Changed style and certain argument names of draw.sim. Changed example…

…s in various functions to be in line with new draw.sim requirements. Updated NEWS.md. Added @Aliases field in paleobuddy.R to be in line with current roxygen requirements.

NAMESPACE

@@ -7,7 +7,7 @@ S3method(summary,sim)
 S3method(tail,sim)
 export(bd.sim)
 export(bd.sim.traits)
-export(binarize)
+export(bin.occurrences)
 export(binner)
 export(draw.sim)
 export(find.lineages)
@@ -24,6 +24,7 @@ export(var.rate.div)
 import(stats)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,rgb)
+importFrom(graphics,legend)
 importFrom(graphics,par)
 importFrom(graphics,plot)
 importFrom(graphics,points)

NEWS.md

@@ -40,6 +40,14 @@ BiSSE, MuSSE, and QuaSSE. See documentation for full reference.
  coming from `bd.sim.traits`) needs to include all states as observed
  for that (see examples in `?sample.clade.traits` and vignettes for
  details).
+- `draw.sim` can now color longevity segments and fossil occurrences
+ based on the trait values of a given trait for each species through
+ time. Customization options include which colors to use for each
+ state, whether to plot fossils as true occurrence times or ranges
+ (already present in 1.0, but now with a dedicated argument for such,
+ `fossilsToDraw`), and where to place trait value legend. See
+ `?draw.sim`, `?bd.sim.traits`, `?sample.clade.traits`, and the
+ `overview` vignette for examples.
 
 ## Adding sampled ancestors to a phylogenetic tree
 
@@ -64,6 +72,13 @@ BiSSE, MuSSE, and QuaSSE. See documentation for full reference.
  reviewer in the manuscript.
 - Examples of new features for version 1.1 (see above) were added.
 
+## Other additions
+
+- `bin.occurrences` allows for ad-hoc binning of fossil occurrences, so
+ one can take a fossil record including only true times, i.e. an output
+ of `sample.clade(..., returnTrue = TRUE)`, and bin it to produce the
+ uncertainty in fossil ages ubiquitous in the true fossil record.
+
 ## Simple fixes
 
 - `sample.clade.R`: added a small bit on help page to explain the

R/binarize.R

@@ -39,18 +39,18 @@
 #' fossils_true <- sample.clade(sim, rho = 1, tMax = 50, returnTrue = TRUE)
 #' 
 #' # bin the true occurrences
-#' fossils_binned <- binarize(fossils_true, bins)
+#' fossils_binned <- bin.occurrences(fossils_true, bins)
 #' 
 #' # compare
 #' fossils_true
 #' fossils_binned
 #' 
-#' @name binarize
-#' @rdname binarize
+#' @name bin.occurrences
+#' @rdname bin.occurrences
 #' @export
 #' 
 
-binarize <- function(fossils, bins) {
+bin.occurrences <- function(fossils, bins) {
  # sort bins in decreasing order
  bins <- sort(bins, decreasing = TRUE)