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'))

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:

4 exports 6 stars 1.40 score 95 dependencies 13 scripts 293 downloads

Last updated 9 months agofrom:04373d0770. Checks:OK: 1 NOTE: 6. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Aug 25 2024
R-4.5-win	NOTE	Aug 25 2024
R-4.5-linux	NOTE	Aug 25 2024
R-4.4-win	NOTE	Aug 25 2024
R-4.4-mac	NOTE	Aug 25 2024
R-4.3-win	NOTE	Aug 25 2024
R-4.3-mac	NOTE	Aug 25 2024

Exports:FishPhyloMaker FishTaxaMaker PD_deficit whichFishAdd

Dependencies:ape base64enc blob bslib cachem cli clusterGeneration coda codetools colorspace combinat cpp11 crayon DBI dbplyr DEoptim deSolve digest doParallel dplyr duckdb duckdbfs evaluate expm fansi farver fastmap fastmatch fishtree fontawesome foreach fs geiger generics ggplot2 ggseqlogo glue gtable highr hms htmltools igraph isoband iterators jquerylib jsonlite knitr labeling lattice lifecycle magrittr maps MASS Matrix memoise mgcv mime mnormt munsell mvtnorm ncbit nlme numDeriv optimParallel phangorn phytools pillar pkgconfig prettyunits progress purrr quadprog R6 rappdirs RColorBrewer Rcpp rfishbase rlang rmarkdown sass scales scatterplot3d stringi stringr subplex tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

How to know which species must be added to phylogeny?

Rendered fromwhichFishAdd_vignette.Rmdusingknitr::rmarkdownon Aug 25 2024.

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

How to map species insertions in phylogenetic tree?

Rendered frommappingInsertions_vignette.Rmdusingknitr::rmarkdownon Aug 25 2024.

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

Using FishPhyloMaker to build phylogenies for finned-ray fishes

Rendered fromFishPhyloMaker_vignette.Rmdusingknitr::rmarkdownon Aug 25 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