Analysis of Deviance, Entropy and Diversity Tables

Description

Provides an analysis of deviance, entropy and diversity for a collection of diversity models (outputs from mdm).

Usage

## S3 method for class 'mdm'
anova(object, ..., topnote = TRUE, cols = c("df","dev","ent","div")[1:4])

Arguments

Details

Specifying a single object gives a sequential analysis of deviance table for that fit. That is, the reductions in the residual sum of deviances, plus the residual deviance The deviances are converted into entropies and diversities, and differences in deviances are converted into differnces in entropies and diversities.

If more than one object is specified, the table has a row for the residual degrees of freedom and sum of deviances for each model. For all but the first model, the change in degrees of freedom and deviances. This only makes statistical sense if the models are nested. It is conventional to list the models from smallest to largest, but this is up to the user.

Value

The analysis of deviance, entropy and diversity for a collection of diversity models.

Note

mdm is a modifed version of multinom in the nnet package.

References

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

Ripley, B. D. (1996) Pattern Recognition and Neural Networks. Cambridge.

Venables, W. N. and Ripley, B. D. (2002) Modern Applied Statistics with S. Fourth edition. Springer.

See Also

multinom, nnet

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)
anova(fit0,fit1,fit2,fit3)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MDM)
Loading required package: nnet
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MDM/anova.mdm.Rd_%03d_medium.png", width=480, height=480)
> ### Name: anova.mdm
> ### Title: Analysis of Deviance, Entropy and Diversity Tables
> ### Aliases: anova.mdm
> ### Keywords: mdm
> 
> ### ** Examples
> 
> library(MDM)
> data(spider6)
> fit0 <- mdm(y2p(spider6[,1:6])~1,data=spider6)
# weights:  12 (5 variable)
> fit1 <- mdm(y2p(spider6[,1:6])~Water,data=spider6)
# weights:  18 (10 variable)
initial  value 50.169265 
iter  10 value 38.780815
iter  20 value 38.409944
final  value 38.409941 
converged
> fit2 <- mdm(y2p(spider6[,1:6])~Water+Herbs,data=spider6)
# 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
> fit3 <- mdm(y2p(spider6[,1:6])~Site,data=spider6)
# weights:  174 (140 variable)
> anova(fit0,fit1,fit2,fit3)
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
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>