NEWS

cladoRcpp 0.15.1 (2018-11-21)

Added R documentation file 00-cladoRcpp-package.Rd, which got lost somewhere in the updates. This contains aliases so that ?cladoRcpp brings up the package information, and also should fix CRAN warnings for BioGeoBEARS like: checking Rd cross-references ... WARNING Missing link or links in documentation object 'BioGeoBEARS-package.Rd': '[cladoRcpp]{cladoRcpp}'

added modifications for trait-dependent dispersal model variants (basically, the cladogenetic transition matrix can be doubled-up, e.g. if a 2-state trait is influencing dispersal. Dispersal multipliers (m1, m2, etc.) are multiplied by the base j value. This takes place as a last step (after j has been used to modify the per-event cladogenetic weights for y, s, and v (narrow sympatry, subset sympatry, and vicariance per-event weights).

Commented out references to citation("rexpokit") and citation("BioGeoBEARS") in examples -- these create unnecessary dependencies in the examples.
Also removed within-documentation hot-links to rexpokit, for the same reason.

These were not material bugs, these were issues noted by CRAN due to updates to R / R CMD check:
removed an 'extern "C"' from basics.h (not needed on a C++ function)
updated DESCRIPTION file as methods/Rcpp/RcppArmadillo do not need to be dependencies; just LinkingTo for Rcpp/RcppArmadillo (to access their C++ headers) and Imports: for Rcpp, so that importFrom(Rcpp, evalCpp) in the NAMESPACE file generated by Rcpp.package.skeleton works after I have used it to build the package source.

added CITATION file and information
updated CITATION file to refer to first publication citing CladoRcpp & BioGeoBEARS: Matzke, Nicholas J. (2013). Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing. Frontiers of Biogeography, 5(4), 242-248. http://escholarship.org/uc/item/44j7n141
changed \link{Rcpp} to Rcpp in the roxygen2 documentation files (which roxygen2 changes into .Rd (R documentation files). Links in documentation didn't work after removing Rcpp from Depends: field.

Version 0.14.2 of package cladoRcpp fixes an AddressSanitizer error found when compiling under gcc48, and some notes found by Uwe Ligges's WinBuilder website, due unused variables, or comparison of int to unsigned int in e.g. for loops. (For the latter, the vector object's .size() function returns an unsigned int, so the forloop should start with for (unsigned int i, ...etc.) )

Version 0.14.1 of package cladoRcpp adds to the function rcpp_states_list_to_DEmat (and thus C++ functions cpp_states_list_to_DEmat_COO and cpp_states_list_to_DEmat) the input of "amat", a matrix of anagenetic transition probabilities for e.g. instantaneous switching from A->B. This allows cladoRcpp users to implement "standard" character transition models, as used in e.g. DNA, morphology characters, etc., as well as in biogeography. Additional of this parameter allows increased modeling capabilities in BioGeoBEARS. I have also added a NEWS file.