Package: phylopairs 0.1.0

Sean A. S. Anderson

phylopairs: Comparative Analyses of Lineage-Pair Traits

Facilitates the testing of causal relationships among lineage-pair traits in a phylogenetically informed context. Lineage-pair traits are characters that are defined for pairs of lineages instead of individual taxa. Examples include the strength of reproductive isolation, range overlap, competition coefficient, diet niche similarity, and relative hybrid fitness. Users supply a lineage-pair dataset and a phylogeny. 'phylopairs' calculates a covariance matrix for the pairwise-defined data and provides built-in models to test for relationships among variables while taking this covariance into account. Bayesian sampling is run through built-in 'Stan' programs via the 'rstan' package. The various models and methods that this package makes available are described in Anderson et al. (In Review), Coyne and Orr (1989) <doi:10.1111/j.1558-5646.1989.tb04233.x>, Fitzpatrick (2002) <doi:10.1111/j.0014-3820.2002.tb00860.x>, and Castillo (2007) <doi:10.1002/ece3.3093>.

Authors:Sean A. S. Anderson [aut, cre]

phylopairs_0.1.0.tar.gz
phylopairs_0.1.0.tar.gz(r-4.5-noble)phylopairs_0.1.0.tar.gz(r-4.4-noble)
phylopairs.pdf |phylopairs.html
phylopairs/json (API)

# Install 'phylopairs' in R:
install.packages('phylopairs', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

1.00 score 143 downloads 8 exports 74 dependencies

Last updated 6 months agofrom:f5eb3e3136. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 23 2024
R-4.5-linux-x86_64OKDec 23 2024

Exports:betareg.stancovmat.checklinreg.stannode.averagerpair.age.in.treetaxapair.vcvtwoterm.plmm.matstwoterm.plmm.stan

Dependencies:abindapebackportsBHcallrcheckmatecliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdescdigestdistributionaldoParallelexpmfansifarverfastmatchforeachgenericsggplot2gluegridExtragtableigraphinlineisobanditeratorslabelinglatticelifecycleloomagrittrmapsMASSMatrixmatrixStatsmgcvmnormtmunsellnlmenumDerivoptimParallelphangornphytoolspillarpkgbuildpkgconfigposteriorprocessxpsquadprogQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsscalesscatterplot3dStanHeaderstensorAtibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
The 'phylopairs' package.phylopairs-package phylopairs
betareg.stanbetareg.stan
covmat.checkcovmat.check
linreg.stanlinreg.stan
node.averagernode.averager
pair.age.in.treepair.age.in.tree
Simulated Datasetsdata1 data2 data3 data4 data5 data6 data7 data8 sim.cov.pairs sim.tree1 simulated.datasets
taxapair.vcvtaxapair.vcv
twoterm.plmm.matstwoterm.plmm.mats
twoterm.plmm.stantwoterm.plmm.stan