Tools

Free Tools | MigClim | Niche overlap | Biomapper | Canogen
 

Free Tools

You will find here the tools our GIS lab and research group make available to the scientific community.

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MigClim

The MigClim tool and manual are now available in beta version. Please contact Robin Engler at "Robin.Engler [--at--] gmail.com" to obtain the beta version and sign-up for the newsletter.
 

MigClim is an ArcGIS extension which allows simulating simulating plant dispersal under climate change and landscape fragmentation scenarios. MigClim allows implementing various parameters, such as dispersal distance, increase in reproductive potential over time, landscape fragmentation or long-distance dispersal.

Reference :

Engler R. and Guisan A., 2009. MIGCLIM: Predicting plant distribution and dispersal in a changing climate. Diversity and Distribution, 15 (4), 590-601.

Engler R., Randin C.F., Vittoz P., Czáka T., Beniston M., Zimmermann N.E., Guisan A., 2009. Predicting future distributions of mountain plants under climate change: does dispersal capacity matter? Ecography, 32 (1), 34-45.

 

NEW: Migclim is now implemented as a R package!!!!

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Niche overlap

R functions to perform measures of niche overlap and niche equivalency/similarity tests.

The methods are described in:

Broennimann O. , Fitzpatrick M.C. , Pearman P.B. , Petitpierre B. , Pellissier L. , Yoccoz N.G. , Thuiller W. , Fortin M.J. , Randin C.R. , Zimmermann N.E. , Graham C.H. , Guisan A. 2012. Measuring ecological niche overlap from occurrence and spatial environmental data. Global Ecology and Biogeography 21(4): 481-497

Short tutorial: 

Put the following R files in a folder with a R shortcut. Use this folder as workspace by setting the path in the proprieties of the shortcut (right click). In this folder also put your datasets of occurences data (delimited text file with column names x,y) and datesets of points representing the study areas with environmental values (column names should be x,y,X1,X2,...,Xn). The user scripts allow setting the analyses and sourcing the functions necessary for the calculations (niche.overlap.functions.R and occ.prep.functions.R). Use user_script_2sp_2A.R if you want to compare niches of 2 species in different areas (e.g. invasive species). Use user_script_Nsp_1A.R if you want to compare niches of n species in the same area.

functions (sourced in user scripts): 

file   niche.overlap.functions.R  (15 Kb)

file   occ.prep.functions.R  (6 Kb)

user scripts: 

file   user_script_2sp_2A.R  (30 Kb)

file   user_script_Nsp_1A.R  (6 Kb)

species & climate data (loaded by user scripts): 

txt   clim.eu.txt  (4911 Kb)

txt   clim.na.txt  (5040 Kb)

txt   CM_2009_05feb.txt  (106 Kb)

txt   sampleglob.txt  (2049 Kb)

txt   sp.txt  (14 Kb)

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Biomapper

Link to the BIOMAPPER software for predicting species occurrences developped by Alex Hirzel at UNIL.

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Canogen

Get the zip CANOGEN AML developped by Andrew D. Weiss and Stuart B. Weiss to predict plant distribution in ARCINFO directly from CANOCO outputs (see Guisan, A., Weiss, S.B. & Weiss, A.D. 1999. GLM versus CCA spatial modeling of plant species distribution. Plant Ecology 143(1) : 107-122)

Credits : Thanks to acknowledge Andy and Stu in any related publication ! Contact weiss.andrew (a) epamail.epa.gov.

zip   canogen.zip  (3 Kb)

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