Removed imports and fixed if(class) tests

Just trying to comply with CRAN suggestions

Author: danlwarren

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rwty
 Type: Package
 Title: R We There Yet? Visualizing MCMC Convergence in Phylogenetics
-Version: 1.0.2
+Version: 1.0.3
 Authors@R: c(person(given = "Dan", family = "Warren", role = c("aut", "cre"), email = "dan.l.warren@gmail.com"),
               person(given = "Anthony", family = "Geneva", role = "aut", email = "anthony.geneva@gmail.com"),
               person(given = "Rob", family = "Lanfear", role = "aut", email = "rob.lanfear@gmail.com"),
@@ -32,18 +32,7 @@ Imports:
     ggdendro,
     GGally,
     parallel,
-    usedist,
-    plotly,
-    png,
-    gifski,
-    gganimate,
-    transformr,
-    sf,
-    units,
-    beepr,
-    DT,
-    TreeDist,
-    magick,
+    TreeDist
 Suggests:
     knitr,
     testthat,

NAMESPACE

@@ -36,6 +36,7 @@ importFrom(TreeDist,InfoRobinsonFoulds)
 importFrom(TreeDist,JaccardRobinsonFoulds)
 importFrom(TreeDist,MASTInfo)
 importFrom(TreeDist,MASTSize)
+importFrom(TreeDist,MatchingSplitDistance)
 importFrom(TreeDist,MatchingSplitInfoDistance)
 importFrom(TreeDist,NNIDist)
 importFrom(TreeDist,NyeSimilarity)

R/check.chains.R

@@ -19,12 +19,12 @@
 check.chains <- function(chains){
 
   # if passed a single trees object, turn it into a list
-  if(class(chains) == "rwty.chain"){
+  if(inherits(chains, "rwty.chain")){
     chains <- list(chains)
   }
 
   # check chains is a list
-  if(class(chains)!='list'){
+  if(!inherits(chains, 'list')){
     stop("'chains' must be a list of rwty.chain objects")        
   }
 

R/clade.freq.R

@@ -23,11 +23,11 @@
 # Modified from prop.part in APE, returning data in a more useful format
 clade.freq <- function (x, start, end, rooted=FALSE, ...) {
 
-  if(class(x) == "rwty.chain"){
+  if(inherits(x, "rwty.chain")){
     x <- x$trees
   }
 
-   if (length(x) == 1 && class(x[[1]]) == "multiPhylo"){
+   if (length(x) == 1 && inherits(x[[1]], "multiPhylo")){
      x <- x[[1]]
    }
 

R/load.trees.R

@@ -4,7 +4,7 @@
 #'
 #' @param file A path to a tree file containing an MCMC chain of trees
 #' @param type An argument that designates the type of tree file.  If "nexus",
-#' trees are loaded using ape's \code{\link[pkg:ape]{read.nexus}} function.  Otherwise, it's \code{\link[pkg:ape]{read.tree}}.
+#' trees are loaded using ape's \code{\link[ape]{read.nexus}} function.  Otherwise, it's \code{\link[ape]{read.tree}}.
 #' If a "format" argument is passed, type will be determined from the format definition.
 #' @param format File format, which is used to find tree and log files.
 #' Currently accepted values are "mb" for MrBayes, "beast" for BEAST, "*beast" for *BEAST, and "revbayes" for RevBayes.
@@ -19,7 +19,7 @@
 #' read in with a skip value of 1.  If no "skip" value is provided but a "format" is supplied, RWTY will
 #' attempt to read logs using the skip value from the format definition.
 #' @return output An rwty.chain object containing the multiPhylo and the table of values from the log file if available.
-#' @seealso \code{\link{read.tree}}, \code{\link{read.nexus}}
+#' @seealso \code{\link[ape]{read.tree}}, \code{\link[ape]{read.nexus}}
 #' @keywords Phylogenetics, MCMC, load
 #'
 #' @export load.trees

R/makeplot.acsf.cumulative.R

@@ -91,9 +91,9 @@ get.acsf <- function(freq.table){
 
 get.csf <- function(freq.table){
   # get a df of absolute differences in pp variation between windows
-  if(class(freq.table) == "rwty.slide"){
+  if(inherits(freq.table, "rwty.slide")){
     dat = freq.table$slide.table
-  }else if(class(freq.table) == "rwty.cumulative"){
+  }else if(inherits(freq.table, "rwty.cumulative")){
     dat = freq.table$cumulative.table
   }else{
     stop("ERROR: unknown type of frequency table passed to process.freq.table()")

R/makeplot.splitfreqs.sliding.R

@@ -92,9 +92,9 @@ single.splitfreq.plot <- function(dat, rank){
 process.freq.table <- function(freq.table, n.clades, rank){
 
     # strip out just the parts of a slide.freq.table or a cumulative.freq.table that we need
-    if(class(freq.table) == "rwty.slide"){
+    if(inherits(freq.table, "rwty.slide")){
         dat = freq.table$slide.table
-    }else if(class(freq.table) == "rwty.cumulative"){
+    }else if(inherits(freq.table, "rwty.cumulative")){
         dat = freq.table$cumulative.table
     }else{
         stop("ERROR: unknown type of frequency table passed to process.freq.table()")
@@ -116,10 +116,10 @@ process.freq.table <- function(freq.table, n.clades, rank){
     dat$clade = rownames(dat)
 
 
-    if(class(freq.table) == "rwty.slide"){
+    if(inherits(freq.table, "rwty.slide")){
         dat = melt(dat, id.vars=c("clade", "sd", "ess"))
         colnames(dat) = c("Clade", "StDev", "ESS", "Generations", "Split.Frequency")
-    }else if(class(freq.table) == "rwty.cumulative"){
+    }else if(inherits(freq.table, "rwty.cumulative")){
         dat = melt(dat, id.vars=c("clade", "sd", "wcsf"))
         colnames(dat) = c("Clade", "StDev", "WCSF", "Generations", "Split.Frequency")
     }

R/tree.dist.matrix.R

@@ -122,8 +122,8 @@
 #' @keywords treespace tree-distance robinson-foulds
 #'
 #' @importFrom TreeDist ClusteringInfoDistance InfoRobinsonFoulds 
-#' JaccardRobinsonFoulds MASTSize MASTInfo MatchingSplitInfoDistance NNIDist 
-#' NyeSimilarity PathDist PhylogeneticInfoDistance SPRDist
+#' JaccardRobinsonFoulds MASTSize MASTInfo MatchingSplitDistance MatchingSplitInfoDistance 
+#' NNIDist NyeSimilarity PathDist PhylogeneticInfoDistance SPRDist
 #' @export tree.dist.matrix
 #' @examples
 #' \dontrun{