" Exercise 18.4

 Statistical Methods in Biology: Design and Analysis of Experiments and Regression
 by S.J. Welham, S.A. Gezan, S.J. Clark & A. Mead (2014)
 Chapman & Hall/CRC Press, Boca Raton, Florida. ISBN: 978-1-4398-0878-8
 Version 1, 22/08/2015 "

" Set working directory - change to location of your data file "
\SET [WORKINGDIRECTORY='d:/stats4biol/data/']

" Read data from working directory "
FILEREAD [NAME='TRANSECT.DAT'; IMETHOD=read] FGROUPS=2(no),yes,no

" Fit log-linear model (with default dispersion = 1) "
MODEL [DISTRIBUTION=poisson; LINK=log] Y=Count
FITINDIVIDUALLY [PRINT=model,accumulated; FPROBABILITY=yes; TPROBABILITY=yes] Distance+fDist

" Residual plots based on standardized deviance residuals "
RKEEP RESIDUALS=res; FITTEDVALUES=fval
DRESIDUALS [RESIDUALS=res; FITTEDVALUES=fval] METHOD=fittedvalues,normal,histogram,absresidual

" Save residual deviance and df "
RKEEP DEVIANCE=ResDev; DF=ResDF

" Test for over-dispersion "
PRINT STRUCTURE=CUCHI(ResDev;ResDF)

" Re-fit in terms of group means "
MODEL [DISTRIBUTION=poisson; LINK=log] Y=Count
FITINDIVIDUALLY [PRINT=model,accumulated; FPROBABILITY=yes; TPROBABILITY=yes] fDist

" Save fitted values "
RKEEP FITTED=fitGLM

" Compare with means from analysis of log-transformed data "
MODEL log10(Count)
FITINDIVIDUALLY [PRINT=model,accumulated; FPROBABILITY=yes; TPROBABILITY=yes] fDist
RKEEP FITTED=fitREGlog
CALC fitREG = 10**(fitREGlog)

" Compare fitted values "
DGRAPH Count,fitGLM,fitREG; Distance; PEN=1,2,3

" Verify that GLM means are group means "
TABULATE [PRINT=mean; CLASS=fDist] Count,fitGLM,fitREG

" End of File "