R Code and Output Supporting: Species Distribution Models: Predictive Snipers or Shots in the Dark?

Loading...
Thumbnail Image
Statistics
View Statistics

Collection period

2013-06-01
2014-09-09

Date completed

2016-08-11

Date updated

Time period coverage

Geographic coverage

Minnesota, USA

Source information

Minnesota moose data was derived from Street et al. (2016).

Journal Title

Journal ISSN

Volume Title

Title

R Code and Output Supporting: Species Distribution Models: Predictive Snipers or Shots in the Dark?

Published Date

2016-08-11

Group

Author Contact

Fieberg, John R
jfieberg@umn.edu

Type

Dataset
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

Related to

Replaces

Publisher

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.

item.page.sponsorshipfunderid

item.page.sponsorshipfundingagency

item.page.sponsorshipgrant

Previously Published Citation

Suggested citation

View/Download file
File View/OpenDescriptionSize
Readme.txtComplete file description14.91 KB
moose12687.csvRadio telemetry data for one moose (Street et al., 2016)1.45 MB
example_1_corr00.htmlMissing predictor example with cor(x1,x2) = 0 for training & test data sets322.06 KB
example_1_corrNN.htmlMissing predictor example with cor(x1,x2) = -0.3 for training & test data sets308.79 KB
example_1_corrPN.htmlMissing predictor example with cor(x1,x2) = 0.3 for training & -0.3 for test data sets310.15 KB
example_2_temp.htmlNon-linear example178.19 KB
example_3_moose.htmlStep-selection example with MN moose data344.66 KB
uhcdatasimulator.htmlCode for the function "uhcdatasimulator"16.31 KB
ecalcrsf.htmlCode for the function "ecalcrsf" to create calibration plots14.91 KB
uhcsim.htmlCode for the function "uhcsim" to randomly sample locations from non-stratified test data14.56 KB
uhcsimstrat.htmlCode for the function "uhcsimstrat" to randomly sample locations from stratified test data14.89 KB
uhcdenscalc.htmlCode for the function "uhcdenscalc" to calculate density estimates for observed locations14.75 KB
uhcdensplot.htmlCode for the function "uhcdensplot" to create UHC plots15.25 KB
uhcdiffdensplot.htmlCode for the function "uhcdiffdensplot" to create alternate UHC plots14.32 KB
uhcplots.zipContains all Program R code files (.R extension) and data to replicate manuscript results462.17 KB
tables.htmlCode to replicate tables in the manuscript (formatted for LaTeX)18.89 KB
UHC_schematic.pdfSchematic of the steps for producing a UHC plot363.41 KB
MNmoose_Arrowhead.pdfMap detailing the location of moose from dataset746.67 KB

Content distributed via the University Digital Conservancy may be subject to additional license and use restrictions applied by the depositor. By using these files, users agree to the Terms of Use. Materials in the UDC may contain content that is disturbing and/or harmful. For more information, please see our statement on harmful content in digital repositories.