Package 'rbacon'

top depth of the slice

bottom depth of the slice

Density of the slice (in g/cm3)

Detailed information of the current run, stored within this session's memory as variable info.

The modelled values of the 210Pb influx

The modelled values of the supported 210Pb

The age for which the accumulation rates need to be returned.

Detailed information of the current run, stored within this session's memory as variable info.

Accumulation rates can be calculated in cm/year or year/cm. By default cmyr=FALSE and accumulation rates are calculated in year per cm.

The ages of the age-depth model. Not provided by default, but can be provided to speed things up if the function is called repeatedly

The calendar scale of graphs and age output-files is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

Warn when ages are outside the core's range. Default silent=TRUE.

Remove NA entries. These are NOT removed by default, ensuring that always the same amount of iterations is returned.

Detailed information of the current run, stored within this session's memory as variable info.

Minimum and maximum calendar age ranges, calculated automatically by default (age.lim=c()).

The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE).

Use kcal BP. Default is kcal=FALSE.

Resolution or amount of greyscale pixels to cover the age scale of the plot. Default age.res=400.

Resolution or amount of greyscale pixels to cover the accumulation rate scale plot. Default age.res=400.

Point below which colours will no longer be printed. Default cutoff=0.001.

The darkest grey value is dark=1 by default; lower values will result in lighter grey but values >1 are not advised.

The function to produce a coloured representation of all age-models. Needs 3 values for the intensity of red, green and blue. Defaults to grey-scales: rgb.scale=c(0,0,0), but could also be, say, scales of red (rgb.scale=c(1,0,0)).

Resolution of the colour spectrum depicting the age-depth model. Default rgb.res=100.

Probability ranges. Defaults to prob=0.95.

If plot.range=TRUE, the confidence ranges (two-tailed; half of the probability at each side) are plotted.

Colour of the confidence ranges.

Line type of the confidence ranges.

If plot.mean=TRUE, the means are plotted.

Colour of the mean accumulation rates.

Type of the mean lines.

If plot.mean=TRUE, the medians are plotted.

Colour of the median accumulation rates.

Type of the median lines.

Axis limits for the accumulation rates.

Axis label for the accumulation rate.

The calendar scale of graphs and age output-files is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

Accumulation rates can be calculated in cm/year or year/cm. By default cmyr=FALSE and accumulation rates are calculated in year per cm. Axis limits are difficult to calculate when cmyr=TRUE, so a manual adaptation of acc.lim might be a good idea.

The default is to plot the calendar age horizontally and accumulation rates vertically. Change to rotate.axes=TRUE value to rotate axes.

The direction of the age axis, which can be reversed using rev.age=TRUE.

The direction of the accumulation rate axis, which can be reversed (rev.acc=TRUE.

Extension of the x-axis. White space can be added to the vertical axis using xaxs="r".

Extension of the y-axis. White space can be added to the vertical axis using yaxs="r".

Type of box to be drawn around the plot ("n" for none, and "l" (default), "7", "c", "u", or "o" for correspondingly shaped boxes).

The age for which accumulation rates need to be returned.

Detailed information of the current run, stored within this session's memory as variable info.

Accumulation rates can be calculated in cm/year or year/cm. By default cmyr=FALSE and accumulation rates are calculated in year per cm.

Remove NA entries. These are NOT removed by default, so that always the same amount of iterations is returned.

The probability ranges to be returned. Defaults to the minima and maxima of the 95% and 68% ranges, as well as the median: probs=c(.025, .16, .84, .975, .5).

The depth for which accumulation rates need to be returned.

Detailed information of the current run, stored within this session's memory as variable info.

Accumulation rates can be calculated in cm/year or year/cm. By default cmyr=FALSE and accumulation rates are calculated in year per cm.

Remove NA entries. These are NOT removed by default, ensuring that always the same amount of iterations is returned.

Detailed information of the current run, stored within this session's memory as variable info.

The depths for which the accumulation rates are to be calculated. Default to the entire core.

Axis limits for the depths.

Axis limits for the accumulation rates.

Label for the depth axis.

Accumulation rates can be calculated in cm/year or year/cm. By default cmyr=FALSE and accumulation rates are calculated in year per cm. Axis limits are difficult to calculate when cmyr=TRUE, so a manual adaptation of acc.lim might be a good idea.

Axis label for the accumulation rate.

The darkest grey value is dark=1 by default; lower values will result in lighter grey but values >1 are not advised.

