eco_region: Filter points within ecoregions

In ropensci/scrubr: Clean Biological Occurrence Records

Filter points within ecoregions

Description

Filter points within ecoregions

Usage

eco_region(x, dataset = "meow", region, lat = NULL, lon = NULL, drop = TRUE)

regions_meow()

regions_fao()

Arguments

x	(data.frame) A data.frame
dataset	(character) the dataset to use. one of: "meow" (Marine Ecoregions of the World), "fao" (). See Details.
region	(character) one or more region names. has the form a:b where a is a variable name (column in the sf object) and b is the value you want to filter to within that variable. See Details.
lat, lon	(character) name of the latitude and longitude column to use
drop	(logical) Drop bad data points or not. Either way, we parse out bad data points as an attribute you can access. Default: TRUE #param ignore.na (logical) To consider NA values as a bad point or not. Default: FALSE

Details

see scrubr_cache for managing the cache of data

Value

Returns a data.frame, with attributes

dataset options

• Marine Ecoregions of the World (meow):

  • data from: https://opendata.arcgis.com/datasets/ed2be4cf8b7a451f84fd093c2e7660e3_0.geojson

• Food and Agriculture Organization (fao):

  • data from: http://www.fao.org/geonetwork/srv/en/main.home?uuid=ac02a460-da52-11dc-9d70-0017f293bd28

region options

• within meow:

  • ECOREGION: many options, see regions_meow()

  • ECO_CODE: many options, see regions_meow()

  • and you can use others as well; run regions_meow() to get the data used within eco_region() and see what variables/columns can be used

• within fao:

  • OCEAN: Atlantic, Pacific, Indian, Arctic

  • SUBOCEAN: 1 through 11 (inclusive)

  • F_AREA (fishing area): 18, 21, 27, 31, 34, 37, 41, 47, 48, 51, 57, 58, 61, 67, 71, 77, 81, 87, 88

  • and you can use others as well; run regions_fao() to get the data used within eco_region() and see what variables/columns can be used

Examples

## Not run: 
if (requireNamespace("mapview") && requireNamespace("sf") && interactive()) {
## Marine Ecoregions of the World
wkt <- 'POLYGON((-119.8 12.2, -105.1 11.5, -106.1 21.6, -119.8 20.9, -119.8 12.2))'
res <- rgbif::occ_data(geometry = wkt, limit=300)$data
res2 <- sf::st_as_sf(res, coords = c("decimalLongitude", "decimalLatitude"))
res2 <- sf::st_set_crs(res2, 4326)
mapview::mapview(res2)
tmp <- eco_region(dframe(res), dataset = "meow",
   region = "ECOREGION:Mexican Tropical Pacific")
tmp2 <- sf::st_as_sf(tmp, coords = c("decimalLongitude", "decimalLatitude"))
tmp2 <- sf::st_set_crs(tmp2, 4326)
mapview::mapview(tmp2)
## filter many regions at once
out <- eco_region(dframe(res), dataset = "meow",
   region = c("ECOREGION:Mexican Tropical Pacific", "ECOREGION:Seychelles"))
out
out2 <- sf::st_as_sf(out, coords = c("decimalLongitude", "decimalLatitude"))
out2 <- sf::st_set_crs(out2, 4326)
mapview::mapview(out2)

## FAO
## FIXME - this needs fixing, broken
wkt <- 'POLYGON((72.2 38.5,-173.6 38.5,-173.6 -41.5,72.2 -41.5,72.2 38.5))'
manta_ray <- rgbif::name_backbone("Mobula alfredi")$usageKey
res <- rgbif::occ_data(manta_ray, geometry = wkt, limit=300, hasCoordinate = TRUE)
dat <- sf::st_as_sf(res$data, coords = c("decimalLongitude", "decimalLatitude"))
dat <- sf::st_set_crs(dat, 4326)
mapview::mapview(dat)
tmp <- eco_region(dframe(res$data), dataset = "fao", region = "OCEAN:Indian")
tmp <- tmp[!is.na(tmp$decimalLongitude), ]
tmp2 <- sf::st_as_sf(tmp, coords = c("decimalLongitude", "decimalLatitude"))
tmp2 <- sf::st_set_crs(tmp2, 4326)
mapview::mapview(tmp2)
}
## End(Not run)

ropensci/scrubr documentation built on Sept. 12, 2022, 2:12 p.m.