" Exercise 8.4

 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
 Data from P. Lutman, Rothamsted Research
 Version 1, 26/06/2015 "

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

" Read data from working directory "
FILEREAD [NAME='WEEDCOMPETITION.DAT'; IMETHOD=read] FGROUPS=no,3(yes),no,no

" Plot data, by species and labelled by species "
DGRAPH Y=Yield; X=Density; PEN=Weed

" Investigate density levels per species "
RESTRICT Density; Weed.in.'BG'
PRINT SORT(UNIQUE(Density))
RESTRICT Density; Weed.in.'CL'
PRINT SORT(UNIQUE(Density))
RESTRICT Density; Weed.in.'CW'
PRINT SORT(UNIQUE(Density))
RESTRICT Density "Remove restriction"

" Create density levels 1-6 for each weed species separately (1=control) plus category for other species"
FACTOR [LEVELS=7; LABELS=!T('Control','19.9','28.8','57.7','92.8','183.0','not BG')] BG
CALC BG = (Weed.in.'BG')*(position(Density;!(0,19.9,28.8,57.7,92.8,183.0))) + (Weed.ni.'BG')*7
FACTOR [LEVELS=7; LABELS=!T('Control','2.1','3.8','4.1','9.6','24.9','not CL')] CL
CALC CL = (Weed.in.'CL')*(position(Density;!(0,2.1,3.8,4.1,9.6,24.9))) + (Weed.ni.'CL')*7
FACTOR [LEVELS=7; LABELS=!T('Control','3.8','10.9','29.8','90.3','130.0','not CW')] CW
CALC CW = (Weed.in.'CW')*(position(Density;!(0,3.8,10.9,29.8,90.3,130.0))) + (Weed.ni.'CW')*7

" Create combined factor of density levels "
FACTOR [LEVELS=6; LABELS=!T('Control','Density 1','Density 2','Density 3','Density 4','Density 5')] fDensity
CALC fDensity = (Weed.in.'BG')*BG + (Weed.in.'CL')*CL + (Weed.in.'CW')*CW

" Check factor allocation "
TABULATE [PRINT=count; CLASS=Weed,fDensity]

" Multi-stratum ANOVA with nested structure "
BLOCKSTRUCTURE Block/Plot
TREATMENTSTRUCTURE Weed/fDensity
ANOVA [FPROBABILITY=yes; PSE=diff,lsd] Y=Yield

" Residual plots based on standardized residuals "
APLOT [RMETHOD=standardized] METHOD=fittedvalues,normal,histogram,absresidual

" Plot treatment means "
AGRAPH [PSE=LSD] X=fDensity; GROUPS=Weed

" Separate out nested comparisons for each species "
BLOCKSTRUCTURE Block/Plot
TREATMENTSTRUCTURE Weed/(BG+CL+CW)
ANOVA [FPROBABILITY=yes; PSE=means,differences,lsd] Y=Yield

" Use Dunnett's test to find differences from control within each set "
AMDUNNETT Weed,BG; CONTROL='BG','Control'
AMDUNNETT Weed,CW; CONTROL='CW','Control'

" End of file "