R Code and Output Supporting: Species Distribution Models: Predictive Snipers or Shots in the Dark?
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: Species Distribution Models: Predictive Snipers or Shots in the Dark?
Published Date
2016-08-11
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Author Contact
Fieberg, John R
jfieberg@umn.edu
jfieberg@umn.edu
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Software Code
Field Study Data
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. "Species distribution models: Predictive snipers or shots in the dark?", 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_3_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 (uhcplots.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. In Review. Species distribution models: predictive snipers or shots in the dark? Ecology Letters.
Street, GM, Fieberg, J, Rodgers, AR, Carstensen, M, Moen, R, and Moore, SA, et al. (2016) Habitat functional response mitigates reduced foraging opportunity: Implications for animal fitness and space use. Landscape Ecology 1-15.
http://doi.org/10.1007/s10980-016-0372-z
Street, GM, Fieberg, J, Rodgers, AR, Carstensen, M, Moen, R, and Moore, SA, et al. (2016) Habitat functional response mitigates reduced foraging opportunity: Implications for animal fitness and space use. Landscape Ecology 1-15.
http://doi.org/10.1007/s10980-016-0372-z
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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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Readme.txt
Complete file description
(14.91 KB)
moose12687.csv
Radio telemetry data for one moose (Street et al., 2016)
(1.45 MB)
example_1_corr00.html
Missing predictor example with cor(x1,x2) = 0 for training & test data sets
(322.06 KB)
example_1_corrNN.html
Missing predictor example with cor(x1,x2) = -0.3 for training & test data sets
(308.79 KB)
example_1_corrPN.html
Missing predictor example with cor(x1,x2) = 0.3 for training & -0.3 for test data sets
(310.15 KB)
example_2_temp.html
Non-linear example
(178.19 KB)
example_3_moose.html
Step-selection example with MN moose data
(344.66 KB)
uhcdatasimulator.html
Code for the function "uhcdatasimulator"
(16.31 KB)
ecalcrsf.html
Code for the function "ecalcrsf" to create calibration plots
(14.91 KB)
uhcsim.html
Code for the function "uhcsim" to randomly sample locations from non-stratified test data
(14.56 KB)
uhcsimstrat.html
Code for the function "uhcsimstrat" to randomly sample locations from stratified test data
(14.89 KB)
uhcdenscalc.html
Code for the function "uhcdenscalc" to calculate density estimates for observed locations
(14.75 KB)
uhcdensplot.html
Code for the function "uhcdensplot" to create UHC plots
(15.25 KB)
uhcdiffdensplot.html
Code for the function "uhcdiffdensplot" to create alternate UHC plots
(14.32 KB)
uhcplots.zip
Contains all Program R code files (.R extension) and data to replicate manuscript results
(462.17 KB)
tables.html
Code to replicate tables in the manuscript (formatted for LaTeX)
(18.89 KB)
UHC_schematic.pdf
Schematic of the steps for producing a UHC plot
(363.41 KB)
MNmoose_Arrowhead.pdf
Map detailing the location of moose from dataset
(746.67 KB)
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