Working on documentation

Author: gvegayon

R/aphylo_mcmc.R

@@ -3,7 +3,7 @@
 #' @details `APHYLO_DEFAULT_MCMC_CONTROL` lists the default values for the MCMC
 #' estimation:
 #' - `nsteps`: \Sexpr{aphylo::APHYLO_DEFAULT_MCMC_CONTROL$nsteps}
-#' - `nsteps`: \Sexpr{aphylo::APHYLO_DEFAULT_MCMC_CONTROL$burnin}
+#' - `burnin`: \Sexpr{aphylo::APHYLO_DEFAULT_MCMC_CONTROL$burnin}
 #' - `thin` : \Sexpr{aphylo::APHYLO_DEFAULT_MCMC_CONTROL$thin}
 #' - `nchains` : \Sexpr{aphylo::APHYLO_DEFAULT_MCMC_CONTROL$nchains}
 #' - `multicore` : \Sexpr{aphylo::APHYLO_DEFAULT_MCMC_CONTROL$multicore}

R/simulation.R

@@ -255,6 +255,7 @@ sim_fun_on_tree <- function(
 #' @templateVar .Pi 1
 #' @templateVar .types 1
 #' @param informative,maxtries Passed to [sim_fun_on_tree].
+#' @param edge.length Passed to [sim_tree].
 #' @return An object of class [aphylo]
 #' @family Simulation Functions 
 #' @export
@@ -267,6 +268,7 @@ sim_fun_on_tree <- function(
 raphylo <- function(
   n           = NULL,
   tree        = NULL,
+  edge.length = NULL,
   tip.type    = NULL,
   node.type   = function(n) sample.int(2, size = n, replace = TRUE, prob = c(.2, .8)) - 1,
   P           = 1L,
@@ -286,7 +288,15 @@ raphylo <- function(
     # Checking if there's n
     if (!length(n))
       stop("When -tree- is not specified, -n- must be specified.")
-    tree  <- sim_tree(n)
+    tree  <- do.call(
+      sim_tree, c(
+        list(n = n),
+        if (is.null(edge.length))
+          list(edge.length = edge.length)
+        else
+          NULL
+        )
+      )
 
   } else if (is.aphylo(tree)) {
 

man/aphylo_mcmc.Rd

@@ -46,13 +46,10 @@ If needed, we can export the data as follows:
 
 ```{r eval=FALSE}
 # Edgelist describing parent->offspring relations
-edges <- x$tree$edge
-colnames(edges) <- c("parent", "offspring")
-write.csv(edges, file = "edgelist.csv", row.names = FALSE)
+write.csv(x$tree, file = "tree.tree", row.names = FALSE)
 
 # Tip annotations
 ann <- with(x, rbind(tip.annotation, node.annotation))
-rownames(ann) <- 1L:nrow(ann)
 write.csv(ann, file = "annotations.csv", row.names = FALSE)
 
 # Event types