RĂ©mi Lesmerises
2016-Feb-04 16:50 UTC
[R] Conditional (paired) design for binomial regression in MCMCglmm
| This is my first attempt asking question in this forum and I do it because thorough research on the web didn't give me any answer.I am trying to accomodate a conditional regression in a Bayesian generalized linear mixed model using Monte Carlo Markov Chain. I am using the package {MCMCglmm} in R. I already did such analysis with the {coxme} package and it worked well, but as I want to access random slope, it seems that I must use such approach to decrease the bias of estimates (Hadfield 2010). I (partly) understand how to code for binomial regression (link logit) in MCMCglmm but I cannot find any indication for paired design. Here an example of my dataset.data(bear) Id Strata Site Real_rand Spruce Fir Road Adele Ade-1 Ade-1 1 3 60 100.49 Adele Ade-1 Ade-1A 0 5 58 89.22 Adele Ade-1 Ade-1B 0 2 37 109.79 Adele Ade-2 Ade-2 1 1 103 198.48 Adele Ade-2 Ade-2A 0 0 192 199.26 Adele Ade-2 Ade-2B 0 0 53 201.61 Sally Sal-7 Sal-7 1 0 2 7.02 Sally Sal-7 Sal-7A 0 40 0 94.40 Sally Sal-7 Sal-7B 0 2 3 16.58 Sally Sal-8 Sal-8 1 2 21 48.74 Sally Sal-8 Sal-8A 0 8 17 112.75 Sally Sal-8 Sal-8B 0 63 0 205.04It is a black bear habitat selection analysis, with used sites (variable Real_rand coded 1) compared with available sites (coded 0). It is a paired design because available sites were randomly drawn within a buffer zone around used site. I wonder if strata, nested in Id, could used as random factor and provide similar result than cox regression. Here an example of what it could looks like:prior <- list(R = list(V = 1, nu = 0.002), G = list(G1 = list(V = 1, nu=0.002), (G2 = list(V = 1, nu=0.002))) mod1 <- MCMCglmm(Real_rand ~ Spruce + Fir + Road, random = ~Strata:Id + us(Road):Id, family = "categorical", data = bear, prior = prior, verbose = FALSE, pr = TRUE)I added a random slope (us(Road):Id) to have individual coefficient for road selection. There is probably many errors, both in the prior formula and the glm call, but if anyone can help me to find a way to code it more correctly, I would be grateful! | ?R?mi L. [[alternative HTML version deleted]]