embryogrowth (version 9.5)

resultNest_mcmc_4p_SSM: Result of the mcmc using the nest database

Description

Fit using the nest database

Usage

resultNest_mcmc_4p_SSM

Format

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

Author

Marc Girondot

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

if (FALSE) {
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_SSM <- searchR(parameters=x, fixed.parameters=pfixed, 
	temperatures=formated, integral=integral.Gompertz, M0=1.7, 
	test=c(Mean=39.33, SD=1.92))
data(resultNest_4p_SSM)
pMCMC <- TRN_MHmcmc_p(resultNest_4p_SSM, accept=TRUE)
# Take care, it can be very long, sometimes several days
resultNest_mcmc_4p_SSM <- GRTRN_MHmcmc(result=resultNest_4p_SSM, 
 adaptive = TRUE, 
	parametersMCMC=pMCMC, n.iter=10000, n.chains = 1, n.adapt = 0,  
	thin=1, trace=TRUE)
data(resultNest_mcmc_4p_SSM)
1-rejectionRate(as.mcmc(resultNest_mcmc_4p_SSM))
as.parameters(resultNest_mcmc_4p_SSM)
layout(mat=matrix(1:4, nrow = 2))
plot(resultNest_mcmc_4p_SSM, parameters = "all", scale.prior = TRUE, las = 1)
layout(mat=1)
plotR(resultNest_4p_SSM, resultmcmc=resultNest_mcmc_4p_SSM, ylim=c(0,4), 
         main="Schoolfield, Sharpe & Magnuson 4-parameters", show.density=TRUE)
}