..3519ecba6 100644
--- a/R/MaximizeParsimony.R
+++ b/R/MaximizeParsimony.R
@@ -999,17 +999,13 @@ 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
+  if (!requireNamespace("shiny", quietly = TRUE)) {
+    stop("Package 'shiny' is required for EasyTrees(). ",
+         "Install it with: install.packages('shiny')",
+         call. = FALSE)
+  }
   shiny::runApp(system.file("Parsimony", package = "TreeSearch"))
 }
 
diff --git a/R/TaxonInfluence.R b/R/TaxonInfluence.R
index 51397ddfc..67710a539 100644
--- a/R/TaxonInfluence.R
+++ b/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 +121,11 @@ TaxonInfluence <- function(
     ...
   ) {
   if (!is.null(savePath)) {
+    if (!requireNamespace("fs", quietly = TRUE)) {
+      stop("Package 'fs' is required when using savePath. ",
+           "Install it with: install.packages('fs')",
+           call. = FALSE)
+    }
     saveDir <- dirname(paste0(savePath, "taxon_name"))
     if (!dir.exists(saveDir)) {
       dir.create(saveDir, recursive = TRUE)
@@ -153,9 +157,13 @@ 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))
       }
diff --git a/R/mpl_morphy_objects.R b/R/mpl_morphy_objects.R
index 66dbf1aa5..e4941d769 100644
--- a/R/mpl_morphy_objects.R
+++ b/R/mpl_morphy_objects.R
@@ -225,10 +225,9 @@ MorphyErrorCheck <- function(action) {
 #' Score a tree: [`MorphyTreeLength()`]
 #' 
 #' @family Morphy API functions
-#' @importFrom stringi stri_paste
 #' @export
 SingleCharMorphy <- function (char, gap = "inapp") {
-  char <- stri_paste(c(char, ";"), collapse = "")
+  char <- paste(c(char, ";"), collapse = "")
   entries <- gregexpr("\\{[^\\{]+\\}|\\([^\\()]+\\)|[^;]", char)
   nTip <- length(entries[[1]])
   morphyObj <- mpl_new_Morphy()
diff --git a/tests/testthat/test-ClusterStrings.R b/tests/testthat/test-ClusterStrings.R
index 6efef66e8..cc356d7bb 100644
--- a/tests/testthat/test-ClusterStrings.R
+++ b/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]))
diff --git a/tests/testthat/test-TaxonInfluence.R b/tests/testthat/test-TaxonInfluence.R
index 6a605ead5..9ec779104 100644
--- a/tests/testthat/test-TaxonInfluence.R
+++ b/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)

From 936acda0876ececbada6258100347e77870595c1 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 4 Nov 2025 16:27:10 +0000
Subject: [PATCH 3/5] Update NAMESPACE to remove imports for suggested packages

Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>
---
 NAMESPACE | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 79e40d690..8efc93b32 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -205,25 +205,15 @@ 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)
 importFrom(stats,runif)
 importFrom(stats,setNames)
 importFrom(stats,weighted.mean)
-importFrom(stringi,stri_paste)
 importFrom(utils,adist)
 importFrom(utils,combn)
 useDynLib(TreeSearch, .registration = TRUE)

From 3673dd31edef56f2bc4b9bd5f301da4aaa4a686e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Tue, 4 Nov 2025 16:31:12 +0000
Subject: [PATCH 4/5] Add clarifying comment for cache implementation

Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>
---
 R/Consistency.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/Consistency.R b/R/Consistency.R
index 717412fcf..ea7ec4751 100644
--- a/R/Consistency.R
+++ b/R/Consistency.R
@@ -109,6 +109,7 @@ Consistency <- function (dataset, tree, nRelabel = 0, compress = FALSE) {
 }
 
 
+# Cache for character length calculations (replaces previous fastmap implementation)
 .CharLengthCache <- new.env(parent = emptyenv())
 
