Removing empty code flags

R/simulation.R

@@ -1,8 +1,7 @@
 #' Random tree generation
-#' 
+#' @details
 #' An alternative to [ape::rtree]. This function was written in C++ and is 
 #' significantly faster than `rtree`. 
-#' 
 #' @param n Integer scalar. Number of leaf nodes.
 #' @param edge.length A Function. Used to set the length of the edges.
 #' 
@@ -60,8 +59,7 @@ sim_tree <- function(n, edge.length = stats::runif) {
 
 }
 
-#' Simulate functions on a ginven tree
-#' 
+#' @title Simulate functions on a ginven tree
 #' @param tree An object of class [phylo][ape::read.tree]
 #' @template parameters
 #' @templateVar .psi 1
@@ -243,7 +241,6 @@ sim_fun_on_tree <- function(
 }
 
 #' Simulation of Annotated Phylogenetic Trees
-#' 
 #' @param n Integer scalar. Number of leafs. If not specified, then 
 #' @param tree An object of class [phylo][ape::read.tree].
 #' @param P Integer scalar. Number of functions to generate.
@@ -370,11 +367,9 @@ rmultiAphylo <- function(R, ...) {
 #' 
 #' @param atree An object of class [aphylo].
 #' @template parameters
-#' @templateVar .psi
-#' 
+#' @templateVar .psi 1
 #' @return An object of class [aphylo] with modified labels.
 #' @examples 
-#' 
 #' set.seed(131)
 #' x <- raphylo(5, P=2, psi=c(0,0))
 #' x$tip.annotation

man-roxygen/edges.r

@@ -1,3 +1,2 @@
-#' \code{}
 #' @param edges Integer matrix with two columns. An edgelist where each row is in the form of \\code{(parent, offspring)}.
 #' 

man-roxygen/parameters.r

@@ -1,4 +1,3 @@
-#' \code{}
 #' <%=ifelse(exists(".annotationslab"), "@param annotations Matrix of size \\eqn{n\\times P + 1}{n*P + 1}. Annotation data, where the first column is the nodeid (should coincide with the coding of the tree), the following columns are function annotations coded as \\code{1} if the node has the function, \\code{0} if the node doesn't has the function and \\code{9} or \\code{NA} otherwise (no information).", "") %>
 #' <%=ifelse(exists(".annotations"),    "@param annotations Matrix of size \\eqn{n\\times P}{n*P}. Annotation data, each column is a functional annotation coded as \\code{1} if the node has the function, \\code{0} if the node doesn't has the function and \\code{9} or \\code{NA} otherwise (no information).", "") %>
 #' <%=ifelse(exists(".tip.annotation"), "@param tip.annotation,node.annotation Annotation data. See [aphylo-class].", "") %>