07_assemblageFetch: Function 'assemblageFetch' retrieves the species set of an...

In rangeMapper: A platform for the study of macroecology of life history traits

Description

Function assemblageFetch retrieves the species set, and the data associated with it, of an arbitrary canvas cell optionally with the associated life history data

Methods

signature(object = "rangeMap", xy = "SpatialPoints", BIO = "character")

assemblageFetch(rangeMap, xy, BIO) returns a data.frame containing the bioid (e.g. species names), canvas id and any associated life history data contained in the BIO table.

signature(object = "rangeMap", xy = "SpatialPoints", BIO = "missing")

If BIO is missing then assemblageFetch(rangeMap, xy) returns only a data.frame containing two columns the bioid (e.g. species names) and the canvas id.

Examples

require(rangeMapper)

projName = "wrens.sqlite"
projLoc = paste(tempdir(), projName, sep = .Platform$file.sep)

dbcon = rangeMap.start(file = projName,dir = tempdir() , overwrite = TRUE)
f = system.file(package = "rangeMapper", "extdata", "wrens", "vector_combined")
global.bbox.save(con = dbcon, bbox = f) 
gridSize.save(dbcon, gridSize = 3) 
canvas.save(dbcon) 
data(wrens)
bio.save(con = dbcon, loc = wrens ,  ID = "sci_name")
r = readOGR(f, "wrens", verbose = FALSE)
processRanges(spdf = r, con =  dbcon, ID = "sci_name")
rangeMap.save(dbcon)

sr = rangeMap.fetch(dbcon)
image(sr, axes = TRUE); grid()

p = list(x = -76.39, y = 9.26)
# or use locator:  p =  locator(1) 

xy = SpatialPoints( do.call(cbind, p), proj4string = CRS("+proj=longlat +datum=NAD83 +no_defs ") )
af = assemblageFetch(rangeMap(projLoc) , xy)
points(p, col = 4, cex = 2)
print(af)

af = assemblageFetch(rangeMap(projLoc) , xy, "wrens")
print(af[, c(1, 4, 6:8)])

rangeMapper documentation built on May 2, 2019, 5 p.m.