 #' Expected length

From be2930e1de8a8fc0f13dd601f2d028b9e67d7420 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 5 Nov 2025 09:28:46 +0000
Subject: [PATCH 5/5] Keep fastmap and stringi for performance; add user
 prompts for package installation

Co-authored-by: ms609 <1695515+ms609@users.noreply.github.com>
---
 DESCRIPTION              |  2 ++
 NAMESPACE                |  2 ++
 R/ClusterStrings.R       | 13 ++-----------
 R/Consistency.R          | 13 +++++++------
 R/MaximizeParsimony.R    |  6 +-----
 R/TaxonInfluence.R       |  6 +-----
 R/TreeSearch_utilities.R | 25 +++++++++++++++++++++++++
 R/mpl_morphy_objects.R   |  3 ++-
 8 files changed, 42 insertions(+), 28 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 641565691..f7f37f8cc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -36,12 +36,14 @@ Depends: R (>= 4.0)
 Imports: 
   ape (>= 5.6),
   cli (>= 3.0),
+  fastmap,
   fastmatch (>= 1.1.3),
   PlotTools,
   Rcpp,
   Rdpack (>= 0.7),
   Rogue (> 2.0.0),
   stats,
+  stringi,
   TreeDist (>= 2.6.3),
   TreeTools (>= 1.16),
 Suggests:
diff --git a/NAMESPACE b/NAMESPACE
index 8efc93b32..bcd152bec 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -205,6 +205,7 @@ importFrom(cli,cli_h1)
 importFrom(cli,cli_progress_bar)
 importFrom(cli,cli_progress_done)
 importFrom(cli,cli_progress_update)
+importFrom(fastmap,fastmap)
 importFrom(fastmatch,"%fin%")
 importFrom(fastmatch,fmatch)
 importFrom(graphics,par)
@@ -214,6 +215,7 @@ importFrom(stats,median)
 importFrom(stats,runif)
 importFrom(stats,setNames)
 importFrom(stats,weighted.mean)
+importFrom(stringi,stri_paste)
 importFrom(utils,adist)
 importFrom(utils,combn)
 useDynLib(TreeSearch, .registration = TRUE)
diff --git a/R/ClusterStrings.R b/R/ClusterStrings.R
index caf8ae952..43953f206 100644
--- a/R/ClusterStrings.R
+++ b/R/ClusterStrings.R
@@ -26,17 +26,8 @@ ClusterStrings <- function (x, maxCluster = 12) {
     stop("`maxCluster` must be at least two.")
   }
   
-  if (!requireNamespace("cluster", quietly = TRUE)) {
-    stop("Package 'cluster' is required for ClusterStrings(). ",
-         "Install it with: install.packages('cluster')",
-         call. = FALSE)
-  }
-  
-  if (!requireNamespace("protoclust", quietly = TRUE)) {
-    stop("Package 'protoclust' is required for ClusterStrings(). ",
-         "Install it with: install.packages('protoclust')",
-         call. = FALSE)
-  }
+  .InstallSuggestedPackage("cluster")
+  .InstallSuggestedPackage("protoclust")
   
   if (length(unique(x)) < maxCluster) {
     nom <- unique(x)
diff --git a/R/Consistency.R b/R/Consistency.R
index ea7ec4751..bd695f758 100644
--- a/R/Consistency.R
+++ b/R/Consistency.R
@@ -109,8 +109,8 @@ Consistency <- function (dataset, tree, nRelabel = 0, compress = FALSE) {
 }
 
 
-# Cache for character length calculations (replaces previous fastmap implementation)
-.CharLengthCache <- new.env(parent = emptyenv())
+#' @importFrom fastmap fastmap
+.CharLengthCache <- fastmap()
 
 #' Expected length
 #' 
@@ -127,6 +127,7 @@ Consistency <- function (dataset, tree, nRelabel = 0, compress = FALSE) {
 #' 
 #' @export
 #' @importFrom stats median
+#' @importFrom stringi stri_paste
 #' @family tree scoring
 #' @template MRS
 ExpectedLength <- function(dataset, tree, nRelabel = 1000, compress = FALSE) {
@@ -150,9 +151,9 @@ ExpectedLength <- function(dataset, tree, nRelabel = 1000, compress = FALSE) {
   }, integer(nLevels)))
   
