library("R2BayesX")
## load forest health data and tree location map
data("ForestHealth")
data("BeechBnd")
## estimate model without spatial effect
fm1 <- bayesx(defoliation ~ stand + fertilized +
humus + moisture + alkali + ph + soil +
sx(age) + sx(inclination) + sx(canopy) +
sx(year) + sx(elevation), family = "cumlogit",
method = "REML", data = ForestHealth)
summary(fm1)
plot(fm1, term = c("sx(age)", "sx(inclination)",
"sx(canopy)", "sx(year)", "sx(elevation)"))
## now include spatial effect
## warning: long runtime
fm2 <- bayesx(defoliation ~ stand + fertilized +
humus + moisture + alkali + ph + soil +
sx(age) + sx(inclination) + sx(canopy) + sx(year) +
sx(elevation) + sx(id, bs = "gk", map = BeechBnd, full = TRUE),
family = "cumlogit", method = "REML", data = ForestHealth)
summary(fm2)
plot(fm2, term = c("sx(age)", "sx(inclination)",
"sx(canopy)", "sx(year)", "sx(elevation)", "sx(id)"),
map = BeechBnd, pos = "topleft")
## compare effects for elevation and inclination
plot(c(fm1, fm2), term = c("sx(elevation)", "sx(inclination)"))
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