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:
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')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 5 months agofrom:f5eb3e3136. Checks:OK: 2. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 23 2024 |
R-4.5-linux-x86_64 | OK | Nov 23 2024 |
Exports:betareg.stancovmat.checklinreg.stannode.averagerpair.age.in.treetaxapair.vcvtwoterm.plmm.matstwoterm.plmm.stan
Dependencies:abindapebackportsBHcallrcheckmatecliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdescdigestdistributionaldoParallelexpmfansifarverfastmatchforeachgenericsggplot2gluegridExtragtableigraphinlineisobanditeratorslabelinglatticelifecycleloomagrittrmapsMASSMatrixmatrixStatsmgcvmnormtmunsellnlmenumDerivoptimParallelphangornphytoolspillarpkgbuildpkgconfigposteriorprocessxpsquadprogQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsscalesscatterplot3dStanHeaderstensorAtibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
The 'phylopairs' package. | phylopairs-package phylopairs |
betareg.stan | betareg.stan |
covmat.check | covmat.check |
linreg.stan | linreg.stan |
node.averager | node.averager |
pair.age.in.tree | pair.age.in.tree |
Simulated Datasets | data1 data2 data3 data4 data5 data6 data7 data8 sim.cov.pairs sim.tree1 simulated.datasets |
taxapair.vcv | taxapair.vcv |
twoterm.plmm.mats | twoterm.plmm.mats |
twoterm.plmm.stan | twoterm.plmm.stan |