combinationWithRandomEffect_Gauss {ArchaeoChron} | R Documentation |
Bayesian modeling for combining Gaussian dates with known variance and with the addition of a random effect. These dates are assumed to be contemporaneous of the target date and have non identical distributions as the variance may be different for each date. In addition, a random effect is introduced in the modelling by a shrinkage distribution as defined by Congdom (2010). The posterior distribution of the modeling is sampled by a MCMC algorithm implemented in JAGS.
combinationWithRandomEffect_Gauss(M, s, refYear=NULL, studyPeriodMin, studyPeriodMax,
numberChains = 2, numberAdapt = 10000, numberUpdate = 10000,
variable.names = c("theta"), numberSample = 50000, thin = 10)
M |
vector of measurement |
s |
vector of measurement errors |
refYear |
vector of year of reference for ages |
studyPeriodMin |
numerical value corresponding to the start of the study period in BC/AD format |
studyPeriodMax |
numerical value corresponding to the end of the study period in BC/AD format |
numberChains |
number of Markov chains simulated |
numberAdapt |
number of iterations in the Adapt period of the MCMC algorithm |
numberUpdate |
number of iterations in the Update period of the MCMC algorithm |
variable.names |
names of the variables whose Markov chains are kept |
numberSample |
number of iterations in the Acquire period of the MCMC algorithm |
thin |
step between consecutive iterations finally kept |
If there are Nbobs measurements M associated with their error s, the model is the following one :
for j in (1:Nbobs)
Mj ~ N(muj, sj^2)
muj ~ N(theta, sigmai^2)
theta ~ U(ta, tb)
sigma ~ UniformShrinkage
This function returns a Markov chain of the posterior distribution. The MCMC chain is in date format BC/AD, that is the reference year is 0. Only values for the variables defined by 'variable.names' are given.
Anne Philippe & Marie-Anne Vibet
Congdom P. D., Bayesian Random Effect and Other Hierarchical Models: An Applied Perspective,Chapman and Hall/CRC, 2010
data(sunspot)
MCMC = combinationWithRandomEffect_Gauss(M=sunspot$Age[1:10], s= sunspot$Error[1:10],
refYear=rep(2016,10), studyPeriodMin=0, studyPeriodMax=1500, variable.names = c('theta'))
plot(MCMC)
gelman.diag(MCMC)