writeBacon: Create the input file for a Bacon model from a LiPD object

In nickmckay/GeoChronR: Tools to Analyze and Visualize Time-Uncertain Data

Create the input file for a Bacon model from a LiPD object

Description

This generates the csv file that is used for input to Bacon. Will be run in interactive mode if necessary parameters aren't specified. Most users will want to use runBacon for their bacon needs.

Usage

writeBacon(
  L,
  bacon.dir = NA,
  chron.num = 1,
  remove.rejected = TRUE,
  overwrite = TRUE,
  cc = NA,
  site.name = L$dataSetName,
  model.num = NA,
  use.marine = NULL,
  ask.reservoir = TRUE,
  ...
)

Arguments

L	a LiPD object
bacon.dir	the directory where Bacon is installed on this computer.
chron.num	the number of the chronData object that you'll be working in
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 cc=1 IntCal20 cc=2 MarineCal20 cc=3 SHCal20
site.name	the name used for the bacon model (and directories)
model.num	chron.numModel do you want to use?
use.marine	use the marine 13C curve? (yes or no, or NULL to choose)
ask.reservoir	ask about reservoir corrections
...	Arguments passed on to selectData var.name string name of the variable to extract paleo.or.chron "paleoData" or "chronData" paleo.or.chron.num an integer that corresponds to paleo.num or chron Data object (L$<paleo.or.chron>[[?]]) has the variable you want? meas.table.num an integer that corresponds to paleo.num measurementTable has the variable you want? table.type What type of table do you want to select data from? ("measurement", "summary" or "ensemble") always.choose Force selection of the variable from a list alt.names A vector of strings for alternative names to search for ens.table.num an integer that corresponds to ensembleTable you want to get the variable from? sum.table.num an integer that corresponds to which summaryTable you want to get the variable from? strict.search Use a strict.search to look for the ageEnsemble and depth variables. TRUE(default) or FALSE.

Value

L the input LiPD file with methods added to the chronModel.

Author(s)

Nick McKay

See Also

Other Bacon: getBaconDir(), loadBaconOutput(), runBacon(), sampleBaconAges(), setBaconDir()

Examples

## Not run: 
writeBacon(L)
#Run in interactive mode

writeBacon(L,chron.num=1,meas.table.num = 1,bacon.dir="~/Bacon/",remove.rejected=TRUE,overwrite=TRUE,cc=NA,site.name=L$dataSetName,model.num=NA)

## End(Not run)

nickmckay/GeoChronR documentation built on Feb. 21, 2025, 6:38 a.m.