y2p
(Package: MDM) :
Scale rows of a species-sites data set
The response matrix for mdm diversity analyses requires that species (columns of the data matrix) are scaled to proportions i.e. that they sum to one for each site (row of the data matrix). Two matrices are particularly useful; these correspond to alpha and gamma diversities. The former is particularly useful for mdm anovas that include the alpha model which is computationally expensive using the function mdm.
● Data Source:
CranContrib
● Keywords:
● Alias: y2p
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simdata
(Package: MDM) :
Species abundance data simulator
Simulates species abundance data along a one-dimensional gradient
● Data Source:
CranContrib
● Keywords:
● Alias: simdata
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2 images
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mdm
(Package: MDM) :
Fits the parameteric diversity model
The parametric diversity model (mdm) is a new method for directly relating diversity to environmental predictors. It is based on three components: (1) parametric diversity, a new parametric model of diversity that can represent any configuration of species proportional abundances, (2) the multinomial logit model (MLM) that can relate species proportional abundances to complex predictors and (3) the link between parametric diversity and the likelihood function of the MLM.
● Data Source:
CranContrib
● Keywords: mdm
● Alias: mdm
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Plots components of entropy by species or sites.
● Data Source:
CranContrib
● Keywords:
● Alias: entropy.plot
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1 images
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eds1
(Package: MDM) :
Calculate alpha, beta and gamma parametric entropies and diversities
Calculates parametric diversities of individual sites of a data set
● Data Source:
CranContrib
● Keywords:
● Alias: eds1
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eds
(Package: MDM) :
Calculate alpha, beta and gamma parametric entropies and diversities
Calculates alpha, beta and gamma parametric diversities of a data set. The matrix or data frame is automatically scaled to row sums of one. Unlike true diversities where weighting is done through the function ed, weighting for parameterized diversity is done within the MDM, or more genrelaly by using case weights.
● Data Source:
CranContrib
● Keywords:
● Alias: eds
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ed1
(Package: MDM) :
Calculate alpha, beta and gamma true entropies and diversities
Calculates true diversities of individual sites of a data set
● Data Source:
CranContrib
● Keywords:
● Alias: ed1
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ed
(Package: MDM) :
Calculate alpha, beta and gamma true entropies and diversities
Calculates alpha, beta and gamma true diversities of a data set. The matrix or data frame is automatically scaled to row sums of one.
● Data Source:
CranContrib
● Keywords:
● Alias: ed
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0 images
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dev2div
(Package: MDM) :
Converts deviances to diversities
Takes either (1) a mdm or (2) a scaler, vector or matrix of deviances, and extracts or converts then to diverities. The relationship between deviance (dev) and diversity (d) is given by div = exp(dev/2/n) where n is the number of units (typically rows of a matrix) over which deviance is being averaged.
● Data Source:
CranContrib
● Keywords:
● Alias: dev2div
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anova.mdm
(Package: MDM) :
Analysis of Deviance, Entropy and Diversity Tables
Provides an analysis of deviance, entropy and diversity for a collection of diversity models (outputs from mdm).
● Data Source:
CranContrib
● Keywords: mdm
● Alias: anova.mdm
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providing 
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