Spatial Ecology Miscellaneous Methods

Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre, core and post modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) and Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland. Read Di Cola et al. (2016) for details.


News

ecospat_1.1 (06.03.2015)

FIXES

  • Fixed bug in "ecospat.grid.clim.dyn()" with the kernel.
  • Fixed error in "ecospat.boyce()" return Boyce index value: Spearman coeficient is the correct one.
  • Fixed bug in "ecospat.cons_Cscore()" p-value correction.
  • Fixed manual of the function "ecospat.calculate.pd()" where arguments definition was incomplete.
  • Fixed data set of species list, now matches the species in the tree dataset.
  • Fixed ouput of "ecospat.plot.mess()" function, now gives individual figures as result.

CHANGES

  • Removed some dependencies of whole packages, and indicated individual functions from packages to be imported.

ecospat_2.0 (26.05.16)

NEW FEATURES

  • Added a new argument in the function "ecospat.niche.similarity.test()", to indicate if the niches are randomized.
  • Added function "ecospat.shift.centroids()", to replace "ecospat.fun.arrows()" for being more precise on the utility of the function.
  • Added two new datasets "ecospat.testNiche.nat" and "ecospat.testNiche.nat", to better exemplify the niche quantification analysis.
  • Added new function "ecospat.ESM.Modeling()" for calibrating simple bivariate models.
  • Added new function "ecospat.ESM.Projection()" for projecting simple bivariate models on new.env.
  • Added new function "ecospat.ESM.EnsembleModeling()" forevaluating and averaging simple bivariate models to ESMs.
  • Added new function "ecospat.ESM.EnsembleProjection()" for projecting calibrated ESMs into new space or time.
  • Added new function "ecospat.SESAM.prr()" for predicting community composition using a 'probability ranking' rule.
  • Added new function "ecospat.cohen.kappa()" for calculating Cohen`s kappa and variance estimates.
  • Added new function "ecospat.max.kappa()" for calculating values for Cohen’s Kappa along different thresholds.
  • Added new function "ecospat.max.tss()" for calculating values for TSS along different thresholds.
  • Added new function "ecospat.meva.table()" for calculating values of a series of different evaluations metrics for a model.
  • Added new function "ecospat.plot.kappa()" for plotting the values for Cohen’s Kappa.
  • Added new function "ecospat.plot.tss()" for plotting the values for TSS.
  • Added new function "ecospat.mpa()" for calculating minimal predicted area.
  • Added new function "ecospat.cor.plot()" for plotting correlation of variables.
  • Added function "ecospat.CommunityEval()", to replace "ecospat.SSDMeval()" for being more precise on the utility of the function.
  • Added new function "ecospat.adj.D2.glm()" for calculating an adjusted D2.
  • Added new function "ecospat.exdet()" to assess climate analogy between a projection extent and a reference extent.

CHANGES

  • Updated NAMESPACE file, import("biomod2"), and dependencies.
  • Updated dependencies of the package.Removed the dependency on the package "gam." Removed the dependency of the function kasc2spixdf("adehabitatMA"). Added the package "gtools".
  • Removed window progress indicator for the function "ecospat.niche.similarity.test()" and "ecospat.niche.equivalency.test()", and added a progress bar in the command line for functions.
  • Removed the function "ecospat.cv.gam()" and the option to run the cv in the function 'ecospat.cv.example()'.

FIXES

  • Corrected the function "ecospat.niche.dyn.index()", value of the intersection = 0.1.

ecospat_2.0.1 (09.06.16)

FIXES

  • Added details to the documentation files in the description section of the function "ecospat.niche.similarity.test()".
  • Fixed spelling error in description of the package (*Collection).
  • Fixed bug in the ESM functions "ecospat.ESM.Modeling()", "ecospat.ESM.EnsembleModeling()" and "ecospat.ESM.EnsembleProjection()", when using raster files as input.
  • Corrected definition of the argument "quant" of the function "ecospat.plot.niche.dyn()".
  • Updated the function "ecospat.grid.clim.dyn()" and the definition of its arguments "th.sp" and "th.env". Also updated its details.

ecospat_2.1.0 (23.09.16)

FIXES

  • Fixed the definition of variables of TRUE/FALSE in the function "ecospat.cv.rf()","ecospat.binary.model()", "ecospat.boyce()", "ecospat.caleval()", "ecospat.CommunityEval()","ecospat.cons_Cscore()", "ecospat.co_occurrences()", "ecospat.cv.gbm()", "ecospat.cv.glm()", "ecospat.cv.me()", "ecospat.ESM.EnsembleModeling()", "ecospat.ESM.EnsembleProjection()", "ecospat.ESM.Modeling()", "ecospat.ESM.Projection()", "ecospat.exdet()", "ecospat.makeDataFrame()", "ecospat.mess()", "ecospat.niche.similarity.test()", "ecospat.occ.desaggregation()", "ecospat.SESAM.prr()".

