This is a high-level function that uses BAM to simulate age uncertainty in layer counted records, and stores this as an age-ensemble in a paleoData measurementTable, and in a model in chronData. If needed input variables are not entered, and cannot be deduced, it will run in interactive mode. BAM produces reasonable results for non-layer counted data, and can generate ensembles for unevenly spaced data, and thus is useful for generating ensembles for tie-point chronologies that are missing the necessary data to calculate ensembles properly. See Comboul et al. (2015) doi:10.5194/cp-10-825-2014 for details.
runBam(
L,
time.var = "year",
paleo.num = NA,
paleo.meas.table.num = NA,
chron.num = 1,
model.num = NA,
ens.table.number = NA,
make.new = FALSE,
n.ens = 1000,
model = NA
)A LiPD object - an R serialization of a single LiPD file. It's a list, and is typically created by `readLipd()`
What is the time variable we're going to use for the basis of the simulation?
the number of the paleoData object that you'll be working in
the number of the measurementTable you'll be working in
the number of the chronData object that you'll be working in
the number of the chronData model where you want to store the model information
the number of the ensembleTable you want to put the output into
Forces the creation of a new model (TRUE or FALSEdefault)
The number of members in the ensemble
a list that describes the model to use in BAM
model$ns: number of samples
model$name: 'poisson' or 'bernoulli'
model$param: probability of growth band being perturbed (default: prob of missing band = prob of doubly-counted band = 0.05)
if model$param is a single argument, then the perturbations are symmetric (prob of missing band = prob of doubly-counted band)
if model$param = [a1 a2] and a1 neq a2 the model is asymmetric
a1 = prob(missing layer) - undercounted
a2 = prob(layer counted multiple times) - overcounted
if model$param: 2xp matrix, then different miscounting prob. are defined for each time series.
model$resize: do not resize: 0 (default), resize to shortest sample: -1, resize to longest sample: 1
model$tm: if a time model is provided, the code returns the corresponding perturbed data
L The single LiPD object that was entered, with ageEnsemble and chronData model added.
Other BAM:
bamCorrect(),
simulateBam()
if (FALSE) { # \dontrun{
#Run in interactive mode:
L = runBam(L)
#Run in noninteractive mode, describing everything:
L = runBam(L,paleo.num = 1, paleo.meas.table.num = 1, model.num = 3, make.new = TRUE,
nEns = 100, model = list(name = "poisson",param = 0.05, resize = 0, ns = n.ens))
} # }