MDM-package: Multinomial Diversity Model

In MDM: Multinomial Diversity Model

Description

The multinomial diversity model is a toolbox for relating diversity to complex predictors. It is based on (1) Shannon diversity; (2) the multinomial logit model, and (3) the link between Shannon diversity and the log-likelihood of the MLM.

Details

Package:	MDM
Type:	Package
Version:	1.0
Date:	2011-09-08
License:	GPL (version 2 or newer)
LazyLoad:	yes

Author(s)

Glenn De'ath: [e-mail]

References

De'ath, G. (2011) The Multinomial Diversity Model: Linking Shannon Diversity To Multiple Predictors

Examples

library(MDM)
data(spider6)
fit0 <- mdm(y2p(spider6[,1:6])~1,data=spider6)
fit1 <- mdm(y2p(spider6[,1:6])~Water,data=spider6)
fit2 <- mdm(y2p(spider6[,1:6])~Water+Herbs,data=spider6)
fit3 <- mdm(y2p(spider6[,1:6])~Site,data=spider6,alpha=TRUE)
anova(fit0,fit1,fit2,fit3)

Example output

Loading required package: nnet
# weights:  12 (5 variable)
# weights:  18 (10 variable)
initial  value 50.169265 
iter  10 value 38.780815
iter  20 value 38.409944
final  value 38.409941 
converged
# weights:  24 (15 variable)
initial  value 50.169265 
iter  10 value 36.791764
iter  20 value 35.415854
iter  30 value 35.415361
final  value 35.415361 
converged
# weights:  174 (140 variable)
Deviances, Entropies and Diversities of Parametric Diversity Models

Response: y2p(spider6[, 1:6]) 

Model 1: y2p(spider6[, 1:6]) ~ 1
Model 2: y2p(spider6[, 1:6]) ~ Water
Model 3: y2p(spider6[, 1:6]) ~ Water + Herbs
Model 4: y2p(spider6[, 1:6]) ~ Site 

   DF DF-Diff    Dev Dev-Diff    Ent Ent-Diff    Div Div-Ratio
1 135         94.105          1.6804          5.3680          
2 130       5 76.820  17.2856 1.3718  0.30867 3.9424    1.3616
3 125       5 70.831   5.9892 1.2648  0.10695 3.5425    1.1129
4   0     125 60.923   9.9075 1.0879  0.17692 2.9681    1.1935

MDM documentation built on May 30, 2017, 4:58 a.m.