Error in LME4
On 14-06-07 04:29 PM, Sunil Mundra wrote:
Hello all, I am new to use LME4 for analysing mixed effect model. I am trying to test impact of Deep-snow treatment, sampling round, and sampling depth on fungal richness. In my experiment: I have two block (C and D), each Block has 3 fence group. I have two treatment one is where snow is deep (causing soil warming) and other in control sample, at each fence. Samples are collected 9 times in summer from two different depth (2cm and 5cm). I hope i am able to explain my experiment well... My first question the the model I am using (see below) here, is OK for this question? Z1 <- lmer(Richness ~ Treatment*Round*Depth + (1|Block/Fence/Treatment/Round), REML= FALSE, data = data) Second when i am running this this argument i am getting following error as mention below. Error in lme4::lFormula(formula = Richness ~ Treatment * Round * Depth + : rank of X = 28 < ncol(X) = 36 I tried to google it, but did not manage to find the solution. I also get similar error (col pivoting) when i was trying CCA analysis for community study with similar predictor and random variables. Help in this regards would be highly appreciated....!!! Regards Sunil
This means that you don't have all 36 combinations of Treatment, Round, and Depth in your experimental design (based on the arithmetic it seems that "Round" is your 9 samples). (You probably only have 28 combinations -- were some treatment/depth combinations missed in some rounds?) If you use a recent version of lme4 you should be able to ask lme4 to drop the aliased/unidentifiable columns -- in fact this should happen automatically. However, you have more problems than this (sorry) * you're probably not going to be able to fit block as a random effect (because there are only two levels) * you shouldn't have the same factor included as both a random and a fixed effect I would suggest (I think) Richness ~ Treatment*Depth + (1|(Block:Fence)/Round) possibly Richness ~ Treatment*Depth + (Treatment*Depth|(Block:Fence)) + (1|Block:Fence:Round) to allow for variation in treatment/depth effects across blocks and block/fence combinations