View source: R/run.bchron.LiPD.R
runBchron | R Documentation |
This is a high-level function that uses Bchron 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 Haslett and Parnell (2008) doi:10.1111/j.1467-9876.2008.00623.x for details.
runBchron(
L,
chron.num = NA,
meas.table.num = NA,
site.name = L$dataSetName,
model.num = NA,
cal.curves = NA,
iter = 10000,
outlier.probs = 0.05,
ask = TRUE,
lab.id.var = "labID",
age.14c.var = "age14C",
age.14c.uncertainty.var = "age14CUnc",
age.var = "age",
age.uncertainty.var = "ageUnc",
depth.var = "depth",
reservoir.age.14c.var = "reservoirAge",
reservoir.age.14c.uncertainty.var = "reservoirAge14C",
rejected.ages.var = "rejected",
depth.units = "cm",
which.table = 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 |
the number of the chronData object that you'll be working in |
meas.table.num |
an integer that corresponds to paleo.num measurementTable has the variable you want? |
site.name |
the name of the site |
model.num |
chron.numModel do you want to use? |
cal.curves |
The calibration curves to be used. Enter either "marine20", intcal20", "shcal20" or "normal". Will prompt if not provided. |
iter |
number of iterations to use in bchron (default = 10000) |
outlier.probs |
probability of outliers amongst the dates |
ask |
ask for user input? (True/False) |
lab.id.var |
Lab Id variable name |
age.14c.var |
Radiocarbon age variable name |
age.14c.uncertainty.var |
Radiocarbon age uncertainty variable name |
age.var |
Calibrated age variable name |
age.uncertainty.var |
Calibrated age uncertainty variable name |
depth.var |
Depth variable name |
reservoir.age.14c.var |
Reservoir age variable name |
reservoir.age.14c.uncertainty.var |
Reservoir age uncertainty variable name |
rejected.ages.var |
Rejected ages variable name |
depth.units |
units for depth |
which.table |
deprecated. Use meas.table.num instead. |
... |
Arguments passed on to
|
L. The single LiPD object that was entered, with methods, ensembleTable, summaryTable and distributionTable added to the chronData model.
Deborah Khider
Andrew Parnell
Nick McKay
## Not run:
#Run in interactive mode:
L = runBchron(L)
#Run in noninteractive mode:
L = runBchron(L,chron.num = 1, site.name = "MyWonderfulSite", model.num = 3, cal.curves = "marine20")
## End(Not run)
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