Dear all, 
 
I have data from the following experimental design and trying to fit a mixed model with lme function according to following steps but struggling. Any help is deeply appreciated.
 
1) Experimental design: I have 40 plants each of which has 4 clones. Each clone planted to one of 4 blocks. Phenotypes were collected from each clone for 3 consecutive years. I have genotypes of plants. I need to relate phenotype to genotype. 
 
2) I am reading data from a file with “read.table” function. Then grouping data as: my.Data<-groupedData( phenotype ~ Block | PlantID, data = as.data.frame( Data ) ) 
 
3) I want to fit Genotype + Year + Genotype:Year as fixed effect. Block + PlantID + Block.PlantID as random effect. 
 
I feel my data grouping is incorrect as model fitting do not work properly. 
 
Some part of my data was added below in case it would help to understand the structure.
 
Any help regarding data grouping and model fitting is deeply appreciated.
 
Kind Regards
 
Seyit Ali
 
 
PlantID Block Year Diameter Genotype 
1 1 1 170 0 
1 2 1 166 0 
1 3 1 168 0 
1 4 1 169 0 
1 1 2 142 0 
1 2 2 115 0 
1 3 2 131 0 
1 4 2 129 0 
1 1 3 138 0 
1 2 3 142 0 
1 3 3 139 0 
1 4 3 135 0 
2 1 1 155 1 
2 2 1 168 1 
2 3 1 158 1 
2 4 1 145 1 
2 1 2 131 1 
2 2 2 150 1 
2 3 2 130 1 
2 4 2 130 1 
2 1 3 123 1 
2 2 3 125 1 
2 3 3 126 1 
2 4 3 129 1 
3 1 1 142 0 
3 2 1 155 0 
3 3 1 150 0 
3 4 1 149 0 
3 1 2 123 0 
3 2 2 129 0 
3 3 2 134 0 
3 4 2 131 0 
3 1 3 126 0 
3 2 3 117 0 
3 3 3 123 0 
3 4 3 126 0 
4 1 1 167 0 
4 2 1 156 0 
4 3 1 161 0 
4 4 1 164 0 
4 1 2 148 0 
4 2 2 133 0 
4 3 2 144 0 
4 4 2 127 0 
4 1 3 137 0 
4 2 3 134 0 
4 3 3 135 0 
4 4 3 135 0 
5 1 1 146 1 
5 2 1 156 1 
5 3 1 152 1 
5 4 1 147 1 
5 1 2 122 1 
5 2 2 131 1 
5 3 2 132 1 
5 4 2 130 1 
5 1 3 127 1 
5 2 3 126 1 
5 3 3 130 1 
5 4 3 136 1 
6 1 1 148 0 
6 2 1 161 0 
6 3 1 140 0 
6 4 1 150 0 
6 1 2 123 0 
6 2 2 130 0 
6 3 2 120 0 
6 4 2 134 0 
6 1 3 123 0 
6 2 3 132 0 
6 3 3 128 0 
6 4 3 128 0 
7 1 1 152 1 
7 2 1 147 1 
7 3 1 153 1 
7 4 1 170 1 
7 1 2 124 1 
7 2 2 130 1 
7 3 2 135 1 
7 4 2 128 1 
7 1 3 128 1 
7 2 3 129 1 
7 3 3 129 1 
7 4 3 129 1 
8 1 1 141 0 
8 2 1 129 0 
8 3 1 135 0 
8 4 1 138 0 
8 1 2 117 0 
8 2 2 124 0 
8 3 2 121 0 
8 4 2 127 0 
8 1 3 124 0 
8 2 3 125 0 
8 3 3 123 0 
8 4 3 121 0 
9 1 1 150 1 
9 2 1 153 1 
9 3 1 147 1 
9 4 1 148 1 
9 1 2 135 1 
9 2 2 131 1 
9 3 2 133 1 
9 4 2 135 1 
9 1 3 130 1 
9 2 3 130 1 
9 3 3 129 1 
9 4 3 128 1 
10 1 1 152 1 
10 2 1 143 1 
10 3 1 148 1 
10 4 1 150 1 
10 1 2 134 1 
10 2 2 128 1 
10 3 2 133 1 
10 4 2 132 1 
10 1 3 129 1 
10 2 3 133 1 
10 3 3 129 1 
10 4 3 130 1 


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Dr. Seyit Ali KAYIS
Selcuk University, Faculty of Agriculture
Kampus/Konya, Turkey



Tel: +90 332 223 2830 Mobile: +90 535 587 1139


Greetings from Konya, Turkey
http://www.ziraat.selcuk.edu.tr/skayis/
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