diff --git a/code/10a-solutions-spatial-glmm-birds.R b/code/10a-solutions-spatial-glmm-birds.R index b94a698..c0490a7 100644 --- a/code/10a-solutions-spatial-glmm-birds.R +++ b/code/10a-solutions-spatial-glmm-birds.R @@ -128,6 +128,10 @@ summary(out.non.sp.nb) # and tuning variances should again be adequate. # Model 3: Spatial Poisson ------------ +# Number of samples per chain +(n.batch * batch.length - n.burn) / n.thin +# Total samples +((n.batch * batch.length - n.burn) / n.thin) * n.chains out.sp.p <- spAbund(formula = ~ scale(tcc) + scale(elev) + I(scale(elev)^2) + scale(ppt) + scale(day) + I(scale(day)^2) + (1 | obs), @@ -219,7 +223,7 @@ str(pred.df) coords.0 <- as.matrix(pred.df[, c('x', 'y')]) # Standardize the covariates by their appropriate means and sds tcc.pred <- (pred.df$tcc - mean(data.NOCA$covs$tcc)) / sd(data.NOCA$covs$tcc) -elev.pred <- (pred.df$tcc - mean(data.NOCA$covs$tcc)) / sd(data.NOCA$covs$tcc) +elev.pred <- (pred.df$elev - mean(data.NOCA$covs$elev)) / sd(data.NOCA$covs$elev) elev.2.pred <- elev.pred^2 ppt.pred <- (pred.df$ppt - mean(data.NOCA$covs$ppt)) / sd(data.NOCA$covs$ppt) # Set day to 0