Bacon  R Documentation 
This is the main agedepth modelling function of the rbacon package.
Bacon( core = "MSB2K", thick = 5, coredir = "", prob = 0.95, d.min = NA, d.max = NA, add.bottom = TRUE, d.by = 1, seed = NA, depths.file = FALSE, depths = c(), depth.unit = "cm", age.unit = "yr", unit = depth.unit, acc.shape = 1.5, acc.mean = 20, mem.strength = 10, mem.mean = 0.5, boundary = NA, hiatus.depths = NA, hiatus.max = 10000, add = c(), after = 1e04/thick, cc = 1, cc1 = "IntCal20", cc2 = "Marine20", cc3 = "SHCal20", cc4 = "ConstCal", ccdir = "", postbomb = 0, delta.R = 0, delta.STD = 0, t.a = 3, t.b = 4, normal = FALSE, suggest = TRUE, accept.suggestions = FALSE, reswarn = c(10, 200), remember = TRUE, ask = TRUE, run = TRUE, defaults = "defaultBacon_settings.txt", sep = ",", dec = ".", runname = "", slump = c(), remove = FALSE, BCAD = FALSE, ssize = 2000, th0 = c(), burnin = min(500, ssize), MinAge = c(), MaxAge = c(), MinYr = MinAge, MaxYr = MaxAge, cutoff = 0.01, plot.pdf = TRUE, dark = 1, date.res = 100, age.res = 200, yr.res = age.res, close.connections = TRUE, verbose = TRUE, ... )
core 
Name of the core, given using quotes. Defaults to one of the cores provided with rbacon, 
thick 
Bacon will divide the core into sections of equal thickness specified by thick (default 
coredir 
Folder where the core's files 
prob 
Confidence interval to report. This should lie between 0 and 1, default 0.95 (95 %). 
d.min 
Minimum depth of agedepth model (use this to extrapolate to depths higher than the top dated depth). 
d.max 
Maximum depth of agedepth model (use this to extrapolate to depths below the bottom dated depth). 
add.bottom 
Add a model section at the bottom of the core, in order to ensure the bottommost date is taken into account. Default 
d.by 
Depth intervals at which ages are calculated. Defaults to 
seed 
Seed used for C++ executions. If it is not assigned ( 
depths.file 
By default, Bacon will calculate the ages for the depths 
depths 
By default, Bacon will calculate the ages for the depths 
depth.unit 
Units of the depths. Defaults to 
age.unit 
Units of the ages. Defaults to 
unit 
Deprecated and replaced by 
acc.shape 
The prior for the accumulation rate consists of a gamma distribution with two parameters.
Its shape is set by acc.shape (default 
acc.mean 
The accumulation rate prior consists of a gamma distribution with two parameters. Its mean is set by acc.mean (default 
mem.strength 
The prior for the memory (dependence of accumulation rate between neighbouring depths) is a beta distribution, which looks much like the gamma distribution.
but its values are always between 0 (no assumed memory) and 1 (100% memory). Its default settings of 
mem.mean 
The prior for the memory is a beta distribution, which looks much like the gamma distribution but
its values are always between 0 (no assumed memory) and 1 (100% memory). Its default settings of 
boundary 
The assumed depths of any boundary, which divides sections of different accumulation rate regimes (e.g., as indicated by major change in the stratigraphy). No hiatus is assumed between these sections, and memory is reset crossing the boundary. Different accumulation priors can be set for the sections above and below the boundary, e.g., 
hiatus.depths 
The assumed depths for any hiatus should be provided as, e.g.,

hiatus.max 
The prior for the maximum length of the hiatus. Hiatus length is a uniform distribution, with equal probabilities between 0 and 
add 
Add a value to the maximum hiatus length if a boundary is chosen. Defaults to 100 yr (or whatever other age unit is chosen). Can be adapted if Bacon complains that the parameters are out of support. 
after 
Sets a short section above and below hiatus.depths within which to calculate ages. For internal calculations  do not change. 
cc 
Calibration curve for C14 dates: 
cc1 
For northern hemisphere terrestrial 14C dates (IntCal20). 
cc2 
For marine 14C dates (Marine20). 
cc3 
For southern hemisphere 14C dates (SHCal20). 
cc4 
Use an alternative curve (3 columns: cal BP, 14C age, error, separated by white spaces and saved as a plaintext file). See 
ccdir 
Directory where the calibration curves for C14 dates 
postbomb 
Use a postbomb curve for negative (i.e. postbomb) 14C ages. 
delta.R 
Mean of corewide age offsets (e.g., regional marine offsets). 
delta.STD 
Error of corewide age offsets (e.g., regional marine offsets). 
t.a 
The dates are treated using the student's t distribution by default ( 
t.b 
The dates are treated using the student's t distribution by default ( 
normal 
By default, Bacon uses the student's tdistribution to treat the dates. Use 
suggest 
If initial analysis of the data indicates abnormally slow or fast accumulation rates, Bacon will suggest to change the prior. 
accept.suggestions 
Automatically accept the suggested values. Use with care. Default 
reswarn 
Bacon will warn you if the number of sections lies outside the safe range (default between 10 and 200 sections;

remember 
Bacon will try to remember which settings you have applied to your cores (default 
ask 
By default Bacon will ask you to confirm that you want to run the core with the provided settings. Disable this using 
run 
In order to load an existing Bacon run instead of producing a new one, you can use 
defaults 
Name of the file containing settings for the core. For internal use only  do not change. 
sep 
Separator between the fields of the plain text file containing the dating information. Default 
dec 
Character for decimal points. Default to 
runname 
Text to add to the corename for specific runs, e.g., 
slump 
Upper and lower depths of any sections of assumed abrupt accumulation, that require excising before agemodelling (and adding after agemodelling). Requires pairs of depths, e.g., 
remove 
Whether or not to remove depths within slumps. Defaults to 
BCAD 
The calendar scale of graphs and age outputfiles is in cal BP (calendar or calibrated years before the present, where the present is AD 1950) by default, but can be changed to BC/AD using 
ssize 
The approximate amount of iterations to store at the end of the MCMC run. Default 2000; decrease for faster (but less reliable) runs or increase for cores where the MCMC mixing (panel at upperleft corner of agemodel graph) appears problematic. 
th0 
Starting years for the MCMC iterations. 
burnin 
Amount of initial, likely suboptimal MCMC iterations that will be removed. 
