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The easiest way to use OBIS data in R is to download a file directly to one’s computer and read it into R. There is an unpublished package available on GitHub (https://github.com/pieterprovoost/robis) that can be installed to retrieve data directly from OBIS in R. For this package to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: Land Cover Type from MRLC NLCDData Category: Land Cover Type Data Description: The National Land Cover Database (NLCD) is a compilation of land cover data collected and maintained by the Multi-Resolution Land Characteristics (MRLC). Data Link: http://www.mrlc.gov/index.php Data Use Policy: http://www.usgs.gov/laws/policies_notices.html Use With R: When using NLCD data with R, the information can be downloaded from the MRLC website (link above). Note that this data set can be memory intensive for an average computer. Due to the size of the data file (i.e., the entire U.S.A.) it may take a considerable amount of time to retrieve and plot. Once rasterized, it is possible to decrease the resolution of the data (depending on your scale of interest) to reduce the size of the file, as demonstrated in the following example, before plotting the data. Decreasing the resolution may not be desirable in many situations so keep in mind the scale and region size of interest. Useful packages for working with this data in R include “raster” in order to rasterize the data. In this example, I have downloaded the entire continental U.S. and presented it at a resolution of 100 m. Install and load relevant packages
Download data
Unzip data
Rasterize the data (package “raster”)
Change the resolution of the data to decrease file size using aggregate()
Plot the NLCD data
Further: The information provided here http://neondataskills.org/R/Raster-Data-In-R/ may be useful in producing a map with more distinct color, as shown below: 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
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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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