Get a smaller tree with popular taxa spanning the diversity

This assumes you will have a data.frame of popularity measures and then sum to combine the columns into a single measure.

popularitree(phy, ntax, measures, pd_weighting = 0.5, nrep = 10000)

Arguments

phy	A phylo object
ntax	The final number of taxa you want
measures	Data.frame of the measures of popularity
pd_weighting	How much to weight the pd vs the popularity
nrep	How many replicates to use

Value

A phylo object pruned to the number of taxa

Examples

big.phy <- rotl::get_study("ot_308")[[1]]
big.phy <- geiger::drop.random(big.phy, ape::Ntip(big.phy) - 20)
measures <- tree_compute_measures(big.phy)
#> 
#> Retrieving data for taxon 'Microtus_juldaschi'
#> 
#> Retrieving data for taxon 'Gerbillurus_setzeri'
#> 
#> Retrieving data for taxon 'Cricetomys_gambianus'
#> 
#> Retrieving data for taxon 'Spalax_giganteus'
#> Not found. Consider checking the spelling or alternate classification
#> 
#> Retrieving data for taxon 'Zygodontomys_brevicauda'
#> 
#> Retrieving data for taxon 'Akodon_dayi'
#> 
#> Retrieving data for taxon 'Oecomys_rex'
#> 
#> Retrieving data for taxon 'Chiropodomys_major'
#> Not found. Consider checking the spelling or alternate classification
#> 
#> Retrieving data for taxon 'Nesokia_bunnii'
#> Not found. Consider checking the spelling or alternate classification
#> 
#> Retrieving data for taxon 'Nesokia_indica'
#> 
#> Retrieving data for taxon 'Ctenomys_perrensis'
#> 
#> Retrieving data for taxon 'Petinomys_genibarbis'
#> Not found. Consider checking the spelling or alternate classification
#> 
#> Retrieving data for taxon 'Exilisciurus_concinnus'
#> 
#> Retrieving data for taxon 'Lepilemur_mustelinus'
#> 
#> Retrieving data for taxon 'Tragelaphus_eurycerus'
#> 
#> Retrieving data for taxon 'Viverricula_indica'
#> 
#> Retrieving data for taxon 'Manis_crassicaudata'
#> 
#> Retrieving data for taxon 'Mormoops_blainvillii'
#> 
#> Retrieving data for taxon 'Chalinolobus_dwyeri'
#> Not found. Consider checking the spelling or alternate classification
#> 
#> Retrieving data for taxon 'Crocidura_beatus'
#> [1] "Retrieving trends data for taxon 'Microtus_juldaschi'"
#> [1] "Retrieving trends data for taxon 'Gerbillurus_setzeri'"
#> [1] "Retrieving trends data for taxon 'Cricetomys_gambianus'"
#> [1] "Retrieving trends data for taxon 'Spalax_giganteus'"
#> [1] "Retrieving trends data for taxon 'Zygodontomys_brevicauda'"
#> [1] "Retrieving trends data for taxon 'Akodon_dayi'"
#> [1] "Retrieving trends data for taxon 'Oecomys_rex'"
#> [1] "Retrieving trends data for taxon 'Chiropodomys_major'"
#> [1] "Retrieving trends data for taxon 'Nesokia_bunnii'"
#> [1] "Retrieving trends data for taxon 'Nesokia_indica'"
#> [1] "Retrieving trends data for taxon 'Ctenomys_perrensis'"
#> [1] "Retrieving trends data for taxon 'Petinomys_genibarbis'"
#> [1] "Retrieving trends data for taxon 'Exilisciurus_concinnus'"
#> [1] "Retrieving trends data for taxon 'Lepilemur_mustelinus'"
#> [1] "Retrieving trends data for taxon 'Tragelaphus_eurycerus'"
#> [1] "Retrieving trends data for taxon 'Viverricula_indica'"
#> [1] "Retrieving trends data for taxon 'Manis_crassicaudata'"
#> [1] "Retrieving trends data for taxon 'Mormoops_blainvillii'"
#> [1] "Retrieving trends data for taxon 'Chalinolobus_dwyeri'"
#> [1] "Retrieving trends data for taxon 'Crocidura_beatus'"
small.phy <- popularitree(phy=big.phy, ntax=5, measures, nrep=100)
par(mfcol=c(1,3))
plot(big.phy)
plot(small.phy)
plot(tree_convert_to_common(small.phy))
#> 
#> Retrieving data for taxon 'Nesokia_indica'
#> 
#> Retrieving data for taxon 'Lepilemur_mustelinus'
#> 
#> Retrieving data for taxon 'Viverricula_indica'
#> 
#> Retrieving data for taxon 'Mormoops_blainvillii'
#> 
#> Retrieving data for taxon 'Crocidura_beatus'