In bomeara/chapter2: Creates an Initial Report for a Clade

all_results <- phydo::run_phydo(params$taxon)

Taxon `r params$taxon`

Wikipedia summary

knitr::include_graphics(all_results$wikipedia_pics)

OpenTree

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)
}

Datelife

if(inherits(all_results$datelife_biggest, "phylo")) {
  plot(all_results$datelife_biggest)
  ape::axisPhylo()
} else {
  print("Datelife did not contain a tree")
}

GenBank

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))

PubMed

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)
}

Realm

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))

Biome

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))