A function which randomizes the values of the given variables within a site-pair table. This function is called from the gdm.varImp function and should not need to be called directly by the user.
● Data Source:
CranContrib
● Keywords: gdm, internal
● Alias: permutateVarSitePair
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This function estimates uncertainty in the I-splines using bootstrapping. The function can run in parallel on multicore machines to reduce computation time (recommended for large number of iterations). I-spline plots with error bands (+/- one standard deviation) are produced showing (1) the variance of Ispline coefficients and (2) a rug plot indicating how sites used in model fitting are distributed along each gradient.
● Data Source:
CranContrib
● Keywords: gdm
● Alias: plotUncertainty
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Randomly selects a number of sites from a given site-pair table and removes them from the site-pair table. This function is called from the plotUncertainty function and should not need to be called directly by the user.
● Data Source:
CranContrib
● Keywords: gdm, internal
● Alias: removeSitesFromSitePair
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This function predicts biological distances between sites or times using a model object returned from gdm. Predictions between site pairs require a data frame containing the values of predictors for pairs of locations, formatted as follows: Distance, Weights, X1, Y1, X2, Y2, Var1Site1, Var2Site1, ..., VarNSite1, Var1Site2, Var2Site2, ..., VarNSite2. Predictions of biological change through time require two raster stacks or bricks for environmental conditions at two time periods, each with a layer for each environmental predictor in the fitted model.
● Data Source:
CranContrib
● Keywords: gdm
● Alias: predict, predict.gdm
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gdm
(Package: gdm) :
For an overview of the functions in the gdm package have a look here: gdm-package.
● Data Source:
CranContrib
● Keywords: gdm
● Alias: gdm
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plot is used to plot the I-splines and fit of a generalized dissimilarity model created using the gdm function.
● Data Source:
CranContrib
● Keywords: gdm
● Alias: plot, plot.gdm
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This function transforms geographic and environmental predictors using (1) the fitted functions from a model object returned from gdm and (2) a data frame or raster stack containing predictor data for a set of sites.
● Data Source:
CranContrib
● Keywords: gdm
● Alias: gdm.transform
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A function which randomizes the rows of a given site-pair table. This function is called from the gdm.varImp function and should not need to be called directly by the user.
● Data Source:
CranContrib
● Keywords: gdm, internal
● Alias: permutateSitePair
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Generalized Dissimilarity Modeling is a statistical technique for modelling spatial variation in biodiversity between pairs of geographical locations. The gdm package currently provides basic functions to fit, summarize, and plot Generalized Dissimilarity Models and to make predictions (in both space and time) and map biological patterns by transforming environmental predictor variables. Future updates will incorporate support for genomic data.
● Data Source:
CranContrib
● Keywords:
● Alias: gdm-package
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Extracts the I-spline values from a gdm object. There is one I-spline for each predictor that has at least one non-zero coefficient in the fitted model.
● Data Source:
CranContrib
● Keywords: gdm
● Alias: isplineExtract
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providing 
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