this code fuses forest inventory data with tree growth data (tree ring or dendrometer band) for the same plots. Code is a rewrite of Clark et al 2007 Ecol Appl into JAGS
Usage
InventoryGrowthFusion(
data,
cov.data = NULL,
time_data = NULL,
n.iter = 5000,
n.chunk = n.iter,
n.burn = min(n.chunk, 2000),
random = NULL,
fixed = NULL,
time_varying = NULL,
burnin_plot = FALSE,
save.jags = "IGF.txt",
z0 = NULL,
save.state = TRUE,
restart = NULL
)Arguments
- data
list of data inputs
- cov.data
covariate data
- time_data
required if time_varying is provided
- n.iter
total number of iterations across all chunks
- n.chunk
number of MCMC steps to evaluate at a time. Will only return LAST. If restarting, second number in vector is chunk to start from
- n.burn
number of steps to automatically discard as burn-in
- random
whether or not to include random effects
- fixed
formula for fixed effects
- time_varying
formula for time-varying effects
- burnin_plot
logical: display a plot of the burnin steps?
- save.jags
logical: Save the generated JAGS script?
- z0
initial conditions for state variable
- save.state
whether or not to include inferred DBH in output (can be large). Enter numeric value to save.state periodically (in terms of n.chunk)
- restart
final mcmc.list from previous execution. NULL for new run. TRUE to save final state for new run.