embryogrowth (version 6.1.1)

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. (2014). A model to predict the thermal reaction norm for the embryo growth rate from field data. Journal of Thermal Biology, 45, 96-102. doi: 10.1016/j.jtherbio.2014.08.005

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(118.431040984352, 498.205702157603, 306.056280989839,
118.189669472381), .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))
data(resultNest_4p)
pMCMC <- TRN_MHmcmc_p(resultNest_4p, accept=TRUE)
# Take care, it can be very long, sometimes several days
result_mcmc_4p <- GRTRN_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$SD, ylim=c(0,0.4), las=1)