phaseModel: Posterior parameter estimation of a phase model

In AdrianTimpson/ADMUR: Ancient Demographic Modelling Using Radiocarbon

Posterior parameter estimation of a phase model

Description

Calibrates 14C dates in a phase and calculates joint posterior parameter probabilities and point estimates (weighted mean) of a simple parameteric phase model

Usage

phaseModel(data, calcurve, prior.matrix, model, plot = FALSE)

Arguments

data	A dataframe of 14C dates. Requires 'age' and 'sd'.
calcurve	A calibration curve object. Choose from intcal20 (default), shcal20, intcal13 or shcal13.
prior.matrix	A matrix of prior probabilities of the two model parameters. Row names and col names are the parameter values.
model	Specify the model used for the phase distribution. Choose from 'norm', 'ellipse'
plot	By default (TRUE) will plot the calibrated 14C dates, the posterior probability surface of the parameters, and the model using the (weighted) mean posterior point esimates.

Details

Function to combine the prior probabilities of the phase model parameters, with the evidence of the 14C dates at that phase.

Value

Returns a list of various objects, including: PD (the Probability Densities of each calibrated 14C date); posterior (the posterior probabilites of the model parameters); and the weighted mean posterior parameter estimates.

Examples

	calcurve <- intcal20

	# 10 random 14C dates
	N <- 10
	age <- uncalibrateCalendarDates(rnorm(N,6350,350), calcurve)
	sd <- rep(25,N)
	data <- data.frame(age,sd)

	# specify the prior probabilities of the parameter values of a gaussian model in a matrix
	mu.range <- c(5500,7000)
	sigma.range <- c(5,700)
	prior.matrix <- matrix(1,150,150); prior.matrix <- prior.matrix/sum(prior.matrix)
	row.names(prior.matrix) <- seq(min(mu.range),max(mu.range),length.out=nrow(prior.matrix))
	colnames(prior.matrix) <- seq(min(sigma.range),max(sigma.range),length.out=ncol(prior.matrix))

	# generate the posterior parameter probabilities
	pm <- phaseModel(data, calcurve, prior.matrix, model='norm', plot=TRUE)
	

AdrianTimpson/ADMUR documentation built on July 2, 2024, 8:39 p.m.