Package: FishPhyloMaker 0.2.0

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
FishPhyloMaker_0.2.0.zip(r-4.7)FishPhyloMaker_0.2.0.zip(r-4.6)FishPhyloMaker_0.2.0.zip(r-4.5)
FishPhyloMaker_0.2.0.tgz(r-4.6-any)FishPhyloMaker_0.2.0.tgz(r-4.5-any)
FishPhyloMaker_0.2.0.tar.gz(r-4.7-any)FishPhyloMaker_0.2.0.tar.gz(r-4.6-any)
FishPhyloMaker_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
FishPhyloMaker/json (API)
NEWS

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

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:

Conda:

5.71 score 10 stars 17 scripts 271 downloads 4 exports 84 dependencies

Last updated from:04373d0770. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE142
source / vignettesOK191
linux-release-x86_64NOTE147
macos-release-arm64NOTE75
macos-oldrel-arm64NOTE105
windows-develNOTE74
windows-releaseNOTE91
windows-oldrelNOTE71
wasm-releaseOK133

Exports:FishPhyloMakerFishTaxaMakerPD_deficitwhichFishAdd

Dependencies:apebase64encblobbslibcachemcliclusterGenerationcodacodetoolscolorspacecombinatcpp11crayonDBIdbplyrDEoptimdeSolvedigestdoParalleldplyrduckdbduckdbfsevaluateexpmfastmapfastmatchfishtreefontawesomeforeachfsgeigergenericsgluehighrhmshtmltoolsigraphiteratorsjquerylibjsonliteknitrlatticelifecyclemagrittrmapsMASSMatrixmemoisemimemnormtmvtnormncbitnlmenumDerivoptimParallelphangornphytoolspillarpkgconfigprettyunitsprogresspurrrquadprogR6rappdirsRcpprfishbaserlangrmarkdownsassscatterplot3dstringistringrsubplextibbletidyrtidyselecttinytexutf8vctrswithrxfunxml2yaml

How to know which species must be added to phylogeny?

Rendered fromwhichFishAdd_vignette.Rmdusingknitr::rmarkdownon May 23 2026.

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

How to map species insertions in phylogenetic tree?

Rendered frommappingInsertions_vignette.Rmdusingknitr::rmarkdownon May 23 2026.

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

Using FishPhyloMaker to build phylogenies for finned-ray fishes

Rendered fromFishPhyloMaker_vignette.Rmdusingknitr::rmarkdownon May 23 2026.

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