querxc: Access Xeno-Canto recordings and metadata

Description

querxc downloads recordings and metadata from Xeno-Canto (http://www.xeno-canto.org/).

Usage

querxc(qword, download = FALSE, X = NULL, file.name = c("Genus", "Specific_epithet"), 
parallel = 1, path = NULL, pb = TRUE)

Arguments

qword

Character vector of length one indicating the genus, or genus and species, to query Xeno-Canto database. For example, Phaethornis or Phaethornis longirostris. (http://www.xeno-canto.org/). More complex queries can be done by using search terms that follow the xeno-canto advance query syntax.This syntax uses tags to search within a particular aspect of the recordings (e.g. country, location, sound type). Tags are of the form tag:searchterm'. For instance, 'type:song' will search for all recordings in which the sound type description contains the word 'song'. Several tags can be included in the same query. The query "phaethornis cnt:belize' will only return results for birds in the genus Phaethornis that were recorded in Belize. See http://www.xeno-canto.org/help/search for a full description and see examples below for queries using terms with more than one word.

download

Logical argument. If FALSE only the recording file names and associated metadata are downloaded. If TRUE, recordings are also downloaded to the working directory as .mp3 files. Default is FALSE. Note that if the recording is already in the working directory (as when the downloading process has been interrupted) it will be skipped. Hence, resuming downloading processes will not start from scratch.

Data frame with a 'Recording_ID' column and any other column listed in the file.name argument. Only the recordings listed in the data frame will be download (download argument is automatically set to TRUE). This can be used to select the recordings to be downloaded based on their attributes.

file.name

Character vector indicating the tags (or column names) to be included in the sound file names (if download = TRUE). Several tags can be included. If NULL only the Xeno-Canto recording identification number ("Recording_ID") is used. Default is c("Genus", "Specific_epithet"). Note that recording id is always used (whether or not is listed by users) to avoid duplicated names.

parallel

Numeric. Controls whether parallel computing is applied when downloading mp3 files. It specifies the number of cores to be used. Default is 1 (i.e. no parallel computing). Currently only applied when downloading files. Might not work improve performance on Windows OS.

path

Character string containing the directory path where the sound files are located. If NULL (default) then the current working directory is used.

Logical argument to control progress bar. Default is TRUE. Note that progress bar is only used when parallel = 1.

Value

If X is not provided the function returns a data frame with the following recording information: recording ID, Genus, Specific epithet, Subspecies, English name, Recordist, Country, Locality, Latitude, Longitude, Vocalization type, Audio file, License, URL, Quality, Time, Date. Sound files in .mp3 format are downloaded into the working directory if download = TRUE or if X is provided; a column indicating the names of the downloaded files is included in the output data frame.

Details

This function queries for avian vocalization recordings in the open-access online repository Xeno-Canto (http://www.xeno-canto.org/). It can return recordings metadata or download the associated sound files. Complex queries can be done by using search terms that follow the xeno-canto advance query syntax (check "qword" argument description). Files are double-checked after downloading and "empty" files are re-downloaded. File downloading process can be interrupted and resume later as long as the working directory is the same. Maps of recording coordinates can be produced using xcmaps.

Examples

Run this code

# NOT RUN {
# Set temporary working directory
setwd(tempdir())

# search without downloading
df1 <- querxc(qword = 'Phaethornis anthophilus', download = FALSE)
View(df1)

# downloading files
querxc(qword = 'Phaethornis anthophilus', download = TRUE)

# check this folder
getwd()

## search using xeno-canto advance query ###
orth.pap <- querxc(qword = 'gen:orthonyx cnt:papua loc:tari', download = FALSE)
 
# download file using the output data frame as input
querxc(X = orth.pap)

# use quotes for queries with more than 1 word (e.g. Costa Rica),note that the 
# single quotes are used for the whole 'qword' and double quotes for the 2-word term inside
#Phaeochroa genus in Costa Rica 
phae.cr <- querxc(qword = 'gen:phaeochroa cnt:"costa rica"', download = FALSE)

# several terms can be searched for in the same field
# search for all female songs in sound type
femsong <- querxc(qword = 'type:song type:female', download = FALSE)
# }