diff --git a/NEWS.md b/NEWS.md index d59dbf5b..74027da1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,12 +1,12 @@ # Quartet v1.0.0 ## New features - - Add functions to generate ternary plots from tree similarity measures + - Add functions to generate ternary plots from tree similarity measures. ## Improvements - - Use tqDist for all quartet calculations - - Remove single "splits" from splits objects - - Simplify installation via github_install - - Add missing details to documentation + - Use tqDist for all quartet calculations. + - Remove single "splits" from splits objects. + - Simplify installation via `github_install`. + - Add missing details to documentation. ## Modifications - Function `SimilarityMetrics` now takes the output of `QuartetStatus(trees)`, diff --git a/R/Metrics.R b/R/Metrics.R index b03a5aec..a616b6d7 100644 --- a/R/Metrics.R +++ b/R/Metrics.R @@ -21,7 +21,7 @@ #' #' * SemiStrict Joint Assertions (SSJA): _s_ / (_s_ + _d_ + _u_) #' -#' (The numerator of the Semistrict Joint Assertions similarity metric is given in +#' (The numerator of the SemiStrict Joint Assertions similarity metric is given in #' Estabrook _et al_. (1985)'s table 2 as _s_ + _d_, but this is interpreted, with #' reference to their text, as a typographic error.) #' @@ -31,7 +31,7 @@ #' * Steel & Penny's Quartet Metric (dQ): (_s_ + _u_) / _Q_ #' #' -#' Although defined using quartets, analagous values can be calculated using +#' Although defined using quartets, analogous values can be calculated using #' partitions by replacing _s_ and _d_ with 2_s_ and (_d1_ + _d2_), #' and _Q_ with _N_. #' Note that, for reasons listed elsewhere (see Smith 2019, supplementary text), diff --git a/vignettes/Critical-distances.Rmd b/vignettes/Critical-distances.Rmd index 80f4b67b..9d7a1a73 100644 --- a/vignettes/Critical-distances.Rmd +++ b/vignettes/Critical-distances.Rmd @@ -49,7 +49,8 @@ par(mar=rep(0.3, 4)) plot(tree_b) ``` -Now create Tree C by adding a 6th tip as a sister to tip `3` on Tree A. +Now create Tree C by adding a 6th tip as a sister to tip `3` on Tree A. + ```{r tree-c} tree_c <- ape::read.tree(text="((1, 2), ((3, 6), (4, 5)));") ``` diff --git a/vignettes/Tree-distance-metrics.Rmd b/vignettes/Tree-distance-metrics.Rmd index 3fccfb49..9d711d53 100644 --- a/vignettes/Tree-distance-metrics.Rmd +++ b/vignettes/Tree-distance-metrics.Rmd @@ -72,7 +72,7 @@ Given two trees, is possible to calculate the difference in path length between each pair of tips. The path difference metric [@Steel1993; `r Phangorn('path.dist')`] is the -square root of the sum of squaresof each of these differences. +square root of the sum of squares of each of these differences. ## Partition metric The Robinson-Foulds (RF or 'partition') metric [@Robinson1981; @Steel1993;