multilevel mixed effects LME and LMER
First I would like to say thank you for taking the time to read it. Here is my problem. I did an experiment to access the impact of an invasive plant on mice behavior and abundacne. Basically I manipulated fruits and vegetation to two levels each(present and absent) on 12 experimental plots The design consisted of 12 plots, divided in 3 blocks. So each block had 4 plots assigned to one of the following treatments. Fruit intact and Vegetation intact Fruit intact and Vegetation removed Fruit removed and Vegetation intact Fruit removed and Vegetation removed Then I sampled mice activity by recording the presence or absence of paw prints on 16 track plates positioned on each plot. I also measured the number of trees on each plot and got their diameter. I created an index for tree cover and I want to use it as covariate. My goal is to determine how the interaction of fruits, vegetation, and time explain the mice behavior. Because my data is binary and I have fixed (fruit, veget, time) and random effects (block, and trackID as repeated measures) I am trying to fit a model using lmer. here is my first attempt model<-lmer(track~veget*fruit*time*(time|plate)*(1|block),family=binomial) My problem is that when I run this model I get more than 1000 degrees of freedom. Which does not make any sense, remember: 16 plates 2 levels for fruits 2 levels for veget 3 blocks 7 months (time) so I don't know what it is going on. Should I group this by plot ID instead of plate? check a sample of the data on the end. Also, how do I fit a covariate in these model. Especially when it comes to data format. I have just one indez per plot, how do I add this to the model. Should I repeat the same value for all the 16 plates in that plot? Thank you very much for any comments. plate track time block fruit veget
1 1 0 1 1 intact intact 2 2 1 1 1 intact intact 3 3 1 1 1 intact intact 4 4 0 1 1 intact intact 5 5 1 1 1 intact intact 6 6 1 1 1 intact intact 7 7 1 1 1 intact intact 8 8 1 1 1 intact intact 9 9 0 1 1 intact intact 10 10 1 1 1 intact intact 11 11 0 1 1 intact intact 12 12 1 1 1 intact intact 13 13 1 1 1 intact intact 14 14 1 1 1 intact intact 15 15 0 1 1 intact intact 16 16 0 1 1 intact intact 17 17 0 1 1 intact removed 18 18 0 1 1 intact removedt 19 19 1 1 1 intact removed 20 20 1 1 1 intact removed 21 21 0 1 1 intact removed 22 22 0 1 1 intact removed 23 23 1 1 1 intact removed 24 24 1 1 1 intact removed 25 25 0 1 1 intact removed 26 26 1 1 1 intact removed 27 27 0 1 1 intact removed 28 28 0 1 1 intact removed 29 29 0 1 1 intact removed 30 30 1 1 1 intact removed 31 31 0 1 1 intact removed 32 32 0 1 1 intact removed 33 33 0 1 1 removed intact 34 34 0 1 1 removed intact 35 35 0 1 1 removed intact
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