SPDsimulationTest {ADMUR}

Goodness of Fit test, using SPD simulation

Description

Calculates the data p-value given a model.

Usage

SPDsimulationTest(data, calcurve, calrange, pars, type, inc=5, N=20000)

Arguments

data

A dataframe of 14C dates. Requires 'age' and 'sd', and at least one of 'site' and 'phase'. Optional 'datingType' comprising '14C' and/or anything else.

calcurve

A calibration curve object. Choose from intcal20 (default), shcal20, intcal13 or shcal13.

calrange

A vector of two calendar dates BP, giving the calendar range of CalArray. Can be in either order.

pars

A single vector of one parameter combination.

type

Choose 'CPL' for a Continuous Piecewise Linear model, 'exp' for an exponential model, or 'uniform' for a uniform model.

inc

Increments to interpolate calendar years. Default = 5

N

The number of simulations to generate.

Details

The returned list provides various summary statistics and timeseries of the observed and simulated data:

timeseries: a data frame containing various CIs and:

calBP: a vector of calendar years BP.

expected.sim: a vector of the expected simulation (mean average of all N simulations).

local.sd: a vector of the local (for each year) standard deviation of all N simulations.

model: a vector of the model PDF.

SPD: a vector of the observed SPD PDF, generated from data.

index: a vector of -1,0,+1 corresponding to the SPD points that are above, within or below the 95% CI of all N simulations.

pvalue: the proportion of N simulated SPDs that have more points outside the 95% CI than the observed SPD has.

observed.stat: the summary statistic for the observed data (number of points outside the 95% CI).

simulated.stat: a vector of summary statistics (number of points outside the 95% CI), one for each simulated SPD.

n.dates.all: the total number of dates in the whole data set. Trivially, the number of rows in data.

n.dates.effective: the effective number of dates within the date range. Will be non-integer since a proportion of some dates will be outside the date range.

n.phases.all: the total number of phases in the whole data set.

n.phases.effective: the effective number of phases within the date range. Will be non-integer since a proportion of some phases will be outside the date range.

n.phases.internal: an integer subset of n.phases.all that have more than 50% of their total probability mass within the date range.

The default N = 20000 can be increased if greater precision is required, however this can be very time costly.

Value

Returns a list. See details.

Examples

# trivial example showing a single date can never be rejected under a uniform model:
data <- data.frame(age=6500, sd=50, phase=1, datingType='14C')
x <- SPDsimulationTest(data, 
	calcurve=intcal20, 
	calrange=c(6000,9000), 
	pars=NULL, 
	type='uniform')
print(x$pvalue)