   .LengthForChar <- function(x) {
-    key <- paste(c(nRelabel, x), collapse = ",")
-    if (exists(key, envir = .CharLengthCache, inherits = FALSE)) {
-      get(key, envir = .CharLengthCache)
+    key <- stri_paste(c(nRelabel, x), collapse = ",")
+    if (.CharLengthCache$has(key)) {
+      .CharLengthCache$get(key)
     } else {
       patterns <- apply(unname(unique(t(
         as.data.frame(replicate(nRelabel, sample(rep(seq_along(x), x))))))),
@@ -169,7 +170,7 @@ ExpectedLength <- function(dataset, tree, nRelabel = 1000, compress = FALSE) {
         contrast = rwContrast,
         class = "phyDat")
       ret <- median(FastCharacterLength(tree, phy))
-      assign(key, ret, envir = .CharLengthCache)
+      .CharLengthCache$set(key, ret)
       ret
     }
   }
diff --git a/R/MaximizeParsimony.R b/R/MaximizeParsimony.R
index 3519ecba6..218cf9165 100644
--- a/R/MaximizeParsimony.R
+++ b/R/MaximizeParsimony.R
@@ -1001,11 +1001,7 @@ Resample <- function(dataset, tree, method = "jack", proportion = 2 / 3,
 #' @rdname MaximizeParsimony
 #' @export
 EasyTrees <- function () {#nocov start
-  if (!requireNamespace("shiny", quietly = TRUE)) {
-    stop("Package 'shiny' is required for EasyTrees(). ",
-         "Install it with: install.packages('shiny')",
-         call. = FALSE)
-  }
+  .InstallSuggestedPackage("shinyjs")
   shiny::runApp(system.file("Parsimony", package = "TreeSearch"))
 }
 
diff --git a/R/TaxonInfluence.R b/R/TaxonInfluence.R
index 67710a539..f27956775 100644
--- a/R/TaxonInfluence.R
+++ b/R/TaxonInfluence.R
@@ -121,11 +121,7 @@ TaxonInfluence <- function(
     ...
   ) {
   if (!is.null(savePath)) {
-    if (!requireNamespace("fs", quietly = TRUE)) {
-      stop("Package 'fs' is required when using savePath. ",
-           "Install it with: install.packages('fs')",
-           call. = FALSE)
-    }
+    .InstallSuggestedPackage("fs")
     saveDir <- dirname(paste0(savePath, "taxon_name"))
     if (!dir.exists(saveDir)) {
       dir.create(saveDir, recursive = TRUE)
diff --git a/R/TreeSearch_utilities.R b/R/TreeSearch_utilities.R
index 0945cfe59..63abfe6f2 100644
--- a/R/TreeSearch_utilities.R
+++ b/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)
+    }
+  }
+}
+
diff --git a/R/mpl_morphy_objects.R b/R/mpl_morphy_objects.R
index e4941d769..66dbf1aa5 100644
--- a/R/mpl_morphy_objects.R
+++ b/R/mpl_morphy_objects.R
@@ -225,9 +225,10 @@ MorphyErrorCheck <- function(action) {
 #' Score a tree: [`MorphyTreeLength()`]
 #' 
 #' @family Morphy API functions
+#' @importFrom stringi stri_paste
 #' @export
 SingleCharMorphy <- function (char, gap = "inapp") {
-  char <- paste(c(char, ";"), collapse = "")
+  char <- stri_paste(c(char, ";"), collapse = "")
   entries <- gregexpr("\\{[^\\{]+\\}|\\([^\\()]+\\)|[^;]", char)
   nTip <- length(entries[[1]])
   morphyObj <- mpl_new_Morphy()