–→\ifelse{html}{&#ndash;}{--}

R/TreeDist-package.R

@@ -6,7 +6,7 @@
 #' distance-based tree spaces.
 #' 
 #' 'TreeDist' primarily employs metrics in the category of
-#' 'generalized Robinson–Foulds distances': they are based on comparing splits
+#' 'generalized Robinson\ifelse{html}{&#ndash;}{--}Foulds distances': they are based on comparing splits
 #' (bipartitions) between trees, and thus reflect the relationship data within 
 #' trees, with no reference to branch lengths.
 #' Detailed documentation and usage instructions are 
@@ -15,7 +15,7 @@
 #' 
 #' ## Generalized RF distances
 #' 
-#' The [Robinson–Foulds distance](https://ms609.github.io/TreeDist/articles/Robinson-Foulds.html)
+#' The [Robinson\ifelse{html}{&#ndash;}{--}Foulds distance](https://ms609.github.io/TreeDist/articles/Robinson-Foulds.html)
 #' simply tallies the number of non-trivial splits (sometimes inaccurately
 #' termed clades, nodes or edges) that occur in both trees -- any splits that are
 #' not perfectly identical contributes one point to the distance score of zero, 
@@ -48,7 +48,7 @@
 #'   + Nye _et al._ (2006) score matchings according to the size of the largest 
 #'     split that is consistent with both of them, normalized against 
 #'     the Jaccard index.  This approach is extended by Böcker _et al_. (2013)
-#'     with the Jaccard–Robinson–Foulds metric (function 
+#'     with the Jaccard\ifelse{html}{&#ndash;}{--}Robinson\ifelse{html}{&#ndash;}{--}Foulds metric (function 
 #'     [`JaccardRobinsonFoulds()`](https://ms609.github.io/TreeDist/reference/JaccardRobinsonFoulds.html)).
 #' 
 #' * [`MatchingSplitDistance()`](https://ms609.github.io/TreeDist/reference/MatchingSplitDistance.html)
@@ -99,9 +99,9 @@
 #'   
 #'   * [ape](http://ape-package.ird.fr/):
 #'     - `cophenetic.phylo()`: Cophenetic distance
-#'     - `dist.topo()`: Path (topological) distance, Robinson–Foulds distance.
+#'     - `dist.topo()`: Path (topological) distance, Robinson\ifelse{html}{&#ndash;}{--}Foulds distance.
 #'   * [phangorn](https://cran.r-project.org/package=phangorn)
-#'     - `treedist()`: Path, Robinson–Foulds and approximate SPR distances.
+#'     - `treedist()`: Path, Robinson\ifelse{html}{&#ndash;}{--}Foulds and approximate SPR distances.
 #'   * [Quartet](https://ms609.github.io/Quartet/): Triplet and Quartet distances, 
 #'   using the tqDist algorithm.
 #'   * [TBRDist](https://ms609.github.io/TBRDist/): TBR and SPR distances on 

R/plot.R

@@ -61,13 +61,13 @@ TreeDistPlot <- function (tr, title = NULL, bold = NULL, leaveRoom = FALSE,
 #' Visualise a matching
 #' 
 #' Depict the splits that are matched between two trees using a specified 
-#' [Generalized Robinson–Foulds](https://ms609.github.io/TreeDist/articles/Generalized-RF.html)
+#' [Generalized Robinson\ifelse{html}{&#ndash;}{--}Foulds](https://ms609.github.io/TreeDist/articles/Generalized-RF.html)
 #' similarity measure.
 #' 
-#' Note that when visualizing a Robinson–Foulds distance (using 
+#' Note that when visualizing a Robinson\ifelse{html}{&#ndash;}{--}Foulds distance (using 
 #' `Func = RobinsonFouldsMatching`), matched splits are assigned a _similarity_
 #' score of 1, which is deducted from the total number of splits to calculate 
-#' the Robinson–Foulds _distance_.  Unmatched splits thus contribute one to 
+#' the Robinson\ifelse{html}{&#ndash;}{--}Foulds _distance_.  Unmatched splits thus contribute one to 
 #' total tree distance.
 #' 
 #' @param Func Function used to construct tree similarity.

R/tree_distance.R

@@ -1,6 +1,7 @@
-#' Generalized Robinson–Foulds distance
+#' Generalized Robinson\ifelse{html}{&#ndash;}{--}Foulds distance
 #' 
-#' An internal function to calculate Generalized Robinson–Foulds distances from
+#' An internal function to calculate Generalized 
+#' Robinson\ifelse{html}{&#ndash;}{--}Foulds distances from
 #' splits.
 #'
 #' Note that no checks will be made to confirm that `splits1` and `splits2`

R/tree_distance_info.R

@@ -1,11 +1,11 @@
-#' Information-based generalized Robinson–Foulds distances
+#' Information-based generalized Robinson\ifelse{html}{&#ndash;}{--}Foulds distances
 #'
 #' Calculate tree similarity and distance measures based on the amount of 
 #' phylogenetic or clustering information that two trees hold in common, as
 #' proposed in Smith (2020).
 #' 
 #' 
-#' [Generalized Robinson–Foulds distances](https://ms609.github.io/TreeDist/articles/Robinson-Foulds.html#generalized-robinson-foulds-distances)
+#' [Generalized Robinson\ifelse{html}{&#ndash;}{--}Foulds distances](https://ms609.github.io/TreeDist/articles/Robinson-Foulds.html#generalized-robinson-foulds-distances)
 #' calculate tree similarity by finding an
 #' optimal matching that the similarity between a split on one tree
 #' and its pair on a second, considering all possible ways to pair splits 

