Tools

Free Tools | R package 'ecospat' | 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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R package 'ecospat'

Miscellaneous methods and utilities for spatial ecology analysis, written by current and former members and collaborators of the ecospat group.

'ecospat' offers the possibility to perform Pre-modelling Analysis, such as Spatial autocorrelation analysis, MESS (Multivariate Environmental Similarity Surfaces) analyses, Phylogenetic diversity Measures, Biotic Interactions. It also provides functions to complement biomod2 in preparing the data, calibrating and evaluating (e.g. boyce index) and projecting the models. Complementary analysis based on model predictions (e.g. co- occurrences analyses) are also provided.

In addition, the ecospat package includes Niche Quantification and Overlap functions that were used in Broennimann et al. 2012 and Petitpierre et al. 2012 to quantify climatic niche shifts between the native and invaded ranges of invasive species.

link on CRAN

 

Examples of how to use the functions:

Code-ecospat.pdf  (657 Ko)

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MigClim

MigClim is an R package which allows 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.

Link on CRAN

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.

Engler R., Hordijk W., Guisan A., 2012. The MIGCLIM R package – seamless integration of dispersal constraints into projections of species distribution models. Ecography, 35 (10), 872–878.

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Niche overlap

The R package 'ecospat' R now includes the functions to perform measures of niche overlap and niche equivalency/similarity tests.

Short tutorial:

Create 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 for the calculations with an example data. 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.

user scripts:

user_script_2sp_2A.R , user_script_Nsp_1A.R

Species & climate example data:

clim.eu.txt, clim.na.txt, CM_2009_05feb.txt, sp.txt, sampleglob.txt

Reference:

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 dataGlobal Ecology and Biogeography 21(4): 481-497. DOI

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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.

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