A function to cache the phylogenies in treebase locally

Description

A function to cache the phylogenies in treebase locally

Usage

cache_treebase(
  file = paste("treebase-", Sys.Date(), ".rda", sep = ""),
  pause1 = 3,
  pause2 = 3,
  attempts = 10,
  max_trees = Inf,
  only_metadata = FALSE,
  save = TRUE
)

Arguments

Details

it's a good idea to let this run overnight

Value

saves a cached file of treebase

Examples

## Not run: 
 treebase <- cache_treebase()

## End(Not run)

clean the fish.base data into pure ASCII

Description

clean the fish.base data into pure ASCII

Usage

clean_data(metadata)

Arguments

Value

the item scrubbed of non-ASCII characters

Download the metadata on treebase using the OAI-MPH interface

Description

Download the metadata on treebase using the OAI-MPH interface

Usage

download_metadata(
  query = "",
  by = c("all", "until", "from"),
  curl = getCurlHandle()
)

Arguments

Details

query must be#' download_metadata(2010-01-01, by="until") all isn't a real query type, but will return all trees regardless of date

Examples

## Not run: 
Near <- search_treebase("Near", "author", max_trees=1)
 metadata(Near[[1]]$S.id)
## or manualy give a sudy id
metadata("2377")

### get all trees from a certain depostition date forwards ##
m <- download_metadata("2009-01-01", by="until")
## extract any metadata, e.g. publication date:
dates <- sapply(m, function(x) as.numeric(x$date))
hist(dates, main="TreeBase growth", xlab="Year")

### show authors with most tree submissions in that date range 
authors <- sapply(m, function(x){
   index <- grep( "creator", names(x))
     x[index] 
})
a <- as.factor(unlist(authors))
head(summary(a))

## Show growth of TreeBASE 
all <- download_metadata("", by="all")
dates <- sapply(all, function(x) as.numeric(x$date))
hist(dates, main="TreeBase growth", xlab="Year")

## make a barplot submission volume by journals
journals <- sapply(all, function(x) x$publisher)
J <- tail(sort(table(as.factor(unlist(journals)))),5)
b<- barplot(as.numeric(J))
text(b, names(J), srt=70, pos=4, xpd=T)

## End(Not run)

remove non-ASCII characters

Description

remove non-ASCII characters

Usage

drop_nonascii(string)

Arguments

Value

the string after dropping all html tags to spaces

drop errors from the search

Description

drop errors from the search

Usage

drop_nontrees(tr)

Arguments

Details

primarily for the internal use of search_treebase, but may be useful

Value

the list of phylogenetic trees returned successfully

Search the dryad metadata archive

Description

Search the dryad metadata archive

Usage

dryad_metadata(study.id, curl = getCurlHandle())

Arguments

Value

a list object containing the study metadata

Examples

## Not run: 
  dryad_metadata("10255/dryad.12")

## End(Not run)

imports phylogenetic trees from treebase. internal function

Description

imports phylogenetic trees from treebase. internal function

Usage

get_nex(
  query,
  max_trees = "last()",
  returns = "tree",
  curl = getCurlHandle(),
  verbose = TRUE,
  pause1 = 1,
  pause2 = 1,
  attempts = 5,
  only_metadata = FALSE
)

Arguments

Value

A list object containing all the trees matching the search (of class phylo)

return the trees in treebase that correspond to the search results get_study is deprecated, and now can be performed more easily using phylo_metadata and oai_metadata search functions.

Description

return the trees in treebase that correspond to the search results get_study is deprecated, and now can be performed more easily using phylo_metadata and oai_metadata search functions.

Usage

get_study(search_results, curl = getCurlHandle(), ...)

Arguments

Details

this function is commonly used to get trees corresponding to the metadata search.

Value

all corresponding phylogenies.

return the study.id from the search results.

Description

get_study_id is deprecated, and now can be performed more easily using phylo_metadata and oai_metadata search functions.

Usage

get_study_id(search_results)

Arguments

Details

this function is commonly used to get trees corresponding to the metadata search.

Value

the study id

Simple function to identify which trees have branch lengths

Description

Simple function to identify which trees have branch lengths

Usage

have_branchlength(trees)

Arguments

Value

logical string indicating which have branch length data

metadata.rda

Description

Contains a cache of all publication metadata the search_metadata() to pull down when run on 2012-05-12.

Usage

metadata(phylo.md = NULL, oai.md = NULL)

Arguments

Details

recreate with: search_metadata()

Value

a data frame of all available metadata, (as a data.table object) columns are: "Study.id", "Tree.id", "kind", "type", "quality", "ntaxa" "date", "publisher", "author", "title".

Examples

## Not run: 
meta <- metadata()
meta[publisher %in% c("Nature", "Science") & ntaxa > 50 & kind == "Species Tree",]

## End(Not run)

Internal function for OAI-MPH interface to the Dryad database

Description

Internal function for OAI-MPH interface to the Dryad database

Usage

metadata_from_oai(query, curl = curl)

Arguments

See Also

dryad_metadata

Search the OAI-PMH metadata by date, publisher, or identifier

Description

Search the OAI-PMH metadata by date, publisher, or identifier

Usage

oai_metadata(
  x = c("date", "publisher", "author", "title", "Study.id", "attributes"),
  metadata = NULL,
  ...
)

Arguments

Value

a list of values matching the query

Search the PhyloWS metadata

Description

Search the PhyloWS metadata

Usage

phylo_metadata(
  x = c("Study.id", "Tree.id", "kind", "type", "quality", "ntaxa"),
  metadata = NULL,
  ...
)

Arguments

Value

a list of the values matching the query

A function to pull in the phyologeny/phylogenies matching a search query

Description

A function to pull in the phyologeny/phylogenies matching a search query

Usage

search_treebase(
  input,
  by,
  returns = c("tree", "matrix"),
  exact_match = FALSE,
  max_trees = Inf,
  branch_lengths = FALSE,
  curl = getCurlHandle(),
  verbose = TRUE,
  pause1 = 0,
  pause2 = 0,
  attempts = 3,
  only_metadata = FALSE
)

Arguments

Value

either a list of trees (multiphylo) or a list of character matrices

Examples

## 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)

Get the metadata associated with the study in which the phylogeny was published.

Description

Get the metadata associated with the study in which the phylogeny was published.

Usage

show_metadata(study.id, curl = getCurlHandle())

Arguments

Details

if the tree is imported with search_treebase, then this is in tree$S.id

treebase.rda

Description

Contains a cache of all phylogenies cache_treebase() function was able to pull down when run on 2012-05-14.

Details

recreate with: cache_treebase()