robis

R package for retrieving data from the OBIS Web Services

Install

devtools::install_github("pieterprovoost/robis")

Usage

Occurrences
Gridded taxon distribution
Bodiversity indices
Export

Occurrences

Find by species name

names <- c("Carcharodon carcharias", "Mola mola", "Ursus maritimus", "Aptenodytes forsteri")
data <- get_occurrences(names)

Find by AphiaID (species only)

Finding species occurrences by AphiaID is considerably faster than by species name. AphiaIDs can be retrieved from WoRMS using taxizesoap or get_aphiaid.R.

data <- get_occurrences(137094)

Find by OBIS Taxon ID

Species:

data <- get_occurrences(409234, id="obis")

Higher level taxa (slow):

data <- get_occurrences(780806, id="obis", children=TRUE)

Find by storedpath

data <- get_occurrences("x739909x738303x741923x762719x766931
  x766932x642142x778875x781762x778804x696387x752492x739483x769778x")

Bounding box

data <- get_occurrences("Carcharodon carcharias", bbox=c(-180,-20,180,20))

Filtering

data <- get_occurrences("Abra alba", 
  filter=list(yearcollected=2010, institutioncode="Scottish Natural Heritage"))

# explicit where clause

data <- get_occurrences("Abra alba", where="monthcollected > 8")

Create occurrence map

map_occurrences(data)

Change color criterium

data <- get_occurrences("Balaenoptera musculus",
  where="resource_id = 22 or resource_id = 2553")
map_occurrences(data, color="resname")

Map bounding box

m <- map_occurrences(data)
m + coord_quickmap(xlim = c(-20, 30), ylim=c(50, 60))

Gridded taxon distribution

data <- get_distribution("Mola mola")
map_distribution(data)

Bodiversity indices

C-squares

data <- get_summaries()
map_summaries(data, "shannon")

Hexgrid

data <- get_hexsummaries()
map_summaries(data, "shannon")

data <- get_hexsummaries(typeName = "hexgrid5")
data <- data[data$centre_latitude > -10,]

map_summaries(data, "es", style=style_jet(seq(0, 50, by=5))) + 
  coord_map("ortho", orientation=c(90, 0, 0)) +
  theme(legend.position="right")

Export

Export to GeoJSON using the rwkt package

See here for an example file

library(devtools)
install_github("pieterprovoost/rwkt")
library(rwkt)

data <- get_occurrences(743268, id="obis", children=TRUE, maxFeatures=5)
geometry <- paste0("GEOMETRYCOLLECTION(", paste(data$geom, collapse=","), ")")
data <- data[,c("id", "yearcollected", "tname", "collectioncode")]

toGeoJSON(geometry, pretty=TRUE, data=data)

{
    "type": "FeatureCollection",
    "features": [
        {
            "type": "Feature",
            "geometry": {
                "type": "Point",
                "coordinates": [
                    33.7082,
                    44.4106
                ]
            },
            "properties": {
                "id": 149287642,
                "yearcollected": 1996,
                "tname": "Ampelisca diadema",
                "collectioncode": "Laspibay-Black Sea"
            }
        },
        {
            "type": "Feature",
            "geometry": {
                "type": "Point",
                "coordinates": [
                    33.7072,
                    44.4096
                ]
            },
            "properties": {
                "id": 149287011,
                "yearcollected": 1996,
                "tname": "Balanus improvisus",
                "collectioncode": "Laspibay-Black Sea"
            }
        },
        {
            "type": "Feature",
            "geometry": {
                "type": "Point",
                "coordinates": [
                    11.109,
                    42.2386
                ]
            },
            "properties": {
                "id": 146490918,
                "yearcollected": 1999,
                "tname": "Chthamalus stellatus",
                "collectioncode": "pp"
            }
        },
        {
            "type": "Feature",
            "geometry": {
                "type": "Point",
                "coordinates": [
                    11.109,
                    42.2386
                ]
            },
            "properties": {
                "id": 146490947,
                "yearcollected": 2000,
                "tname": "Balanus",
                "collectioncode": "pp"
            }
        },
        {
            "type": "Feature",
            "geometry": {
                "type": "Point",
                "coordinates": [
                    11.109,
                    42.2386
                ]
            },
            "properties": {
                "id": 146491001,
                "yearcollected": 2001,
                "tname": "Chthamalus stellatus",
                "collectioncode": "pp"
            }
        }
    ]
}