search_treebase(input, by, returns = c("tree", "matrix"), exact_match = FALSE, max_trees = Inf, branch_lengths = FALSE, curl = getCurlHandle(), verbose = TRUE, pause1 = 2, pause2 = 1, attempts = 3, only_metadata = FALSE)
either a list of trees (multiphylo) or a list of character matrices
A function to pull in the phyologeny/phylogenies matching a search query
Choose the search type. Options are:
The package provides partial support for character matrices provided by TreeBASE. At the time of writing, TreeBASE permits ambiguous DNA characters in these matrices, such as `CG` indicating either a C or G, which is not supported by any R interpreter, and thus may lead to errors. for a description of all possible search options, see https://spreadsheets.google.com/pub?key=rL--O7pyhR8FcnnG5-ofAlw.
## Not run: # ## defaults to return phylogeny# Huelsenbeck <- search_treebase("Huelsenbeck", by="author")# # ## can ask for character matrices:# wingless <- search_treebase("2907", by="id.matrix", returns="matrix")# # ## Some nexus matrices don't meet read.nexus.data's strict requirements,# ## these aren't returned# H_matrices <- search_treebase("Huelsenbeck", by="author", returns="matrix")# # ## Use Booleans in search: and, or, not# ## Note that by must identify each entry type if a Boolean is given# HR_trees <- search_treebase("Ronquist or Hulesenbeck", by=c("author", "author"))# # ## We'll often use max_trees in the example so that they run quickly,# ## notice the quotes for species.# dolphins <- search_treebase('"Delphinus"', by="taxon", max_trees=5)# ## can do exact matches# humans <- search_treebase('"Homo sapiens"', by="taxon", exact_match=TRUE, max_trees=10)# ## all trees with 5 taxa# five <- search_treebase(5, by="ntax", max_trees = 10)# ## These are different, a tree id isn't a Study id. we report both# studies <- search_treebase("2377", by="id.study")# tree <- search_treebase("2377", by="id.tree")# c("TreeID" = tree$Tr.id, "StudyID" = tree$S.id)# ## Only results with branch lengths# ## Has to grab all the trees first, then toss out ones without branch_lengths# Near <- search_treebase("Near", "author", branch_lengths=TRUE)# ## End(Not run)