queryFiles: Paths to recordings or images

In tereom/querysnmb: Functions to query the SNMB database

Description

queryFiles returns paths to recordings, images or videos. For this function to work you need to be connected to madmex folder, this is because the function searches for existing files in the madmex directories.

Usage

queryFiles(database, file_type, state = "all", organization = "all",
  cgl_id = "all", year_visit = 2010:2016, month_visit = 1:12,
  photo = TRUE, video = TRUE, ultrasonic = FALSE, original = FALSE)

Arguments

database	Connection to an existing postgresql or sqlite database (as returned by src_postgres or src_sqlite.
file_type	String specifing which file paths should be retrieved, value should be "recordings" or "images" (includes images and videos from the camera trap).
organization	Character vector of organizations to include in the search (CONAFOR, CONANP, FMCN), defaults to "all".
cgl_id	Character vector of conglomerate ids to include in the searh, defaults to "all".
year_visit	Numeric vector indicating the year(s) to include in the search, defaults to 2014:2016.
month_visit	Numeric vector indicating the month(s) to include in the search, defaults to 1:12.
photo, video, ultrasonic	Binary variables, if file_type = "images", photo = FALSE, video = TRUE indicates to only search for videos, similarly video = FALSE, photo = TRUE excludes videos from results, defult sets both to TRUE. In case of recordings it is only possible to download one type of file (acoustic OR ultrasonic), defaults to download acoustic, this is ultrasonic = FALSE.
original	Indicates if a column with the original file name should be included in the results.

Value

A data.frame containing the following columns: file_type, state, institucion (organization), cgl_id (conglomerate id), date (date of visit), lat, lon (coordinates of the conglomerate), and archivo_nombre_original (if original = TRUE, the original file name).

Examples

# connect to sqlite database (snmb)
database <- dplyr::src_sqlite(system.file("extdata", "snmb.sqlite",
  package = "querysnmb"))
files_images_videos <- queryFiles(database, file_type = "images",
  cgl_id = "405", year_visit = 2014)
files_videos <- queryFiles(database, file_type = "images", cgl_id = "2286",
  year_visit = 2014, photo = FALSE)
files_acoustic <- queryFiles(database, file_type = "recordings",
  ultrasonic = FALSE, year_visit = 2014)
## Not run: 
# connect to postgreSQL database (snmb)
PASS_SNMB = Sys.getenv("PASS_SNMB")
database <- dplyr::src_postgres(dbname = "snmb", host = "dbms", user =
  "snmb", password = PASS_SNMB)
files_acoustic_name <- queryFiles(database, file_type = "recordings",
  ultrasonic = FALSE, year_visit = 2014, original = TRUE)

## End(Not run)

tereom/querysnmb documentation built on May 31, 2019, 8:39 a.m.