Description: A wide range of functions for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and data, for continuous, discrete, and multivariate characters. A broad range of plotting methods for phylogenies and comparative data include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for computing consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.

MASS, methods, mnormt, nlme, numDeriv, optimParallel, parallel,

Author: Greg M. Silsbe, Sairah Y. Malkin
Description: Fits PE and RLC data to one of a four published PE models.
Simulates incident irradiance as a function of time and space.
Calculates phytoplankton production by transposing modeled PE or RLC data
to a water column with a user-defined theoretical in-situ irradiance field.

Title: Estimating the proportion of true null hypotheses for FDR
Suggests: multtest, numDeriv, limSolve (>= 1.5.2), Matrix (>=
Description: This package implements method(s) to (approximately
unbiasedly) estimate the proportion of true null hypotheses,
i.e., the pi0, when a very large number of hypotheses are
simultaneously tested, especially for the purpose of (local)
false discovery rate control for microarray data. It also
contains functions to estimate the distribution of
noncentrality parameters from a large number of parametric