embryogrowth (version 5.0)

result_mcmc_4p: Result of the mcmc using the nest database

Description

Fit using the nest database

Usage

result_mcmc_4p

format

A list of class mcmcComposite with mcmc result for data(nest) with 4 parameters and Gompertz model of growth

Details

Result of the mcmc using the nest database

References

Girondot, M. & Kaska, Y. Submitted. A model to predict temperature dependency on embryo growth rate and incubation duration from field data.

Examples

library(embryogrowth)
data(nest)
formated <- FormatNests(nest)
# The initial parameters value can be:
# "T12H", "DHA",  "DHH", "Rho25"
# Or
# "T12L", "DT", "DHA",  "DHH", "DHL", "Rho25"
x <- structure(c(118.768297442004, 475.750095909406, 306.243694918151,
116.055824800264), .Names = c("DHA", "DHH", "T12H", "Rho25"))
# pfixed <- c(K=82.33) or rK=82.33/39.33
pfixed <- c(rK=2.093313)
resultNest_4p <- searchR(parameters=x, fixed.parameters=pfixed,
	temperatures=formated, derivate=dydt.Gompertz, M0=1.7,
	test=c(Mean=39.33, SD=1.92), method = "BFGS", maxiter = 200)
data(resultNest_4p)
pMCMC <- embryogrowth_MHmcmc_p(resultNest_4p, accept=TRUE)
# Take care, it can be very long, sometimes several days
result_mcmc_4p <- embryogrowth_MHmcmc(result=resultNest_4p,
	parametersMCMC=pMCMC, n.iter=10000, n.chains = 1, n.adapt = 0,
	thin=1, trace=TRUE)
data(result_mcmc_4p)
plot(result_mcmc_4p, parameters="T12H", main="", xlim=c(290, 320), bty="n")
plotR(resultNest_4p, SE=result_mcmc_4p$TimeSeriesSE, ylim=c(0,0.3), las=1)