C++ Implementations of Phylogenetic Cladogenesis Calculations
c(person("Nicholas J.", "Matzke", email="nickmatzke.ncse@gmail.com", role=
c("aut", "cre", "cph")))
Various cladogenesis-related calculations that are slow in pure R are implemented in C++ with Rcpp. These include the calculation of the probability of various scenarios for the inheritance of geographic range at the divergence events on a phylogenetic tree, and other calculations necessary for models which are not continuous-time markov chains (CTMC), but where change instead occurs instantaneously at speciation events.  Typically these models must assess the probability of every possible combination of (ancestor state, left descendent state, right descendent state).  This means that there are up to (# of states)^3 combinations to investigate, and in biogeographical models, there can easily be hundreds of states, so calculation time becomes an issue.  C++ implementation plus clever tricks (many combinations can be eliminated a priori) can greatly speed the computation time over naive R implementations.  CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it!  Type: citation(package="cladoRcpp") to get the citation information.

Classical Age-Depth Modelling of Cores from Deposits
c(
person("Maarten", "Blaauw", email = "maarten.blaauw@qub.ac.uk", role = c("aut", "cre")),
person("J. Andres", "Christen", role = "ctb"),
person("Judith", "Esquivel Vazquez", role = "ctb"),
person("Simon", "Goring", role = "ctb"))
Performs 'classical' age-depth modelling of dated sediment deposits - prior to applying more sophisticated techniques such as Bayesian age-depth modelling. Any radiocarbon dated depths are calibrated. Age-depth models are constructed by sampling repeatedly from the dated levels, each time drawing age-depth curves. Model types include linear interpolation, linear or polynomial regression, and a range of splines. See Blaauw (2010). <doi:10.1016/j.quageo.2010.01.002>.
Maarten Blaauw [aut, cre],
J. Andres Christen [ctb],
Judith Esquivel Vazquez [ctb],
Simon Goring [ctb]