all_results <- phydo::run_phydo(params$taxon)
r params$taxon
knitr::include_graphics(all_results$wikipedia_pics)
Taxon r params$taxon
has r all_results$otol$ntaxa
terminal taxa in OpenTree. This is based on taxonomy plus r nrow(all_results$otol$studies)
studies.
if(nrow(all_results$otol$studies)>0) { pander::pander(all_results$otol$studies, split.table = Inf) }
if(inherits(all_results$datelife_biggest, "phylo")) { plot(all_results$datelife_biggest) ape::axisPhylo() } else { print("Datelife did not contain a tree") }
In GenBank, there are r all_results$genbank_count
species listed for this group.
pander::pander(data.frame(seqs=all_results$genbank_count_by_gene))
There are r all_results$pubmed$count
articles that match r params$taxon
AND phylogeny on PubMed. Here are the most recent.
pubmed.df <- all_results$pubmed$recent.papers if(nrow(pubmed.df)>0) { pubmed.df <- pubmed.df[order(pubmed.df$Date, decreasing=TRUE),] pander::pander(pubmed.df, split.table = Inf) }
Here is information about realms (biogeographic regions) by species; frequency of record in each realm.
realm <- all_results$location_realm_biome$realm for (i in sequence(nrow(realm))) { realm[i,] <- realm[i,]/sum(realm[i,], na.rm=TRUE) } pander::pander(data.frame(realm))
Here is information about biomes by species; frequency of records in each biome.
biome <- all_results$location_realm_biome$biome for (i in sequence(nrow(biome))) { biome[i,] <- biome[i,]/sum(biome[i,], na.rm=TRUE) } pander::pander(data.frame(biome))
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