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

Package: popularitree 0.0.0.9000

Brian OMeara

popularitree: Subsamples a tree to get popular taxa

Often you want to show a reduced summary tree. Taxa chosen should span all the tree (for example, a tree of mammals should not have just primates) but also be recognizable groups to your audience. This lets you select a final tree size you want, criteria you want to use, and finds the tree that maximizes the criteria.

Authors:Brian O'Meara [aut, cre]

# Install 'popularitree' in R:

install.packages('popularitree', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bomeara/popularitree/issues

On CRAN:

1.70 score 7 exports 85 dependencies

Last updated from:ce3e5899c0. Checks:7 ERROR, 2 OK. Indexed: no.

Target	Result	Time
linux-devel	ERROR	185
source / vignettes	OK	196
linux-release	ERROR	191
macos-release	ERROR	86
macos-oldrel	ERROR	98
windows-devel	ERROR	117
windows-release	ERROR	139
windows-oldrel	ERROR	118
wasm-release	OK	146

Exports:generate_sample popularitree species_get_common species_gtrends_popularity species_ncbi_common_exists tree_compute_measures tree_convert_to_common

Dependencies:anytime ape askpass backports BH checkmate cli cluster codetools cpp11 crayon crul curl data.table digest dplyr farver future future.apply generics ggplot2 globals glue gtable gtrendsR hms httpcode httr igraph isoband jsonlite labeling lattice lifecycle listenv magrittr MASS Matrix mgcv mime natserv nlme openssl osqp parallelly permute phangorn picante pillar pkgconfig plyr prettyunits progress progressr R6 RColorBrewer Rcpp RcppArmadillo rentrez ritis rlang rncl rotl rredlist S7 scales solrium stringi sys taxize tibble tidyselect triebeard urltools utf8 vctrs vegan viridisLite WikipediR wikitaxa withr worrms XML xml2 zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Generate a sample of species, weighted by their score	generate_sample
Get a smaller tree with popular taxa spanning the diversity	popularitree
Return common name if known, otherwise return scientific name	species_get_common
Get a sum of hits of a species relative to a standard	species_gtrends_popularity
Return 1 if a species has a common name in NCBI, 0 otherwise	species_ncbi_common_exists
Compute popularity measures	tree_compute_measures
Convert tips to common names if possible	tree_convert_to_common