KAYIS Seyit Ali
2013-Feb-28 20:56 UTC
[R] data grouping and fitting mixed model with lme function
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. Any help regarding data grouping and model fitting is deeply appreciated. Kind Regards Seyit Ali ------------------------------------------------------------------------ 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/ ------------------------------------------------------------------------ ________________________________ [[alternative HTML version deleted]]
(Apologise for re-sending. I am re-sending in case subject name did not give enough information. Any shared experience with lme is deeply appreciated) 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. Any help regarding data grouping and model fitting is deeply appreciated. Kind Regards Seyit Ali ------------------------------------------------------------------------ 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/ ------------------------------------------------------------------------ [[alternative HTML version deleted]]
You did not get any replies because this is largely off topic. Please stop posting here and post to the r-sig-mixed-models list instead. -- Bert On Fri, Mar 1, 2013 at 9:33 AM, KAYIS Seyit Ali <s_a_kayis at yahoo.com> wrote:> (Apologise for re-sending. I am re-sending in case subject name did not give enough information. Any shared experience with lme is deeply appreciated) > > 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. > > Any help regarding data grouping and model fitting is deeply appreciated. > > Kind Regards > > Seyit Ali > > > > ------------------------------------------------------------------------ > 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/ > ------------------------------------------------------------------------ > [[alternative HTML version deleted]] > > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm