Dear R users, I am looking for some advice on the proper construction of a mixed model in R, using the difference in means as the response and treating within-means residuals as a random effect.
I have a dataframe (my own, a snippet of which is given below) that is composed of observations of pollen viability in flowers along tree branches. Flowers (1 to 3 per position) were collected from apical and basal positions along the same branch, and I'm predicting that the within-branch difference between the mean viabilities at each position is a function of the distance separating the positions, with tree as a random effect. A collection of observations for a single branch is: tree branch position dist viability 10 T113 B.T113.May.16 apical 6.46 0.9733333 11 T113 B.T113.May.16 apical 6.46 1.0000000 12 T113 B.T113.May.16 apical 6.46 0.9766667 13 T113 B.T113.May.16 basal 6.46 0.9933333 14 T113 B.T113.May.16 basal 6.46 0.9929078 Up til now, I've been calculating within-position means for each branch and constructing a separate dataframe with one observation per branch, so for the above the new dataframe would contain a single entry tree branch mean.basal mean.apical dist T113 B.T113.May.16 0.9931206 0.9833333 6.46 and then I'm doing lme(mean.apical - mean.basal ~ dist, random=~1|tree) I get sensible results in line with my predictions, but it occurs to me that I might be losing information here, and that this might be better expressed by calculating the within-position means within the model and treating the within-position-among-flower residuals as a random effect, either common to the entire model or grouped in various ways. However, I can't come up with a way to express this in lme. To be honest, I am also unsure as to whether this makes any statistical sense to attempt. I'd appreciate any advice, thank you. Regards, Douglas G. Scofield, PhD Department of Biology [EMAIL PROTECTED] Indiana University off: (812) 856-0115 1001 E. 3rd St. fax: (812) 855-6705 Bloomington, IN 47405-3700 cell 1: (812) 219-5373 cell 2: (786) 514-9141 ------------------------------------------------- A piece of my dataframe is below: > ex tree branch position dist viability 1 T112 A.T112.May.16 apical 1.26 0.9900000 2 T112 A.T112.May.16 apical 1.26 0.9860140 3 T112 A.T112.May.16 apical 1.26 1.0000000 4 T112 A.T112.May.16 basal 1.26 0.9900000 5 T112 C.T112.May.16 apical 1.94 0.9800000 6 T112 C.T112.May.16 basal 1.94 1.0000000 7 T113 A.T113.May.16 apical 3.36 1.0000000 8 T113 A.T113.May.16 apical 3.36 0.9942197 9 T113 A.T113.May.16 basal 3.36 1.0000000 10 T113 B.T113.May.16 apical 6.46 0.9733333 11 T113 B.T113.May.16 apical 6.46 1.0000000 12 T113 B.T113.May.16 apical 6.46 0.9766667 13 T113 B.T113.May.16 basal 6.46 0.9933333 14 T113 B.T113.May.16 basal 6.46 0.9929078 15 T113 C.T113.May.16 apical 5.00 1.0000000 16 T113 C.T113.May.16 apical 5.00 0.9966667 17 T113 C.T113.May.16 basal 5.00 0.9933333 18 T113 C.T113.May.16 basal 5.00 0.9929078 19 T113 D.T113.May.16 apical 5.84 0.9933333 20 T113 D.T113.May.16 apical 5.84 0.9966667 21 T113 D.T113.May.16 basal 5.84 0.9933333 22 T113 D.T113.May.16 basal 5.84 0.9929078 23 T113 E.T113.May.16 apical 4.50 1.0000000 24 T113 E.T113.May.16 apical 4.50 0.9818182 25 T113 E.T113.May.16 apical 4.50 0.9966667 26 T113 E.T113.May.16 basal 4.50 1.0000000 27 T113 E.T113.May.16 basal 4.50 0.9955752 28 T113 E.T113.May.16 basal 4.50 0.9900000 29 T113 F.T113.May.16 apical 5.01 0.9933333 30 T113 F.T113.May.16 apical 5.01 1.0000000 31 T113 F.T113.May.16 basal 5.01 1.0000000 32 T113 F.T113.May.16 basal 5.01 0.9955752 33 T113 F.T113.May.16 basal 5.01 0.9900000 34 T115 A.T115.Jun.02 apical 4.24 0.9333333 35 T115 A.T115.Jun.02 apical 4.24 0.9933333 36 T115 A.T115.Jun.02 basal 4.24 0.9900000 37 T115 A.T115.Jun.02 basal 4.24 0.9766667 38 T115 B.T115.Jun.02 apical 2.31 0.9866667 39 T115 B.T115.Jun.02 apical 2.31 0.9801325 40 T115 B.T115.Jun.02 basal 2.31 0.9900000 41 T115 B.T115.Jun.02 basal 2.31 0.8267974 ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
