Dear r-users,

My experiment is an germination experiment in which three types of seeds were
stratified at one temperature for 0, 3 and 6 weeks, respectively, following
germination tests at six test temperatures. The question is, are the main factors
(seed type 3 [‘morphs’below] , stratification time 3 , test temperature 6 ) and
interactions significant.
Proportional data with categorical explanatory variables - a three factorial
analysis of deviance.

Thanks to Micheal Crawley and his books:

bidens<-read.table("K:/Bidens
tripartita/Stratifikation/Bidens_Strat_Stat_log.txt", header=T)
attach(bidens)
names(bidens)
y<-cbind(germinated, total-germinated)
model<-glm(y~morph*strat*test, quasibinomial)
summary(model)

dataframe looks as followed

strat
morph
test
germinated
total

zero
peripher
zero
                                                                   0
                                                                  28

zero
peripher
four
                                                                   0
                                                                  29

zero
peripher
eight
                                                                   0
                                                                  29

zero
peripher
twelve
                                                                   0
                                                                  28

zero
peripher
sixteen
                                                                   3
                                                                  26

zero
peripher
twenty
                                                                  27
                                                                  27

zero
inter
zero
                                                                   0
                                                                  29

zero
inter
four
                                                                   0
                                                                  30

zero
inter
eight
                                                                   0
                                                                  28

zero
inter
twelve
                                                                   0
                                                                  26

zero
inter
sixteen
                                                                   0
                                                                  30

zero
inter
twenty
                                                                  15
                                                                  16

zero
inter
zero
                                                                   0
                                                                  25

zero
inter
four
                                                                   0
                                                                  28

zero
inter
eight
                                                                   0
                                                                  31

zero
inter
twelve
                                                                   0
                                                                  28

zero
inter
sixteen
                                                                   8
                                                                  26

zero
inter
twenty
                                                                  28
                                                                  29

zero
peripher
zero
                                                                   0
                                                                  29



The r-output looks like that:

Call:
glm(formula = y ~ morph * strat * test, family = quasibinomial)

Deviance Residuals:
       Min          1Q      Median          3Q         Max
-4.8938080  -0.2407111   0.0001187   0.1658504   4.6929694

Coefficients:
                                       Estimate Std. Error   t value Pr(>|t|)
(Intercept)                           4.974e-16  3.258e-01  1.53e-15 1.000000
morphinter                           -2.461e+00  6.902e-01    -3.565 0.000650 ***
morphperipher                        -1.638e+00  5.567e-01    -2.942 0.004386 **
stratthree                           -2.207e+01  6.339e+03    -0.003 0.997232
stratzero                            -2.204e+01  6.332e+03    -0.003 0.997232
testsixteen                           2.214e+01  6.334e+03     0.003 0.997221
testtwelve                            2.833e+00  7.822e-01     3.622 0.000541 ***
testtwenty                            2.214e+01  6.334e+03     0.003 0.997221
morphinter:stratthree                 2.299e+01  6.339e+03     0.004 0.997116
morphperipher:stratthree              1.592e+00  8.963e+03  1.78e-04 0.999859
morphinter:stratzero                  2.390e+00  8.957e+03  2.67e-04 0.999788
morphperipher:stratzero               1.646e+00  8.963e+03  1.84e-04 0.999854
morphinter:testsixteen                2.406e+00  8.962e+03  2.68e-04 0.999787
morphperipher:testsixteen             1.605e+00  8.960e+03  1.79e-04 0.999858
morphinter:testtwelve                 2.995e+00  1.344e+00     2.229 0.028946 *
morphperipher:testtwelve              8.456e-01  1.042e+00     0.812 0.419651
morphinter:testtwenty                 2.450e+00  8.958e+03  2.73e-04 0.999783
morphperipher:testtwenty              1.605e+00  8.960e+03  1.79e-04 0.999858
stratthree:testsixteen                4.432e+00  8.961e+03  4.95e-04 0.999607
stratzero:testsixteen                -1.192e+00  8.956e+03 -1.33e-04 0.999894
stratthree:testtwelve                 1.907e+01  6.339e+03     0.003 0.997608
stratzero:testtwelve                 -2.848e+00  8.962e+03 -3.18e-04 0.999747
stratthree:testtwenty                 2.206e+01  1.097e+04     0.002 0.998402
stratzero:testtwenty                  2.754e+00  8.956e+03  3.08e-04 0.999755
morphinter:stratthree:testsixteen    -2.323e+01  1.098e+04    -0.002 0.998317
morphperipher:stratthree:testsixteen  1.605e+01  1.417e+04     0.001 0.999100
morphinter:stratzero:testsixteen     -1.948e+00  1.267e+04 -1.54e-04 0.999878
morphperipher:stratzero:testsixteen  -1.837e+00  1.267e+04 -1.45e-04 0.999885
morphinter:stratthree:testtwelve     -2.341e+01  6.339e+03    -0.004 0.997064
morphperipher:stratthree:testtwelve  -1.488e+00  8.963e+03 -1.66e-04 0.999868
morphinter:stratzero:testtwelve       1.478e+01  1.097e+04     0.001 0.998929
morphperipher:stratzero:testtwelve   -8.431e-01  1.268e+04 -6.65e-05 0.999947
morphinter:stratthree:testtwenty     -2.298e+01  1.417e+04    -0.002 0.998710
morphperipher:stratthree:testtwenty  -1.594e+00  1.552e+04 -1.03e-04 0.999918
morphinter:stratzero:testtwenty      -1.643e+00  1.267e+04 -1.30e-04 0.999897
morphperipher:stratzero:testtwenty   -1.530e+00  1.267e+04 -1.21e-04 0.999904
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

(Dispersion parameter for quasibinomial family taken to be 2.387982)

    Null deviance: 3155.83  on 107  degrees of freedom
Residual deviance:  193.19  on  72  degrees of freedom
AIC: NA

Number of Fisher Scoring iterations: 18


But in a first step the only thing I like to know is:



                                       Estimate Std. Error   t value Pr(>|t|)
(Intercept)
morph
strat
test
Morph*strat  and so on

What is my fault?


Thank you very much for your help

Markus




Dr. Markus Brändel
Biocenter Klein Flottbek and Botanical Garden
University of Hamburg
Ohnhorststr. 18
22609 Hamburg
Germany

Phone: +4940 42816-577
Fax:	+4940 42816-254

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