MinAge 
Minimum age limit for Bacon runs, default at current year in cal BP. To set plot limits, use 
MaxAge 
Maximum age limit for Bacon runs, default at 1,000,000 cal BP. To set plot limits, use 
MinYr 
Deprecated  use MinAge instead. 
MaxYr 
Deprecated  use MaxAge instead. 
cutoff 
Avoid plotting very low probabilities of date distributions (default 
plot.pdf 
Produce a pdf file of the agedepth plot. Defaults to 
dark 
Darkness of the greyscale agedepth model. The darkest grey value is 
date.res 
Date distributions are plotted using 
age.res 
Resolution or amount of greyscale pixels to cover the age scale of the agemodel plot. Default 
yr.res 
Deprecated  use age.res instead 
close.connections 
Internal option to close connections after a run. Default 
verbose 
Provide feedback on what is happening (default 
... 
options for the agedepth graph. See agedepth and calib.plot 
Bacon is an approach to agedepth modelling that uses Bayesian statistics in order to reconstruct Bayesian accumulation histories for deposits, through combining radiocarbon and other dates with prior information ('Blaauw' and 'Christen', 2011).
Bacon divides a core into many thin vertical sections (by default of thick=5
cm thickness),
and through millions of Markov Chain Monte Carlo (MCMC) iterations estimates
the accumulation rate (in years/cm; so more correctly, sedimentation times) for each of these sections.
Combined with an estimated starting date for the first section, these accumulation rates then form the agedepth model.
The accumulation rates are constrained by prior information on the accumulation rate (acc.mean, acc.shape
) and its
variability between neighbouring depths, or "memory" (mem.mean, mem.strength
). Hiatuses can be introduced as well, also constrained by prior information (hiatus.max
).
Although Bacon works with any kind of absolute dates (e.g., OSL, tephra or other dates on a calendar scale),
it is often used to agemodel 14Cdated sequences. Radiocarbon dates should be calibrated using either IntCal20
(for terrestrial northern hemisphere material; Reimer et al., 2020), Marine20 (for marine dates; Hughen et al., 2020),
SHCal20 (for southern hemisphere dates; Hogg et al., 2020) or any other calibration curve (see below), while modern 14C
dates are calibrated using one of the postbomb calibration curves (NH1, NH2 or NH3 for the northern hemisphere,
SH12 or SH3 for the southern hemisphere; Hua et al., 2013). See http://calib.org/CALIBomb/ if you are unsure which
postbomb curve you need. If Bacon finds postbomb dates (negative 14C ages) and you haven't specified a postbomb curve,
you will be prompted. Provide postbomb curves as, e.g., postbomb=1
for the NH1 postbomb curve (2 for NH2, 3 for NH3, 4 for SH12, 5 for SH3).
For calendar dates, i.e. dates that are already on the calendar scale and thus should not be calibrated, setcc=0
.
From version 2.5.1 on (i.e., since February 2021), the default memory prior has changed to mem.mean=0.5
and mem.strength=10
. Previously used c++ code contained a bug which caused the prior information for the memory not to be taken into account correctly. Now that this bug has been repaired, the default memory prior has been updated such that it should work for most types of cores, and should result in similar output to previous versions of Bacon. There is no need to redo previous runs. However, it is considered good practice to test the impact of different settings on a site's agedepth model (e.g., thick, acc.mean, acc.shape, mem.mean, acc.strength).
An agedepth model graph, its age estimates, and a summary.
Maarten Blaauw, J. Andres Christen
Blaauw, M. and Christen, J.A., Flexible paleoclimate agedepth models using an autoregressive gamma process. Bayesian Anal. 6 (2011), no. 3, 457–474.
Christen, J.A., Perez E., S., 2010. A new robust statistical model for radiocarbon data. Radiocarbon 51, 10471059.
Reimer et al., 2020. The IntCal20 Northern Hemisphere radiocarbon age calibration curve (0–55 cal kBP). Radiocarbon 62. doi: 10.1017/RDC.2020.41
Hogg et al. 2020 SHCal20 Southern Hemisphere calibration, 055,000 years cal BP. Radiocarbon 62. doi: 10.1017/RDC.2020.59
Hughen et al. 2020 Marine20the marine radiocarbon age calibration curve (055,000 cal BP). Radiocarbon 62. doi: 10.1017/RDC.2020.68
Hua, Q., Barbetti, M., Rakowski, A.Z., 2013. Atmospheric radiocarbon for the period 19502010. Radiocarbon 55(4), doi: 10.2458/azu_js_rc.v55i2.16177
Jones, V.J., Stevenson, A.C., Battarbee, R.W., 1989. Acidification of lakes in Galloway, south west Scotland  a diatom and pollen study of the postglacial history of the Round Loch of Glenhead. Journal of Ecology 77: 123.
Bacon(ask=FALSE, coredir=tempfile()) Bacon(cc=2, delta.R=80, delta.STD=40, coredir=tempfile())
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