I'm modelling species spatio-temporal density in a montane forest. First, I identified the most important topographic parameter using a training and validation dataset.
Usually for my models, I have to specify the practical range and the marginal standard deviation to reduce the probability that the spatial effect explains the data better than the covariates as follows:
spde = inla.spde2.pcmatern(mesh, prior.range = c(prior.median.range, .5), prior.sigma = c(
prior.median.sd, .5))
I use the following formula after setting up a spatial and temporal mesh:
U <- 0.001
hyper.prec <- list(theta = list(prior="pc.prec", param=c(U, 0.05)))
formula <- Den ~ -1 + Intercept + f(TPI, model = "rw1", hyper = hyper.prec) + f(i, model=spde, group = i.group, control.group = list (model = "ar1"))
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where TPI is topographic position index.
My result is below. As you can see, Rho is not significant (go to the bottom below the first output). I assume that this means that my spatial random effect changes over time?
Also, because of the marginal standard deviation that I use, I usually do not get the spatial variance as being important (again at the bottom below the first output). I have included a pdf of my spatial random field. Given that the variance is not significant, how should I interpret the random field? Do the areas of higher or lower spatial autocorrelation mean anything, and can this be construed as density changing at various locations resulting in some areas having much similar/different densities than others?
Additional information: I use a relatively small number of clumped plots. I use the center of each plot and a polygon of the forest area to build my mesh.
Thanks,
Kurt
Call:
c("inla(formula = formula, family = family, contrasts =
inla.setOption(scale.model.default = TRUE), ", " data = inla.stack.data(stack.est, spde
= spde), verbose = TRUE, ", " control.compute = list(cpo = TRUE, dic = TRUE, config =
TRUE), ", " control.predictor = list(A = inla.stack.A(stack.est), compute = TRUE), ", "
keep = FALSE)")
Time used:
Pre = 8.42, Running = 125, Post = 2.52, Total = 136
Fixed effects:
mean sd 0.025quant 0.5quant 0.975quant mode kld
Intercept 0.513 0.006 0.501 0.513 0.526 0.513 0
Random effects:
Name Model
TPI RW1 model
i SPDE2 model
Model hyperparameters:
mean sd 0.025quant 0.5quant 0.975quant mode
Precision for the Gaussian observations 93.209 9.330 76.206 92.75 112.880 91.841
Precision for TPI 1696.909 315.876 1166.916 1665.80 2401.157 1604.169
Range for i 4.292 8.345 0.407 2.06 21.978 0.865
Stdev for i 0.000 0.000 0.000 0.00 0.000 0.000
GroupRho for i 0.051 0.737 -0.997 0.15 0.989 -1.000
Expected number of effective parameters(stdev): 5.33(0.519)
Number of equivalent replicates : 52.58
Deviance Information Criterion (DIC) ...............: -465.51
Deviance Information Criterion (DIC, saturated) ....: 288.30
Effective number of parameters .....................: 6.41
Marginal log-Likelihood: 71.87
CPO and PIT are computed
Posterior marginals for the linear predictor and
the fitted values are computed
*********************************************************************************
mean sd 0.025quant 0.5quant 0.975quant
obs.var 1.083548e-02 1.078099e-03 8.872058e-03 1.078004e-02 1.310143e-02
tpi.var 6.094432e-04 1.118437e-04 4.169475e-04 6.001132e-04 8.547283e-04
spde.var.nom 3.582072e-08 8.279055e-08 -7.685764e-10 6.868704e-09 2.237234e-07
spde.range.nom 4.202139e+00 6.985897e+00 3.832717e-01 2.028437e+00 2.162595e+01
AR.rho 5.106370e-02 7.368315e-01 -9.968896e-01 1.502972e-01 9.886810e-01