Title: Biogeographic Regionalization and Macroecology
and biodiversity conservation (Daru et al. 2020) <doi:10.1101/2020.02.12.945691>.
It is based on the methods described in Daru et al. (2020) <doi:10.1038/s41467-020-15921-6>.
The original conceptual work is described in Daru et al. (2017) <doi:10.1016/j.tree.2017.08.013>
on patterns and processes of biogeographical regionalization. Additionally, the package
Imports: ape, phangorn, Matrix, betapart, parallel, methods, raster,
colorspace, vegan, sp, igraph, rgdal, rgeos
Suggests: tinytest, knitr, rmarkdown, mapproj
Packaged: 2020-07-19 10:30:54 UTC; barnabasdaru

and biodiversity conservation (Daru et al. 2020) <doi:10.1111/2041-210X.13478>.
colorspace, vegan, sp, igraph, clustMixType, dismo,
Suggests: tinytest, knitr, rmarkdown, mapproj, survival, gbm, rJava
Packaged: 2021-05-01 00:02:10 UTC; barnabasdaru

Title: The Probability of Transmission Given Phylogenetic Linkage
Authors@R: c(person("John R", "Giles", role=c("aut", "ctb"), email="jrgiles@uw.edu"),
person("Shirlee", "Wohl", role=c("aut", "ctb"), email="swohl@jhu.edu"),
Description: Implements novel tools that estimate the probability of true transmission between two cases given
phylogenetic linkage and the expected number of true transmission links in a sample. Methods described in
Wohl, Giles, and Lessler (2021) <doi:10.1371/journal.pcbi.1009182>.
Imports: reshape2, ggplot2, cowplot, RColorBrewer
Packaged: 2021-11-20 22:11:17 UTC; johngiles

Title: Graph-Based Permutation Tests for Microbiome Data
Description: Provides functions for graph-based multiple-sample
testing and visualization of microbiome data, in particular data
stored in 'phyloseq' objects. The tests are based on those
<http://www.jstor.org/stable/2958919>, and the tests are described
in more detail in Callahan et al. (2016)
Imports: ggnetwork (>= 0.5.1), igraph (>= 1.1.2), intergraph (>= 2.0.2)
Packaged: 2018-03-14 20:44:06 UTC; juliefukuyama

Packaged: 2018-06-26 21:30:59 UTC; juliefukuyama

Title: Exploring the Phylogenetic Signal in Continuous Traits
Description: A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.
Imports: Rcpp (>= 0.11.0), adephylo, igraph, ape, phylobase, boot,
RCurl, graphics, grDevices, methods, stats, utils