R/tree_distance_nye.R

@@ -1,7 +1,7 @@
 #' Nye _et al_. (2006) tree comparison
 #' 
 #' `NyeSimilarity()` and `NyeSplitSimilarity()` implement the 
-#' [Generalized Robinson–Foulds](https://ms609.github.io/TreeDist/articles/Robinson-Foulds.html#generalized-robinson-foulds-distances)
+#' [Generalized Robinson\ifelse{html}{&#ndash;}{--}Foulds](https://ms609.github.io/TreeDist/articles/Robinson-Foulds.html#generalized-robinson-foulds-distances)
 #' tree comparison metric of Nye _et al_. (2006).
 #' In short, this finds the optimal matching that pairs each branch from
 #' one tree with a branch in the second, where matchings are scored according to
@@ -103,14 +103,14 @@ NyeSplitSimilarity <- function (splits1, splits2,
                 reportMatching = reportMatching)
 }
 
-#' Jaccard–Robinson–Foulds metric
+#' Jaccard\ifelse{html}{&#ndash;}{--}Robinson\ifelse{html}{&#ndash;}{--}Foulds metric
 #' 
 #' Calculate the 
-#' [Jaccard–Robinson–Foulds metric](https://ms609.github.io/TreeDist/articles/Generalized-RF.html#jaccard-robinson-foulds-metric)
+#' [Jaccard\ifelse{html}{&#ndash;}{--}Robinson\ifelse{html}{&#ndash;}{--}Foulds metric](https://ms609.github.io/TreeDist/articles/Generalized-RF.html#jaccard-robinson-foulds-metric)
 #' (B&ouml;cker _et al_. 2013), a 
-#' [Generalized Robinson–Foulds metric](https://ms609.github.io/TreeDist/articles/Robinson-Foulds.html#generalized-robinson-foulds-distances).
+#' [Generalized Robinson\ifelse{html}{&#ndash;}{--}Foulds metric](https://ms609.github.io/TreeDist/articles/Robinson-Foulds.html#generalized-robinson-foulds-distances).
 #' 
-#' In short, the Jaccard–Robinson–Foulds metric is a generalized Robinson-Foulds
+#' In short, the Jaccard\ifelse{html}{&#ndash;}{--}Robinson\ifelse{html}{&#ndash;}{--}Foulds metric is a generalized Robinson-Foulds
 #' metric: it finds the optimal matching that pairs each split in one tree with
 #' a similar split in the second.
 #' Matchings are scored according to the size of the largest split that is 
@@ -132,7 +132,7 @@ NyeSplitSimilarity <- function (splits1, splits2,
 #' @param k An arbitrary exponent to which to raise the Jaccard index.
 #' Integer values greater than one are anticipated by B&ouml;cker _et al_.
 #' The Nye _et al_. metric uses `k = 1`.
-#' As k increases towards infinity, the metric converges to the Robinson–Foulds
+#' As k increases towards infinity, the metric converges to the Robinson\ifelse{html}{&#ndash;}{--}Foulds
 #' metric.
 #' @param allowConflict Logical specifying whether to allow conflicting splits
 #' to be paired. If `FALSE`, such pairings will be allocated a similarity

R/tree_distance_rf.R

@@ -1,9 +1,11 @@
-#' Robinson–Foulds distances, with adjustments for phylogenetic information
+#' Robinson\ifelse{html}{&#ndash;}{--}Foulds distances, with adjustments for phylogenetic information
 #' content
 #' 
-#' Calculate the Robinson–Foulds distance, or the equivalent similarity 
-#' measure, with options to (i) annotate matched splits; (ii) weight splits
-#' according to their phylogenetic information content (Smith 2020).
+#' Calculate the Robinson\ifelse{html}{&#ndash;}{--}Foulds distance, or
+#' the equivalent similarity measure, with options to
+#' (i) annotate matched splits; 
+#' (ii) weight splits according to their phylogenetic information content 
+#' (Smith 2020).
 #' 
 #' Note that if `reportMatching = TRUE`, the `pairScores` attribute returns
 #' a logical matrix specifying whether each pair of splits is identical.

inst/treespace/app.R

@@ -160,7 +160,7 @@ Sand2014 <- Reference(
     year = 2014
 )
 Smith2020 <- Reference('Smith, M.R.', 2020,
-  'Information theoretic Generalized Robinson–Foulds metrics for comparing phylogenetic trees',
+  'Information theoretic Generalized Robinson-Foulds metrics for comparing phylogenetic trees',
   'Bioinformatics', pages = 'In production', doi = "10.1093/bioinformatics/btaa614")
 Smith2021 <- Reference('*Smith, M.R.', 2021,
   'The importance of methodology when analyzing landscapes of phylogenetic trees',