R Code and Output Supporting: Used-habitat calibration plots: A new procedure for validating species distribution, resource selection, and step-selection models
2016-08-11
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2013-06-01
2014-09-09
2014-09-09
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2016-08-11
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Minnesota, USA
Source information
Minnesota moose data was derived from Street et al. (2016).
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Title
R Code and Output Supporting: Used-habitat calibration plots: A new procedure for validating species distribution, resource selection, and step-selection models
Published Date
2016-08-11
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Author Contact
Fieberg, John R
jfieberg@umn.edu
jfieberg@umn.edu
Type
Dataset
Programming Software Code
Field Study Data
Programming Software Code
Field Study Data
Abstract
Species distribution models (SDMs) are one of a variety of statistical methods that link individuals, populations, and species to the habitats they occupy. In Fieberg et al. "Used-habitat calibration plots: A new procedure for validating species distribution, resource selection, and step-selection models", we introduce a new method for model calibration, which we call Used-Habitat Calibration plots (UHC plots) that can be applied across the entire spectrum of SDMs. Here, we share the Program R code and data necessary to replicate all three of the examples from the manuscript that together demonstrate how UHC plots can help with three fundamental challenges of habitat modeling: identifying missing covariates, non-linearity, and multicollinearity.
Description
Each example.html file (“example_”) uses various uhcplot functions (html files with description “code for function”). The example with the MN moose data (example_4_moose.html) also uses data for one Minnesota moose from 2013 and 2014 (in moose12687.csv). The tables (tables.html) are created with regression output files created and saved with the codes provided in the example.html files. The zipped folder (UHCPlotsPaper_R.zip) contains all of the Program R files (.R extension) for each of the html files. MNmoose_Arrowhead.pdf details the location of the moose from dataset. See the readme.txt for more information.
Referenced by
Fieberg, Forester, Street, Johnson, ArchMiller, and Matthiopoulos. Used-habitat calibration plots: A new procedure for validating species distribution, resource selection, and step-selection models. Ecography. DOI:10.1111/ecog.03123.
http://doi.org/10.1111/ecog.03123
http://doi.org/10.1111/ecog.03123
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Funding information
This work was funded in part by the University of Minnesota-Twin Cities and the Minnesota Environment and Natural Resources Trust Fund. The Minnesota Department of Natural Resources assisted with collaring and monitoring of the moose.
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Suggested citation
Fieberg, John R; Forester, James D; Street, Garrett M; Johnson, Douglas H; ArchMiller, Althea A; Matthiopoulos, Jason. (2016). R Code and Output Supporting: Used-habitat calibration plots: A new procedure for validating species distribution, resource selection, and step-selection models. Retrieved from the Data Repository for the University of Minnesota (DRUM), http://doi.org/10.13020/D6T590.
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Readme.txt
Description of Dataset
(14.57 KB)
UHC_schematic.pdf
Schematic of the steps for producing a UHC plot
(363.41 KB)
example_1_corr00.html
Complete R Code for missing predictor example with cor(x1,x2) = 0 for training & test data sets
(82.94 KB)
example_1_corrNN.html
Complete R Code for missing predictor example with cor(x1,x2) = -0.3 for training & test data sets
(80.26 KB)
example_1_corrPN.html
Complete R Code for missing predictor example with cor(x1,x2) = 0.3 for training & -0.3 for test data sets
(81.05 KB)
example_2_temp.html
Complete R Code for Non-linear example
(83.49 KB)
example_3_spatial_split.html
Complete R Code for spatial example
(776.01 KB)
example_4_moose.html
Complete R Code for the step-selection example with MN moose data
(343.1 KB)
moose12687.csv
Radio telemetry data for one moose (Street et al., 2016)
(1.44 MB)
MNmoose_Arrowhead.pdf
Map detailing the location of moose from dataset
(746.67 KB)
ecalcrsf.html
Complete R Code that creates calibration plots
(14.92 KB)
tables.html
R Code to replicate tables in the manuscript (formatted for LaTeX)
(17.89 KB)
uhcplots_0.1.0.tar.gz
Bundled package for R package uhcplots
(886.3 KB)
UHCPlotsPaper_R.zip
All Program R code files (.R extension) and data to replicate manuscript results
(24.47 KB)
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