neotoma (version 1.6.2)

read_bacon: Function to read in defined Bacon outputs.

Description

Reads in Bacon output and formats it for inclusion in a download object.

Usage

read_bacon(x, path = ".", add = FALSE, chron_name = "Bacon",
  as_default = TRUE, download = NULL, sections = NULL,
  age_field = "median", interp = TRUE)

Arguments

x

A folder path that contains a Bacon age file.

path

The location of the Cores folder.

add

Should the results be added to an existing download? Defaults to FALSE.

chron_name

The name for the chronology if the Bacon file is being added to a download.

as_default

Should the chronology become the default?

download

The target download if add is TRUE.

sections

If there are multiple Bacon runs in a folder, identify the file by the number of sections in the run.

age_field

Should the age be assigned to the "median" or the "wmean"?

interp

If the depths don't match up, should we interpolate from the Bacon output? (default TRUE)

Details

The function expects that you are in a working directory containing a "Cores" which would then contain output files from Bacon runs. The output can either be added to an existing record (for example, replacing the default age model returned by Neotoma), or it can be loaded on its own. If the depths for the loaded file do not match with the depths in the `download`'s `sample.meta` then the user can use the `interp` parameter to interpolate between depths. This method uses linear interpolation.

Examples

# Download the record for Lake O' Pines:
lake_o_dl <- get_download(15925)

# This assumes that you have Bacon installed in a folder and have
# set it to your working directory.

write_agefile(lake_o_dl[[1]], path = ".", chronology = 1, 
              corename = "LAKEPINES", cal.prog = 'Bacon') 

source("Bacon.R") 

# These defaults just help the core run quickly, they're not neccesarily good parameters.
Bacon("LAKEPINES", acc.mean = 10, thick = 50, depths.file = TRUE, suggest = FALSE, ask = FALSE)

lake_o_dl <- read_bacon("LAKEPINES", add = TRUE, download = download, sections = 17)