This package is considered a duplicate. The official version of this package is found at:https://gabrielnakamura.r-universe.dev/FishPhyloMaker

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
FishPhyloMaker_0.2.0.zip(r-4.5)FishPhyloMaker_0.2.0.zip(r-4.4)FishPhyloMaker_0.2.0.zip(r-4.3)
FishPhyloMaker_0.2.0.tgz(r-4.4-any)FishPhyloMaker_0.2.0.tgz(r-4.3-any)
FishPhyloMaker_0.2.0.tar.gz(r-4.5-noble)FishPhyloMaker_0.2.0.tar.gz(r-4.4-noble)
FishPhyloMaker_0.2.0.tgz(r-4.4-emscripten)FishPhyloMaker_0.2.0.tgz(r-4.3-emscripten)
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'))

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:

5.44 score 7 stars 13 scripts 209 downloads 4 exports 89 dependencies

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

Target	Result	Date
Doc / Vignettes	OK	Dec 23 2024
R-4.5-win	NOTE	Dec 23 2024
R-4.5-linux	NOTE	Dec 23 2024
R-4.4-win	NOTE	Dec 23 2024
R-4.4-mac	NOTE	Dec 23 2024
R-4.3-win	NOTE	Dec 23 2024
R-4.3-mac	NOTE	Dec 23 2024

Exports:FishPhyloMaker FishTaxaMaker PD_deficit whichFishAdd

Dependencies:ape askpass base64enc blob bslib cachem cli clusterGeneration coda codetools colorspace combinat cpp11 crayon curl DBI dbplyr DEoptim deSolve digest doParallel dplyr duckdb duckdbfs evaluate expm fansi fastmap fishtree fontawesome foreach fs geiger generics glue highr hms htmltools httr igraph iterators jquerylib jsonlite knitr lattice lifecycle magrittr maps MASS Matrix memoise mime mnormt mvtnorm ncbit nlme numDeriv openssl optimParallel phangorn phytools pillar pkgconfig prettyunits progress purrr quadprog R6 rappdirs Rcpp RcppArmadillo rfishbase rlang rmarkdown sass scatterplot3d stringi stringr subplex sys tibble tidyr tidyselect tinytex utf8 vctrs withr xfun yaml

How to know which species must be added to phylogeny?

Rendered fromwhichFishAdd_vignette.Rmdusingknitr::rmarkdownon Dec 23 2024.

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

How to map species insertions in phylogenetic tree?

Rendered frommappingInsertions_vignette.Rmdusingknitr::rmarkdownon Dec 23 2024.

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

Using FishPhyloMaker to build phylogenies for finned-ray fishes

Rendered fromFishPhyloMaker_vignette.Rmdusingknitr::rmarkdownon Dec 23 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Obtaining fish phylogeny according to a local pool of species	FishPhyloMaker
Generate a list of species Auxiliary function to obtain taxonomic classification and check the names of species present in species pool	FishTaxaMaker
Abundance of stream fish species in Parana and Paraguay streams	neotropical_comm
Title Calculate the amount of phylogenetic deficit in assemblages	PD_deficit
List of fish species with occurrence in Afrotropical ecoregion	spp_afrotropic
Data frame with species names needed to assemble the phylogenetic tree	taxon_data_PhyloMaker
Function to inform which species must be added to the mega-tree phylogeny in the insertion process.	whichFishAdd