Update package so it can be published again on CRAN

DESCRIPTION

@@ -1,14 +1,6 @@
 Package: TDAmapper
-Title: Analyze High-Dimensional Data Using Discrete Morse Theory
-Version: 1.0
-Date: 2015-05-26
-Authors@R: c(person("Paul", "Pearson", email = "pearsonp@hope.edu", 
-    role = c("aut", "cre","trl")), person("Daniel", "Muellner", 
-    role = c("aut","ctb")), person("Gurjeet","Singh", role = c("aut","ctb")))
-Author: Paul Pearson [aut, cre, trl],
-    Daniel Muellner [aut, ctb],
-	Gurjeet Singh [aut, ctb]
-Maintainer: Paul Pearson <pearsonp@hope.edu>
+Version: 1.1
+License: GPL-3
 Description: Topological Data Analysis using Mapper (discrete Morse theory).
     Generate a 1-dimensional simplicial complex from a filter 
     function defined on the data:  1. Define a filter function (lens) on the 
@@ -18,9 +10,16 @@ Description: Topological Data Analysis using Mapper (discrete Morse theory).
     between vertices.  The function mapper1D uses a filter function with
     codomain R, while the the function mapper2D uses a filter function with
     codomain R^2.
+Title: Analyze High-Dimensional Data Using Discrete Morse Theory
+Date: 2024-09-24
+Authors@R: c(person("Paul", "Pearson", email = "pearsonp@hope.edu", role = c("aut", "cre", "trl", "cph")),
+             person("Daniel", "Muellner", role = c("aut","ctb")),
+             person("Gurjeet","Singh", role = c("aut","ctb")),
+             person("Iago", "Giné-Vázquez", role = "ctb", email = "iago.gin-vaz@protonmail.com", comment = c(ORCID = "0000-0002-6725-2638")))
 Depends: R (>= 3.1.2)
-Suggests: fastcluster, igraph
-License: GPL-3
-LazyData: true
+Suggests: fastcluster, igraph, networkD3, knitr
 URL: https://github.com/paultpearson/TDAmapper/
 BugReports: https://github.com/paultpearson/TDAmapper/issues
+VignetteBuilder: knitr
+Encoding: UTF-8
+RoxygenNote: 7.3.2

NAMESPACE

@@ -1,7 +1,12 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(mapper)
 export(mapper1D)
 export(mapper2D)
 export(mapperEdges)
 export(mapperVertices)
+importFrom(graphics,hist)
+importFrom(stats,as.dist)
+importFrom(stats,cutree)
+importFrom(stats,dist)
+importFrom(stats,hclust)

NEWS.md

@@ -0,0 +1,4 @@
+# TDAmapper v1.1
+
+* Minimal update solving warnings in [CRAN Check Results](https://cran-archive.r-project.org/web/checks/2022/2022-06-13_check_results_TDAmapper.html) with the goal of returning the package to [CRAN](https://cran.r-project.org).
+

R/cluster_cutoff_at_first_empty_bin.R

@@ -5,7 +5,9 @@
 #' @param heights Height values in hierarchical clustering.
 #' @param diam Maximum distance between points in a level set.
 #' @param num_bins_when_clustering Controls how many bins there are in the histogram used to determine cutoff. values
-#' 
+#'
+#' @importFrom graphics hist
+#'
 #' @return Numerical value for cutoff point of hierarchical cluster diagram.
 #'
 #' @author Paul Pearson, \email{pearsonp@@hope.edu}

R/mapper.R

@@ -34,7 +34,7 @@
 #'
 
 
-mapper <- function(dist_object, filter_values, num_intervals, percent_overlap, num_bins_when_clustering) {
+mapper <- function(distance_matrix, filter_values, num_intervals, percent_overlap, num_bins_when_clustering) {
     ##### begin documentation ############
     # inputs
     # f : X \subset R^n \to R^k, a filter function on a data set with numpoints observations
@@ -164,7 +164,7 @@ mapper <- function(dist_object, filter_values, num_intervals, percent_overlap, n
         if (num_points_in_this_level > 1) {
             # heirarchical clustering
             level_dist_object <- as.dist(
-                as.matrix(dist_object)[points_in_this_level,points_in_this_level])
+                as.matrix(distance_matrix)[points_in_this_level,points_in_this_level])
             level_max_dist <- max(level_dist_object)
             level_hclust   <- hclust( level_dist_object, method="single" )
             level_heights  <- level_hclust$height

R/mapper1D.R

@@ -8,6 +8,8 @@
 #' @param percent_overlap A number between 0 and 100 specifying how much adjacent intervals should overlap.
 #' @param num_bins_when_clustering A positive integer that controls whether points in the same level set end up in the same cluster.
 #'
+#' @importFrom stats as.dist cutree dist hclust
+#'
 #' @return An object of class \code{TDAmapper} which is a list of items named \code{adjacency} (adjacency matrix for the edges), \code{num_vertices} (integer number of vertices), \code{level_of_vertex} (vector with \code{level_of_vertex[i]} = index of the level set for vertex i), \code{points_in_vertex} (list with \code{points_in_vertex[[i]]} = vector of indices of points in vertex i), \code{points_in_level} (list with \code{points_in_level[[i]]} = vector of indices of points in level set i, and \code{vertices_in_level} (list with \code{vertices_in_level[[i]]} = vector of indices of vertices in level set i.
 #'
 #' @author Paul Pearson, \email{pearsonp@@hope.edu}

R/mapper2D.R

@@ -8,6 +8,8 @@
 #' @param percent_overlap a number between 0 and 100 specifying how much adjacent intervals should overlap
 #' @param num_bins_when_clustering a positive integer that controls whether points in the same level set end up in the same cluster
 #'
+#' @importFrom stats as.dist cutree dist hclust
+#'
 #' @return An object of class \code{TDAmapper} which is a list of items named \code{adjacency} (adjacency matrix for the edges), \code{num_vertices} (integer number of vertices), \code{level_of_vertex} (vector with \code{level_of_vertex[i]} = index of the level set for vertex i), \code{points_in_vertex} (list with \code{points_in_vertex[[i]]} = vector of indices of points in vertex i), \code{points_in_level} (list with \code{points_in_level[[i]]} = vector of indices of points in level set i, and \code{vertices_in_level} (list with \code{vertices_in_level[[i]]} = vector of indices of vertices in level set i.
 #'
 #' @author Paul Pearson, \email{pearsonp@@hope.edu}

R/mapperVertices.R

@@ -6,6 +6,8 @@
 #'
 #' @param m An object of class TDAmapper that is the output of the mapper 
 #' function.
+#' @param pt_labels Point labels for vertices. Character class or coercible
+#' to character
 #'
 #' @return A data frame describing the vertices in the graph of the mapper 
 #' output and the point labels that will be displayed when the mouse