runOxcal | R Documentation |
This is a high-level function that uses oxcal to simulate an age model, and stores this as an age-ensemble in a model in chronData. If needed input variables are not entered, and cannot be deduced, it will run in interactive mode. See Bronk Ramsey et al. 2008 doi:10.1016/j.quascirev.2007.01.019
runOxcal(
L,
chron.num = NA,
meas.table.num = NA,
oxcal.path = "~/OxCal/",
model.num = NA,
remove.rejected = TRUE,
overwrite = TRUE,
max.ens = 1000,
static.reservoir.age = NA,
static.reservoir.age.unc = NA,
surface.age = NA,
surface.age.unc = NA,
surface.age.depth = 0,
depth.interval = NA,
events.per.unit.length = NA,
events.per.unit.length.uncertainty = 0,
outlier.prob = 0.05,
cal.curve = "IntCal20",
oxcal.code.export.path = NA,
...
)
L |
A LiPD object - an R serialization of a single LiPD file. It's a list, and is typically created by 'readLipd()' |
chron.num |
Which chron number to get data from |
meas.table.num |
an integer that corresponds to paleo.num measurementTable has the variable you want? |
oxcal.path |
path to oxcal binaries |
model.num |
chron.numModel do you want to use? |
remove.rejected |
don't write out dates that are marked as rejected |
overwrite |
overwrite files and directories |
max.ens |
the maximum number of ensembles to load in (default = 1000) |
static.reservoir.age |
optionally assign a deltaR to all radiocarbon dates |
static.reservoir.age.unc |
optionally assign a deltaR uncertainty to all radiocarbon dates |
surface.age |
specify the age of the surface |
surface.age.unc |
surface age uncertainty |
surface.age.depth |
depth of the surface age |
depth.interval |
Depth interval to use to create depths.to.model (default = 10) |
events.per.unit.length |
How many events per unit length for the Poisson model? This controls the flexibility on the model, the lower the number the more flexibile. |
events.per.unit.length.uncertainty |
Uncertainty on events.per.unit.length in orders of magnitude. This makes for better models but *greatly* increases the run time. If NA or < 0 it runs without uncertainty (default = NA) |
outlier.prob |
What's the probability of a date being an outlier if not otherwise specified (default= 0.05) |
cal.curve |
What calibration curve to use? Current options are "intcal20" (default), "marine20", "shcal20", "intcal13", "marine13", or "shcal13" |
oxcal.code.export.path |
optionally output the oxcal code by specifying a path (default = NA) |
... |
Arguments passed on to
|
L The single LiPD object that was entered, with methods, ensembleTable, summaryTable and distributionTable added to the chronData model.
View a full-fledged example of how to use this function.
Nick McKay
Other oxcal:
createOxcalModel()
,
getModelParametersFromOxcalText()
,
loadOxcalOutput()
,
oxCalDateExpression()
## Not run:
#Run in interactive mode:
L = runOxcal(L)
#Run in noninteractive mode, describing everything:
L = runOxcal(L,chron.num = 1, meas.table.num = 1, model.num = 3, bacon.dir = "~/Bacon/",site.name = "MSB2K", cc = 1)
## End(Not run)
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