Dear all,
I am trying to fit a zibinomial model with MCMCglmm. Everything
works fine when I do the non-inflated model. But the zi models
throws an error. Any suggestions on what when wrong?
Best regards,
Thierry
library(MCMCglmm)
nYear <- 20
nSite <- 50
nVisit <- 5
Start <- qlogis(0.7)
TrendOC <- -0.1
Detect <- 0.6
sdSite <- 1
Design <- expand.grid(Year= seq_len(nYear), Site = seq_len(nSite),
Visit = seq_len(nVisit))
RFSiteOC <- rnorm(nSite, sd = sdSite)
Design$Occupancy <- plogis(with(Design, Start + (Year - 1) * TrendOC
+ RFSiteOC[Site]))
Design$Detect <- Detect
Design$Site <- factor(Design$Site)
set.seed(123456)
Design$Present <- rbinom(nrow(Design), size = 1, prob =
Design$Occupancy) * rbinom(nrow(Design), size = 1, prob =
Design$Detect) == 1
#this works fine
prior <- list(R = list(V = 1, fix = 1), G = list(G1 = list(V = 1, nu
= 0.002)))
m <- MCMCglmm(Present ~ Year, random = ~Site, rcov = ~units, data =
Design, family = "categorical", prior = prior)
plot(m)
#this throws an error
priorzi <- list(R = list(V = diag(2), fix = 2), G = list(G1 = list(V
= 1, nu = 0.002)))
mzi <- MCMCglmm(Present ~ Year, random = ~Site, rcov =
~idh(trait):units, data = Design, family = "zibinomial", prior =
priorzi)
#the error
Error in rowSums(data[, match(response.names[0:1 + nt], names(data))]) :
error in evaluating the argument 'x' in selecting a method for
function 'rowSums': Error in `[.data.frame`(data, ,
match(response.names[0:1 + nt], names(data))) :
undefined columns selected
R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Dutch_Belgium.1252 LC_CTYPE=Dutch_Belgium.1252
[3] LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C
[5] LC_TIME=Dutch_Belgium.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] MCMCglmm_2.12 corpcor_1.5.7 ape_2.7-2 coda_0.14-4
[5] Matrix_0.9996875-0 lattice_0.19-28 tensorA_0.36 rj_0.5.5-4
loaded via a namespace (and not attached):
[1] gee_4.13-16 grid_2.13.0 nlme_3.1-101 tools_2.13.0
----------------------------------------------------------------------------
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium
Research Institute for Nature and Forest
team Biometrics & Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no
more than asking him to perform a post-mortem examination: he may be
able to say what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does
not ensure that a reasonable answer can be extracted from a given
body of data.
~ John Tukey