CHANGES in cladoRcpp VERSION 0.15.1 -- 2018-11-21
NEW FEATURES
o none
BUG FIXES
o none
OTHER CHANGES
o 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}'
CHANGES in cladoRcpp VERSION 0.15 -- 2018-10-03
NEW FEATURES
o 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).
BUG FIXES
o none
OTHER CHANGES
o Code hosted on GitHub as well. (https://github.com/nmatzke/cladoRcpp )
o Changed Maintainer email to nickmatzke.ncse@gmail.com (more permanent)
CHANGES in cladoRcpp VERSION 0.14.4 -- 2014-05-17
NEW FEATURES
o none
BUG FIXES
o Commented out references to citation("rexpokit") and citation("BioGeoBEARS") in
examples -- these create unnecessary dependencies in the examples.
o Also removed within-documentation hot-links to rexpokit, for the same reason.
OTHER CHANGES
o none
CHANGES in cladoRcpp VERSION 0.14.3 -- 2014-05-16
NEW FEATURES
o none
BUG FIXES
o These were not material bugs, these were issues noted by CRAN due to
updates to R / R CMD check:
o removed an 'extern "C"' from basics.h (not needed on a C++ function)
o 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.
OTHER CHANGES
o added CITATION file and information
o 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
o 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.
CHANGES in cladoRcpp VERSION 0.14.2
NEW FEATURES
o 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.) )
BUG FIXES
o none
OTHER CHANGES
o none
CHANGES in cladoRcpp VERSION 0.14.1
NEW FEATURES
o 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.
BUG FIXES
o none
OTHER CHANGES
o none