ageModel | R Documentation |
ageModel(
ages,
ageSds,
positions,
positionThicknesses = rep(0, length(positions)),
ids,
distTypes = rep("G", length(ages)),
MC = 10000,
burn = 2000,
probability = 0.95,
adapt = TRUE,
mhSD = rep(0.001, length(unique(ids))),
psiSD = 0.001,
muSD = 0.001,
predictPositions = seq(min(positions), max(positions), length = 500),
truncateUp = 0,
extrapUp = 100,
truncateDown = 1e+10,
extrapDown = 100
)
ages |
Vector of ages |
ageSds |
Vector of 1-sigma values for ages. Must be the same length and given in the same order as |
positions |
Vector of stratigraphic positions for ages. Must be the same length and given in the same order as |
positionThicknesses |
Vector of stratigraphic uncertainties for each age. Specified as half thicknesses. Must be the same length and given in the same order as |
ids |
Vector of sample names for each age. All samples with the same ids will be combined into a single age PDF. Must be the same length and given in the same order as |
distTypes |
c('G','U') Vector of distribution types to model each age as. Choices are 'G' for Gaussian, and 'U' uniform. Must be the same length and given in the same order as |
MC |
Number of MCMC iteration to run for. Defaults to 10000 |
burn |
Number of initial iterations to discard. Defaults to 2000 |
adapt |
Should the proposal standard deviation for model parameters be determined using the adaptive proposal algorithm of Haario et al., 1998. Defaults to TRUE |
mhSD |
Metropolis-Hastings proposal standard deviation for the age parameters. If adapt = TRUE it will be determined by the model run. Otherwise a vector of standard deviations must be specified with length = |
psiSD |
Metropolis-Hastings proposal standard deviation for the Compound Poisson-Gamma scale parameter. If adapt = TRUE it will be determined by the model run. |
muSD |
Metropolis-Hastings proposal standard deviation for the Compound Poisson-Gamma mean parameter. If adapt = TRUE it will be determined by the model run. |
predictPositions |
Vector of stratigraphic positions to evaluate the model at. Defaults to 500 evenly spaced points from the bottom to top of the section |
truncateUp |
Truncation age for extrapolating above the top of the section. Defaults to 0 |
extrapUp |
Number of extrapolations to perform above the top of the section. defaults to 100 |
truncateDown |
Truncation age for extrapolation below the bottom of the section. Defaults to 1e10 (a really big number) |
extrapDown |
Number of extrapolations to perform below the bottom of the section. defaults to 100 |
prob |
Desired confidence to return. Defaults to 95 |
HDI = specified probability highest density interval for the model run
model = Raw model predictions for each MCMC iteration
thetas = The posterior values for each dated horizon from each MCMC run. burn is not removed.
predictPositions = Stratigraphic positions where the model was evaluated. Same as predictPositions
mu, psi = The posterior values for the Compound Poisson-Gamma mean and scale parameters. burn is not removed.
ageGrid = Grid that age PDFs were evaluated over. Useful for plotting
likelihoods = Age PDFs for each set of dated samples. Useful for plotting
nAges = Number of ages that were combined into each sample. Useful for plotting
masterPositions = Stratigraphic positions for each set of combined ages. Useful for plotting
ids = Vector of unique sample names. Useful for plotting Run a modified version of the Bchronology algorithm from the R package "Bchron" (Haslett and Parnell, 2008)
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