Package: FishPhyloMaker 0.2.0

Gabriel Nakamura

FishPhyloMaker: Phylogenies for a List of Finned-Ray Fishes

Provides an alternative to facilitate the construction of a phylogeny for fish species from a list of species or a community matrix using as a backbone the phylogenetic tree proposed by Rabosky et al. (2018) <doi:10.1038/s41586-018-0273-1>.

Authors:Gabriel Nakamura [aut, cre], Aline Richter [aut], Bruno Soares [aut]

FishPhyloMaker_0.2.0.tar.gz
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FishPhyloMaker.pdf |FishPhyloMaker.html✨
FishPhyloMaker/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/gabrielnakamura/fishphylomaker/issues

Datasets:
  • neotropical_comm - Abundance of stream fish species in Parana and Paraguay streams
  • spp_afrotropic - List of fish species with occurrence in Afrotropical ecoregion
  • taxon_data_PhyloMaker - Data frame with species names needed to assemble the phylogenetic tree

On CRAN:

5.37 score 6 stars 13 scripts 224 downloads 4 exports 83 dependencies

Last updated 11 months agofrom:04373d0770. Checks:OK: 1 NOTE: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 24 2024
R-4.5-winNOTEOct 24 2024
R-4.5-linuxNOTEOct 24 2024
R-4.4-winNOTEOct 24 2024
R-4.4-macNOTEOct 24 2024
R-4.3-winNOTEOct 24 2024
R-4.3-macNOTEOct 24 2024

Exports:FishPhyloMakerFishTaxaMakerPD_deficitwhichFishAdd

Dependencies:apebase64encblobbslibcachemcliclusterGenerationcodacodetoolscolorspacecombinatcpp11crayonDBIdbplyrDEoptimdeSolvedigestdoParalleldplyrduckdbduckdbfsevaluateexpmfansifastmapfishtreefontawesomeforeachfsgeigergenericsgluehighrhmshtmltoolsigraphiteratorsjquerylibjsonliteknitrlatticelifecyclemagrittrmapsMASSMatrixmemoisemimemnormtmvtnormncbitnlmenumDerivoptimParallelphangornphytoolspillarpkgconfigprettyunitsprogresspurrrquadprogR6rappdirsRcpprfishbaserlangrmarkdownsassscatterplot3dstringistringrsubplextibbletidyrtidyselecttinytexutf8vctrswithrxfunyaml

How to know which species must be added to phylogeny?

Rendered fromwhichFishAdd_vignette.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2021-08-27
Started: 2021-03-31

How to map species insertions in phylogenetic tree?

Rendered frommappingInsertions_vignette.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2021-08-27
Started: 2021-04-02

Using FishPhyloMaker to build phylogenies for finned-ray fishes

Rendered fromFishPhyloMaker_vignette.Rmdusingknitr::rmarkdownon Oct 24 2024.

Last update: 2021-09-08
Started: 2021-03-30