diff --git a/R/tree_distance_info.R b/R/tree_distance_info.R index 22fa1b4c..4fdd2d19 100644 --- a/R/tree_distance_info.R +++ b/R/tree_distance_info.R @@ -13,7 +13,7 @@ #' #' The methods implemented here use the concepts of #' [entropy and information](https://ms609.github.io/TreeDist/articles/information.html) -#' \insertCite{Mackay2003}{TreeDist} to assign a similarity score between each +#' \insertCite{Mackay2003}{BigTreeDist} to assign a similarity score between each #' pair of splits. #' #' The returned tree similarity measures state the amount of information, diff --git a/R/tree_distance_msd.R b/R/tree_distance_msd.R index 7a7ed5a7..fede185a 100644 --- a/R/tree_distance_msd.R +++ b/R/tree_distance_msd.R @@ -2,7 +2,7 @@ #' #' Calculate the #' [Matching Split Distance](https://ms609.github.io/TreeDist/articles/Generalized-RF.html#matching-split-distance) -#' \insertCite{Bogdanowicz2012,Lin2012}{TreeDist} for unrooted binary trees. +#' \insertCite{Bogdanowicz2012,Lin2012}{BigTreeDist} for unrooted binary trees. #' #' Trees need not contain identical leaves; scores are based on the leaves that #' trees hold in common. Check for unexpected differences in tip labelling diff --git a/R/tree_distance_nye.R b/R/tree_distance_nye.R index 0cb5958b..183caf4c 100644 --- a/R/tree_distance_nye.R +++ b/R/tree_distance_nye.R @@ -2,7 +2,7 @@ #' #' `NyeSimilarity()` and `NyeSplitSimilarity()` implement the #' [Generalized Robinson–Foulds](https://ms609.github.io/TreeDist/articles/Robinson-Foulds.html#generalized-robinson-foulds-distances) -#' tree comparison metric of \insertCite{Nye2006;textual}{TreeDist}. +#' tree comparison metric of \insertCite{Nye2006;textual}{BigTreeDist}. #' 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 #' the size of the largest split that is consistent with both of them, @@ -112,7 +112,7 @@ NyeSplitSimilarity <- function(splits1, splits2, #' #' Calculate the #' [Jaccard–Robinson–Foulds metric](https://ms609.github.io/TreeDist/articles/Generalized-RF.html#jaccard-robinson-foulds-metric) -#' \insertCite{Bocker2013}{TreeDist}, a +#' \insertCite{Bocker2013}{BigTreeDist}, a #' [Generalized Robinson–Foulds metric](https://ms609.github.io/TreeDist/articles/Robinson-Foulds.html#generalized-robinson-foulds-distances). #' #' In short, the Jaccard–Robinson–Foulds diff --git a/man/JaccardRobinsonFoulds.Rd b/man/JaccardRobinsonFoulds.Rd index 5b7774b0..23c6190c 100644 --- a/man/JaccardRobinsonFoulds.Rd +++ b/man/JaccardRobinsonFoulds.Rd @@ -70,7 +70,7 @@ or \code{splits1} and \code{splits2}. \description{ Calculate the \href{https://ms609.github.io/TreeDist/articles/Generalized-RF.html#jaccard-robinson-foulds-metric}{Jaccard–Robinson–Foulds metric} -\insertCite{Bocker2013}{TreeDist}, a +\insertCite{Bocker2013}{BigTreeDist}, a \href{https://ms609.github.io/TreeDist/articles/Robinson-Foulds.html#generalized-robinson-foulds-distances}{Generalized Robinson–Foulds metric}. } \details{ diff --git a/man/NyeSimilarity.Rd b/man/NyeSimilarity.Rd index 00314716..a836e48b 100644 --- a/man/NyeSimilarity.Rd +++ b/man/NyeSimilarity.Rd @@ -69,7 +69,7 @@ or \code{splits1} and \code{splits2}. \description{ \code{NyeSimilarity()} and \code{NyeSplitSimilarity()} implement the \href{https://ms609.github.io/TreeDist/articles/Robinson-Foulds.html#generalized-robinson-foulds-distances}{Generalized Robinson–Foulds} -tree comparison metric of \insertCite{Nye2006;textual}{TreeDist}. +tree comparison metric of \insertCite{Nye2006;textual}{BigTreeDist}. 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 the size of the largest split that is consistent with both of them,