The 'apcluster' package implements Frey's and Dueck's
Affinity Propagation clustering in R.  The algorithms are
largely analogous to the 'Matlab' code published by Frey and
Dueck. The package further provides leveraged affinity
propagation and an algorithm for exemplar-based agglomerative
clustering that can also be used to join clusters obtained
from affinity propagation. Various plotting functions are
available for analyzing clustering results.

An Implementation of the Additive Polynomial Design Matrix
c(
person("Tyler", "Matta", email = "tyler.matta@gmail.com", role = c("aut", "cre")),
person("Quinn", "Lathrop", role = c("ctb")),
person("Yeow Meng", "Thum", role = c("ctb")))
An implementation of the additive polynomial (AP) design matrix. It
constructs and appends an AP design matrix to a data frame for use with
longitudinal data subject to seasonality.
Tyler Matta [aut, cre],
Quinn Lathrop [ctb],
Yeow Meng Thum [ctb]

Emmanuel Paradis <paradis@isem.univ-montp2.fr>
Julien Claude <claude@isem.univ-montp2.fr>
Yvonnick Noel <noel@univ-lille3.fr>
Ben Bolker <bolker@zoo.ufl.edu>
Ape provides functions for reading, and plotting phylogenetic
trees in parenthetic format (standard Newick format), analyses of
comparative data in a phylogenetic framework, analyses of diversification
and macroevolution, computing distances from allelic and nucleotide data,
reading nucleotide sequences from GenBank via internet, and several tools
such  as Mantel's test, computation of minimum spanning tree, or the
population parameter theta based on various approaches.

Emmanuel Paradis <paradis@isem.univ-montp2.fr>
Korbibian Strimmer <strimmer@stat.uni-muenchen.de>
Julien Claude <claude@isem.univ-montp2.fr>
Yvonnick Noel <noel@univ-lille3.fr>
Ben Bolker <bolker@zoo.ufl.edu>
Ape provides functions for reading, writing, and plotting
phylogenetic trees in parenthetic format (standard Newick format),
analyses of comparative data in a phylogenetic framework, analyses of
diversification and macroevolution, computing distances from allelic
and nucleotide data, reading nucleotide sequences from GenBank via
internet, and several tools such  as Mantel's test, computation of
minimum spanning tree, or the population parameter theta based on
various approaches.