inst/seedlings.r

In mtalluto/tree_seedling_metamodel: Code package for tree seedling metamodel

## Main script for running the model integration examples
library("treeSeedlingMetamodelData")
library("treeSeedlingMetamodel")
library(LaplacesDemon)
data(seedlings, envir = environment())


sp <- seedlings$species[1]


# do the following for each species
	naiveDat <- naive_ld_dat(seedlings$sdm_adults[[sp]])

	# note that this is an EXAMPLE - it is impossible to do this automatically, because fitting LD models 
	# is done by trial and error
	naiveMod <- LaplacesDemon::LaplacesDemon(naive_lp, naiveDat, LaplacesDemon::GIV(naive_lp, naiveDat, PGF=TRUE), 
		Algorithm = "AM", specs=list(Adaptive = 50, Periodicity = 50), Iterations = 100)

	# for some guidance, use consort()
	Consort(naiveMod)

	# set initial values and re-fit with a non-adaptive algorithm
	Initial.Values <- as.initial.values(naiveMod)
	naiveMod <- LaplacesDemon::LaplacesDemon(naive_lp, naiveDat, Initial.Values, Covar=naiveMod$Covar, Iterations=100000,
		Status=5000, Algorithm="RWM")


	## survival model
	survDat <- survival_ld_dat(seedlings$survival[[sp]])
	survMod <- LaplacesDemon::LaplacesDemon(survival_lp, survDat, LaplacesDemon::GIV(survival_lp, survDat, PGF=TRUE), 
		Algorithm = "AM", specs=list(Adaptive = 50, Periodicity = 50), Iterations = 100)

	# set initial values and re-fit with a non-adaptive algorithm
	Initial.Values <- as.initial.values(survMod)
	survMod <- LaplacesDemon::LaplacesDemon(survival_lp, survDat, Initial.Values, Covar=survMod$Covar, Iterations=100000,
		Status=5000, Algorithm="RWM")

	## recruitment model
	popDat <- recruitment_ld_dat(seedlings$population[[sp]])
	popMod <- LaplacesDemon::LaplacesDemon(recruitment_lp, popDat, LaplacesDemon::GIV(recruitment_lp, popDat, PGF=TRUE), 
		Algorithm = "AM", specs=list(Adaptive = 50, Periodicity = 50), Iterations = 100, Status=1000)

	# set initial values and re-fit with a non-adaptive algorithm
	Initial.Values <- as.initial.values(popMod)
	popMod <- LaplacesDemon::LaplacesDemon(recruitment_lp, popDat, Initial.Values, Covar=popMod$Covar, Iterations=100000,
		Status=5000, Algorithm="RWM")

	# integrated model
	intDat <- integrated_ld_dat(seedlings$sdm_adults[[sp]], seedlings$survival[[sp]], seedlings$population[[sp]])
	intMod <- LaplacesDemon::LaplacesDemon(integrated_lp, intDat, LaplacesDemon::GIV(integrated_lp, intDat, PGF=TRUE), 
		Algorithm = "AM", specs=list(Adaptive = 50, Periodicity = 50), Iterations = 100)

	# set initial values and re-fit with a non-adaptive algorithm
	Initial.Values <- as.initial.values(intMod)
	intMod <- LaplacesDemon::LaplacesDemon(integrated_lp, intDat, Initial.Values, Covar=intMod$Covar, Iterations=100000,
		Status=5000, Algorithm="AFSS", Specs=list(A=Inf, B=Null, m=100, n=0, w=1))