Minor documentation fixes

R/get-phybreak.R

@@ -49,7 +49,8 @@ get.tree <- function(phybreak.object, samplenr = 0) {
 #' @param whichpars Which parameters to return. Either a vector with parameter names, or \code{"all"} for all parameters, or 
 #'   \code{"posterior"} for parameters for which a posterior is sampled.
 #' @export
-get.parameters <- function(phybreak.object, samplenr = 0, whichpars = "posterior") {
+get.parameters <- function(phybreak.object, samplenr = 0, 
+                           whichpars = "posterior") {
   if (!inherits(phybreak.object, "phybreak")) {
     stop("object must be of class \"phybreak\"")
   }
@@ -173,9 +174,11 @@ get.mcmc <- function(phybreak.object, thin = 1, nkeep = Inf) {
 #' 
 #' tree0 <- get.phylo(MCMCstate)
 #' seqdata <- get.seqdata(MCMCstate)
-#' phangorn::pml(tree0, seqdata, rate = 0.75*get.parameters(MCMCstate)["mu"]) 
+#' phangorn::pml(tree0, seqdata, 
+#'               rate = 0.75*get.parameters(MCMCstate)["mu"]) 
 #' logLik(MCMCstate, genetic = TRUE, withinhost = FALSE, 
-#'        sampling = FALSE, generation = FALSE) #should give the same result as 'pml'
+#'        sampling = FALSE, generation = FALSE) 
+#'               #should give the same result as 'pml'
 #' @export
 get.phylo <- function(phybreak.object, samplenr = 0, simmap = FALSE) {
   ### tests

R/transtree.R

@@ -14,8 +14,10 @@
 #'     infector in the posterior distribution.
 #'   \item \code{"edmonds"} starts from the most frequent infector (method \code{"count"}), multiple roots and 
 #'     cycles are removed by selecting one by one the next most frequent option that minimizes the loss in support 
-#'     (\href{https://en.wikipedia.org/wiki/Edmonds/'_algorithm}{Edmonds' algorithm}). Support is measured by the frequency of the infector in the posterior distribution.
-#'   \item{"mpc"} gives the maximum parent credibility tree as described in \href{http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004613}{Hall et al (2015)}. This is the tree 
+#'     (\href{https://en.wikipedia.org/wiki/Edmonds'_algorithm}{Edmonds' algorithm}). Support is measured by the 
+#'     frequency of the infector in the posterior distribution.
+#'   \item{"mpc"} gives the maximum parent credibility tree as described in 
+#'     \href{http://dx.doi.org/10.1371/journal.pcbi.1004613}{Hall et al (2015)}. This is the tree 
 #'     in the set of posterior samples that has maximum support = product of frequencies among all posterior samples. 
 #'     Support is measured by the frequency of the infector in the posterior distribution.
 #'   \item{"mtcc"} gives the maximum transmission cluster credibility tree. This is equivalent to the maximum clade