runBacon | R Documentation |
This is a high-level function that uses Bacon 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 Blaauw and Christen (2011) doi:10.1214/11-BA618 for details.
runBacon(
L,
chron.num = NA,
meas.table.num = NA,
bacon.dir = NA,
site.name = L$dataSetName,
model.num = NA,
remove.rejected = TRUE,
overwrite = TRUE,
cc = NA,
max.ens = 1000,
use.marine = NULL,
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",
ask.reservoir = TRUE,
bacon.thick = NA,
bacon.acc.mean = NA,
...
)
L |
a LiPD object |
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? |
bacon.dir |
the directory where Bacon is installed on this computer. |
site.name |
the name used for the bacon model (and directories) |
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 |
cc |
An integer, or vector of integers corresponding to age that describes the calibration curve. You can specify here (see below) or if it's NA the code will guess based on archiveType
|
max.ens |
the maximum number of ensembles to load in (default = 1000) |
use.marine |
use the marine 13C curve? (yes or no, or NULL to choose) |
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 |
ask.reservoir |
ask about reservoir corrections |
bacon.thick |
thickness parameter to pass to bacon (How thick is each chunk to model) |
bacon.acc.mean |
prior mean accumulation rate estimate for bacon |
... |
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
Maarten Blaauw (Bacon)
Other Bacon:
getBaconDir()
,
loadBaconOutput()
,
sampleBaconAges()
,
setBaconDir()
,
writeBacon()
## Not run:
#Run in interactive mode:
L = runBacon(L)
#Run in noninteractive mode, describing everything:
L = runBacon(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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