querySpecies: Query tables by species.

In tereom/querysnmb: Functions to query the SNMB database

Description

Search for species records in Invaders, Footprints, Specimens or Camera Trap tables, in the results each register matches a file, and they include characteristics of the animal or plant to which the file makes reference. The results also include the path to the image file (stored in the madmex folder), also, if the computer is connected to the madmex folder when caling the function, the results will include the path to the scanned paperwork filled in field.

Usage

queryInvaders(database, state = "all", organization = "all",
  cgl_id = "all", year_visit = 2010:2016, month_visit = 1:12,
  noms = "all")

queryFootprints(database, state = "all", organization = "all",
  cgl_id = "all", year_visit = 2010:2016, month_visit = 1:12,
  noms = "all")

querySpecimens(database, state = "all", organization = "all",
  cgl_id = "all", year_visit = 2010:2016, month_visit = 1:12,
  noms = "all")

queryCamera(database, state = "all", organization = "all", cgl_id = "all",
  year_visit = 2010:2016, month_visit = 1:12, noms = "all")

Arguments

database	Connection to an existing postgresql or sqlite database (as returned by src_postgres or src_sqlite.
state	Character vector of Mexican states to include in the searh, defaults to "all".
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.
noms	String indicating the species names to look for (ex: "vaca|equus")

Value

A data.frame where each line corresponds to a conglomerate-date, filtered by state, organization, cgl_id, year, and month, the data.frame includes conglomerate name, coordinates of the conglomerate center, date of visit, organization, state, municipality, monitoring type, vegetation, perturbated, species common and scientific name, ....

Examples

# connect to sqlite database (snmb)
database <- dplyr::src_sqlite(system.file("extdata", "snmb.sqlite",
  package = "querysnmb"))
invaders <- queryInvaders(database)
specimens <- querySpecimens(database, state = "Chiapas")

## Not run: 
connect to database (snmb)
PASS_SNMB = Sys.getenv("PASS_SNMB")
database <- dplyr::src_postgres(dbname = "snmb", host = "dbms", user =
  "snmb", password = PASS_SNMB)
invaders <- queryInvaders(database, noms = "vaca|bos|perro",
  year_visit = 2014:2015, organization = c("CONANP", "FMCN"))
footprints <- queryFootprints(database, noms = "vaca|bos|equus|caballo")

## End(Not run)

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