Package: PCPS 1.0.8
PCPS: Principal Coordinates of Phylogenetic Structure
Set of functions for analysis of Principal Coordinates of Phylogenetic Structure (PCPS).
Authors:
PCPS_1.0.8.tar.gz
PCPS_1.0.8.zip(r-4.5)PCPS_1.0.8.zip(r-4.4)PCPS_1.0.8.zip(r-4.3)
PCPS_1.0.8.tgz(r-4.4-any)PCPS_1.0.8.tgz(r-4.3-any)
PCPS_1.0.8.tar.gz(r-4.5-noble)PCPS_1.0.8.tar.gz(r-4.4-noble)
PCPS_1.0.8.tgz(r-4.4-emscripten)PCPS_1.0.8.tgz(r-4.3-emscripten)
PCPS.pdf |PCPS.html✨
PCPS/json (API)
| # Install 'PCPS' in R: |
| install.packages('PCPS', repos = c('https://vanderleidebastiani.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/vanderleidebastiani/pcps/issues
Last updated 4 years agofrom:71329266a3. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 22 2024 |
| R-4.5-win | NOTE | Nov 22 2024 |
| R-4.5-linux | NOTE | Nov 22 2024 |
| R-4.4-win | OK | Nov 22 2024 |
| R-4.4-mac | OK | Nov 22 2024 |
| R-4.3-win | OK | Nov 22 2024 |
| R-4.3-mac | OK | Nov 22 2024 |
Exports:check.formuladefine.cladeFUN.ADONISFUN.ADONIS2.globalFUN.ADONIS2.marginFUN.GLMFUN.GLS.marginalFUN.GLS.sequentialFUN.LME.marginalFUN.LME.sequentialFUN.MANTELFUN.RDAmatrix.p.nullmatrix.p.sigmutate.names.matrix.p.nullorganize.pcpspcoa.sigpcpc.curve.calcpcpspcps.curvepcps.sigscores.pcpsselect.pcpsmethodself.belongingwcmdscale.org
Dependencies:abindade4apeaskpasscliclustercpp11crayoncurldigestdplyrfansiFDgenericsgeometrygluehmshttrjsonlitelatticelifecyclelinproglpSolvemagicmagrittrMASSMatrixmgcvmimenlmeopensslpermutephylobasepicantepillarpixmappkgconfigplyrprettyunitsprogresspurrrR6RcppRcppArmadilloRcppProgressreshape2rlangrnclRNeXMLspstringistringrSYNCSAsystibbletidyrtidyselectutf8uuidvctrsveganwithrXMLxml2
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Internal function | check.formula |
| Define clade | define.clade |
| Auxiliar function to generate sets of null P matrix or null PCPS | matrix.p.null |
| Association between phylogeny-weighted species composition and environmental predictors | FUN.ADONIS FUN.ADONIS2.global FUN.ADONIS2.margin FUN.GLM FUN.GLS.marginal FUN.GLS.sequential FUN.LME.marginal FUN.LME.sequential FUN.MANTEL FUN.RDA matrix.p.sig pcps.sig print.pcpssig |
| Internal function | mutate.names.matrix.p.null |
| Function for organize data for Package PCPS | organize.pcps |
| Significant dimensions in principal coordinate analysis | pcoa.sig print.pcoasig print.summarypcoasig summary.pcoasig |
| Principal Coordinates of Phylogenetic Structure | pcps plot.pcps print.pcps print.summarypcps scores.pcps summary.pcps |
| Curve of phylogenetic signal at metacommunity level | pcpc.curve.calc pcps.curve plot.pcpscurve print.pcpscurve summary.pcpscurve |
| Internal function | select.pcpsmethod |
| Degree of self belonging of species | self.belonging |
| Internal function for organize the results of wcmdscale function | wcmdscale.org |
