Spatial Data: Ocean Biogeographic Information System (OBIS)Data Category: Species Occurrences Data Description: OBIS is a part of UNESCO’s Intergovernmental Oceanographic Commission, allowing users to search marine species datasets from all of the world’s oceans. Users can identify biodiversity hotspots and large-scale ecological patterns, analyze dispersions of species over time and space, and plot species’ locations with temperature, salinity, and depth. Data Link: http://www.iobis.org/ Data Use Policy: http://www.iobis.org/node/639 Use with R: The easiest way to use OBIS data in R is to download a file directly to one’s computer and read it into R. There is an unpublished package available on GitHub (https://github.com/pieterprovoost/robis) that can be installed to retrieve data directly from OBIS in R. For this package to install, the user must also download and install rtools, which allows for creating and building R packages not in CRAN.
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Spatial Data: Avian Species Occurrences in North America from the Breeding Bird Survey.Data Category: Avian Species Occurrences Data Description: BBS stands for the Breeding Bird Survey, which is managed by the United States Geological Survey and provides free open-access data on North American bird species. Occurrence data are summarized by species’ relative abundance (i.e. raw counts) collected annually at survey routes distributed across the continent. Data Link: ftp://ftpext.usgs.gov/pub/er/md/laurel/BBS/DataFiles/ Data Use Policy: https://www.pwrc.usgs.gov/bbs/RawData/ Use with R: BBS data on species occurrences (and other data with respect to survey routes and sampling) can be downloaded directly from the FTP website by using the R packages
Paleobiology DatabaseData Category: Species Occurrences Data Description: The Paleobiology Database holds data about fossils, including their taxonomic classification and location. Locations are specified as present-day coordinates. Since the age of each specimen is also included, the location can be figured out by transforming land masses appropriately. Spatial coordinates and estimated age both come from the original description of the fossils, so the precision of these measurements varies accordingly. When working with fossil data, remember that the effort that was put in to looking for fossils in a particular region can have a pretty big impact on recorded occurrences, as can the geologic conditions at the point in time that the species lived. Data Link: http://www.paleobiodb.org Data Use Policy: Data in the paleobiodb can be publicly used under a Creative Commons license. They request to be notified, for record-keeping purposes, of publications using their data. For more information, see the FAQ. Use with R: The paleobiodb R paxkage makes retrieving data from the PBDB pretty easy. Below is an example of retrieving data on molluscs from the silurian (~443.8 million years ago). For use with software other than R, a menu for filtering and downloading data is available here.
The paleobiodb package has a lot of useful tools built in. For instance, it can give you a graph of the temporal resolution of your data:
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Spatial Ecology @ MSUClick on "Category" below to search for R code compiled by the Zarnetske Spatial & Community Ecology Lab and students in MSU's Spatial Ecology graduate course (FOR870/FW870) Category
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