Calc_MinDose4(input.data,
sigmab,
log = TRUE,
sample.id = "unknown sample",
gamma.xlb = 0.1,
gamma.xub = 100,
mu.xlb = 1,
mu.xub = 100,
sigma.xlb = 0.001,
sigma.xub = 5.00,
init.gamma = 5,
init.mu = 10,
init.sigma = 0.6,
init.p0 = 0.01,
calc.ProfileLikelihoods = TRUE,
console.ProfileLikelihoods = FALSE,
console.extendedOutput = FALSE,
output.file = FALSE,
output.filename = "default",
output.plot = FALSE,
output.indices = 4)output.indices.output.filename-4R(-UL).res file. See output.filename.calc.ProfileLikelihoods=TRUE. Indices: 1 = gamma, 2 = gamma/mu, 3 = gamma/mu/sigma, 4 = gamma/mu/sigma/p0gamma: minimum dose on the log scale
mu: mean of the non-truncated normal distribution
sigma: spread in ages above the minimum
p0: proportion of grains at gamma
}
(Un-)logged model
In the original version of the three-parameter minimum dose model, the basic data are the natural logarithms of the De estimates and relative standard errors of the De estimates. This model will be applied if log = TRUE.
If log = FALSE, the modified un-logged model will be applied instead. This has essentially the same form as the original version. gamma and sigma are in Gy and gamma becomes the minimum true dose in the population.
While the original (logged) version of the mimimum dose model may be appropriate for most samples (i.e. De distributions), the modified (un-logged) version is specially designed for modern-age and young samples containing negative, zero or near-zero De estimates (Arnold et al. 2009, p. 323).
Boundaries
Depending on the data, the upper and lower bounds for gamma (gamma.xlb and gamma.xub) and mu (mu.xlb and mu.xub) need to be specified. If the final estimate of gamma or mu is on the boundary, gamma.xlb and gamma.xub (mu.xlb and mu.xub respectively) need to be adjusted appropriately, so that gamma and mu lie within the bounds. The same applies for sigma boundaries (sigma.xlb and sigma.xub)
Initial values
The log likelihood calculations use the nlminb function. Accordingly, initial values for the four parameters init.gamma, init.sigma, init.mu and init.p0 need to be specified.## load example data
data(ExampleData.DeValues)
## apply the logged minimum dose model
Calc_MinDose4(ExampleData.DeValues,
sigmab = 0.05, gamma.xub = 10000, mu.xub = 10000, init.p0 = 0.4,
output.file = FALSE,output.plot = FALSE)Run the code above in your browser using DataLab