  • Removed window progress indicator for the function "ecospat.occ.desaggregation()" and "ecospat.sample.envar()".

NEW FEATURES

  • Added new function "ecospat.rcls.grd()" for reclassifying grid files.
  • Added new function "ecospat.recstrat_regl()" to randomly take an equal number of samples of regular number.
  • Added new function "ecospat.recstrat_prop()" to randomly take an equal number of samples of proportional number.
  • Added new function "ecospat.Cscore()" to test for nonrandom patterns of species co-occurrence in a presence-absence matrix.
  • Added a new argument in the function "ecospat.niche.similarity.test()", to test for niche conservatism or divergence.
  • Added a new argument in the function "ecospat.niche.equivalency.test()", to test for niche conservatism or divergence.

ecospat_2.1.1 (02.11.16)

FIXES

  • Fixed the definition of variables of TRUE/FALSE in the files R/ecospat.ESM.R, R/ecospat.sampling.R and R/ecospat.occprep.R.

ecospat_2.2.0 (08.11.17)

NEW FEATURES

  • Added new function "ecospat.rangesize" to estimate the range.size of a species using standard IUCN criteria.
  • Added new function "ecospat.occupied.patch()" to determine the occupied patch of a species.
  • Added new function "ecospat.mdr()" to implement a minimum cost arborescence analysis.
  • Added new dataset "ecospat.testMrd.nat" to exemplify the minimum cost arborescence analysis.

CHANGES

  • Re-named the function "ecospat.exdet()" to "ecospat.climan()".

FIXES

  • Updated the functions "ecospat.occ.desaggregation()", "ecospat.binary.model()" and "ecospat.boyce()".
  • Fixed bug in "ecospat.grid.clim.dyn()" that shifted the gridded distribution one pixel away from the observed points.

ecospat_3.0 (19.06.18)

NEW FEATURES

  • Added new funtions "ecospat.niche.zProjGeo" and "ecospat.niche.dynIndexProjGeo" to project niche quantification (calculated with ecospat.grid.clim.dyn) onto the geographical space
  • Added a new dataset ecospat.testEnvRaster including a stack of 5 topoclimatic rasters at 250m resolution for the Western Swiss Alps
  • Added new functions "ecospat.CCV.modeling", "ecospat.CCV.createDataSplitTable", "ecospat.CCV.communityEvaluation.bin", and "ecospat.CCV.communityEvaluation.prob" to perform community cross-validation (CCV) as in Scherrer et al. 2018.

Added a new function "ecospat.ESM.VarContrib" to calculate the variable contribution of each variable and method in an ESM model

CHANGES

FIXES

  • Fixed several bugs in "ecospat.ESM.R","ecospat.ESM.Projection.Rd", "ecospat.ESM.EnsembleModeling.Rd",and "ecospat.ESM.EnsembleProjection.Rd"
  • Fixed bug in "ecospat.mess" that included x and y coordinates as environmental factors

Reference manual

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install.packages("ecospat")

3.0 by Olivier Broennimann, 10 months ago


http://www.unil.ch/ecospat/home/menuguid/ecospat-resources/tools.html


Report a bug at https://github.com/ecospat/ecospat


Browse source code at https://github.com/cran/ecospat


Authors: Olivier Broennimann [cre, aut, ctb] , Valeria Di Cola [aut, ctb] , Blaise Petitpierre [ctb] , Frank Breiner [ctb] , Daniel Scherrer [ctb] , Manuela D`Amen [ctb] , Christophe Randin [ctb] , Robin Engler [ctb] , Wim Hordijk [ctb] , Heidi Mod [ctb] , Julien Pottier [ctb] , Mirko Di Febbraro [ctb] , Loic Pellissier [ctb] , Dorothea Pio [ctb] , Ruben Garcia Mateo [ctb] , Anne Dubuis [ctb] , Luigi Maiorano [ctb] , Achilleas Psomas [ctb] , Charlotte Ndiribe [ctb] , Nicolas Salamin [ctb] , Niklaus Zimmermann [ctb] , Antoine Guisan [aut]


Documentation:   PDF Manual  


Task views: Phylogenetics, Especially Comparative Methods


GPL license


Imports adehabitatHR, adehabitatMA, biomod2, dismo, ecodist, maptools, randomForest, spatstat, raster, rms, MigClim, gtools, PresenceAbsence, methods, doParallel, foreach, iterators, parallel, classInt, vegan, poibin, snowfall

Depends on ade4, ape, gbm, sp

Suggests rgdal, rJava, XML, knitr, alphahull, rgeos, igraph


Suggested by biomod2.


See at CRAN