jhpoelen’s gists

jhpoelen / coastalPredators.R

Last active August 15, 2016 15:09

	rglobi::query('START predatorTaxon = node:taxons(name="Homo sapiens")
	MATCH predatorTaxon<-[:CLASSIFIED_AS]-predator-[:ATE\|PREYS_ON]->prey-[:CLASSIFIED_AS]->preyTaxon,
	predator-[:COLLECTED_AT]->location-[:HAS_ENVIRONMENT]->envo
	WHERE envo.name= "coast"
	WITH envo, preyTaxon, predatorTaxon
	MATCH preyTaxon<-[:CLASSIFIED_AS]-pred2-[:ATE]->prey2-[:CLASSIFIED_AS]->preyOfPreyTaxon
	RETURN envo.externalId, envo.name, preyTaxon.commonNames?, preyTaxon.path?, predatorTaxon.name as predatorName, preyTaxon.name as preyName, count(distinct preyOfPreyTaxon.name) as preyOfPreyCount')

jhpoelen / completeNerd.html

Last active May 11, 2016 03:10

	<html>
	<head>
	<link rel="stylesheet" href="http://libs.cartocdn.com/cartodb.js/v3/themes/css/cartodb.css"/>
	<script src="http://libs.cartocdn.com/cartodb.js/v3/cartodb.js"></script>
	<script src="https://rawgit.com/jhpoelen/eol-globi-data-js/master/globi-data-dist.js"></script>
	<style>
	html, body {
	width: 100%;
	height: 100%;
	padding: 0;

jhpoelen / .block

Last active March 1, 2016 02:03

Phoibos2 Specimen Identifier Graph (manual only)

license: gpl-3.0

jhpoelen / .block

Last active March 1, 2016 01:10 — forked from mbostock/.block

Phoibos2 Specimen Identifier Graph (small)

license: gpl-3.0

jhpoelen / McLarenFoodWeb.R

Created February 16, 2016 22:18

McLaren Park Observations and Interactions

	# retrieve trophic interactions related to species
	# that were recorded at or near McLaren Park
	# using GloBI and GBIF

	install.packages(c('rglobi', 'rgbif'))

	mcLarenWKT <- 'POLYGON((-122.435 37.726,-122.406 37.726, -122.406 37.710, -122.435 37.710, -122.435 37.726))'
	mcLarenObs <- rgbif::occ_search(geometry= mcLarenWKT)

	gbifSpeciesKeys <- na.omit(unique(mcLarenObs$data$speciesKey))

jhpoelen / filter.json

Last active August 29, 2015 14:23

GBIF download script - requests archive that includes all of GBIF spatial records without (spatial) issues.

	{
	"creator":"jhpoelen",
	"notification_address": ["[email protected]"],
	"predicate":
	{
	"type":"and",
	"predicates": [
	{"type":"equals","key":"HAS_GEOSPATIAL_ISSUE","value":"false"},
	{"type":"equals","key":"HAS_COORDINATE","value":"true"}
	]

jhpoelen / speciesList.R

Last active August 29, 2015 14:20

	#install rglobi (see ropensci.org for more info)
	install.packages(c('rglobi'))

	# read species list after exporting as csv
	krak <- read.csv(file='Krak_list_DELETE.csv', stringsAsFactors=F)
	# pick unique families
	taxonList <- unique(krak$Family)

	# find and aggregate interactions for each species . . . one by one
	interactions <- Reduce(function(accum, taxon) {

jhpoelen / gbif_globi_example.R

Last active August 29, 2015 14:20

Example of how to use GBIF to generate a species list for a specific are and use GloBI to retrieve interactions for those species. Please refer to http://ropensci.org to learn more about the packages.

	# install rgbif and rglobi libraries (see http://ropensci.org for more info)
	install.packages(c('rgbif', 'rglobi'))

	# define geometric bounding box (around california)
	geo1 <- "POLYGON((-126 32, -114 32, -114 41, -126 41, -126 32))"

	# retrieve a bunch of occurrences of Mustelidae with the geometric area
	mustelidaeOcc <- rgbif::occ_search(scientificName='Mustelidae', fields='minimal', geometry = geo1)$data

	# get any interactions records involving unique taxa occurrences at bbox geo1

jhpoelen / interactMap.geojson

Created January 20, 2015 17:50

interaction map

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jhpoelen / createDistributionMap.R

Last active August 29, 2015 14:10

Generate Global Biotic Interaction Distribution Maps

	# see Jorrit H. Poelen, James D. Simons and Chris J. Mungall. (2014). Global Biotic Interactions: An open infrastructure to share and
	# analyze species-interaction datasets. Ecological Informatics. http://dx.doi.org/10.1016/j.ecoinf.2014.08.005

	# rasterize locations, retrieve stats for bounding boxes, plot graphs
	if (!'package:raster' %in% search()) {
	install.packages(c('raster','maps'), repos='http://cran.us.r-project.org')
	library('raster')
	library('maps')
	}

Jorrit Poelen jhpoelen