Example of use of package-in-development taxize

taxize_example.R

# A species list, which ecologies often have, but may not know the family names, or if they do, 
# they (meaning me) may spell the names wrong from time to time
> splist <- c("annona_cherimola", 'annona_muricata', "quercus_robur", 
  "shorea_robusta", "pandanus_patina", "oryza_sativa", "durio_zibethinus",
  "rubus_ulmifolius", "asclepias_curassavica", "pistacia_lentiscus")

# Get the Taxonomic Serial Number for each species, which are unique (note that there could be many TSN's within a species 
# for each subspecies for example. So you may want to query for you species using get_itis_xml in the demos on the github
# site and then make sure you get the TSN for the right subspecies or species
> tsns <- laply(splist, get_tsn, searchtype = "sciname", by_ = "name", 
  .progress = "text")

  |===========================================================================================| 100%

# Get Phylomatic formatted strings for each species (e.g., family/genus/genus_epithet)
> dat_ <- laply(tsns, get_phymat_format, format='rsubmit', .progress="text")
  |===========================================================================================| 100%

# Send the strings to Phylomatic website via an API, and retrieve the newick tree (alternatively, get xml output)
> tree <- get_phylomatic_tree(dat_, 'TRUE', 'GET', 'new', 'TRUE')
Loading required package: ape

# Plot the tree, or do anything else you want to do!
> plot(tree)