Point below which colours will no longer be printed. Default cutoff=0.001.

The function to produce a coloured representation of all age-models. Needs 3 values for the intensity of red, green and blue. Defaults to grey-scales: rgb.scale=c(0,0,0), but could also be, say, scales of red (rgb.scale=c(1,0,0)).

Resolution of the colour spectrum depicting the age-depth model. Default rgb.res=100.

Probability ranges. Defaults to prob=0.95.

If plot.range=TRUE, the confidence ranges (two-tailed; half of the probability at each side) are plotted.

Colour of the confidence ranges.

Line type of the confidence ranges.

If plot.mean=TRUE, the means are plotted.

Colour of the mean accumulation rates.

Type of the mean lines.

If plot.mean=TRUE, the medians are plotted.

Colour of the median accumulation rates.

Type of the median lines.

The default is to plot the accumulation rates horizontally and the depth vertically (rotate.axes=FALSE). Change rotate.axes value to rotate axes.

The direction of the depth axis can be reversed from the default (rev.d=TRUE.

The direction of the accumulation rate axis can be reversed from the default (rev.acc=TRUE).

Extension of x-axis. By default, add some extra white-space at both extremes (xaxs="r"). See ?par for other options.

Extension of y-axis. By default, add no extra white-space at both extremes (yaxs="i"). See ?par for other options.

Type of box to be drawn around the plot ("n" for none, and "l" (default), "7", "c", "u", or "o" for correspondingly shaped boxes).

Add a white line to remove spurious lines at the extreme of the graph. Defaults to TRUE.

The depth for which accumulation rates need to be returned.

Detailed information of the current run, stored within this session's memory as variable info.

Accumulation rates can be calculated in cm/year or year/cm. By default cmyr=FALSE and accumulation rates are calculated in year per cm.

Remove NA entries. These are NOT removed by default, so that always the same amount of iterations is returned.

The probability ranges to be returned. Defaults to the minima and maxima of the 95% and 68% ranges, as well as the median: probs=c(.025, .16, .84, .975, .5).

The sequence of depths for which accumulation rates need to be returned. Defaults to whatever info$dseq is, which most often is a sequence from the top to the bottom of the core at 1 cm increments.

Detailed information of the current run, stored within this session's memory as variable info.

Accumulation rates can be calculated in cm/year or year/cm. By default cmyr=FALSE and accumulation rates are calculated in year per cm.

Remove NA entries. These are NOT removed by default, so that always the same amount of iterations is returned.

The probability ranges to be returned. Defaults to the minima and maxima of the 95% and 68% ranges, as well as the median: probs=c(.025, .16, .84, .975, .5).

The number of decimals to report. Defaults to round=2.

Whether or not to write the summary to a file, in the core's directory and ending in '_accrates.txt'.

Character to separate the entries within the file. Defaults to a tab, sep="\t".

Reported mean of the date. Can be multiple dates. Negative numbers indicate postbomb dates (if cc > 0).

Reported error of the date. Can be multiple dates.

Depth of the date.

The calibration curve to use: cc=1 for IntCal20 (northern hemisphere terrestrial), cc=2 for Marine20 (marine), cc=0 for none (dates that are already on the cal BP scale).

Detailed information of the current run, stored within this session's memory as variable info.

Threshold for plotting of probability values. Defaults to above=1e-3.

Use a postbomb curve for negative (i.e. postbomb) 14C ages. 0 = none, 1 = NH1, 2 = NH2, 3 = NH3, 4 = SH1-2, 5 = SH3

By default, Bacon uses the t-distribution (Christen and Perez 2009) to treat the dates. Use normal=TRUE to use the normal/Gaussian distribution. This will generally give higher weight to the dates.

Mean of core-wide age offsets (e.g., regional marine offsets).

Error of core-wide age offsets (e.g., regional marine offsets).

The dates are treated using the t distribution by default (normal=FALSE). The t model has two parameters, t.a and t.b, set at 3 and 4 by default (see Christen and Perez, 2010). If you want to assign narrower error distributions (more closely resembling the normal distribution), set t.a and t.b at for example 33 and 34 respectively (e.g., for specific dates in your .csv file). For symmetry reasons, t.a must always be equal to t.b-1.

The dates are treated using the t distribution by default (normal=FALSE). The t-distribution has two parameters, t.a and t.b, set at 3 and 4 by default (see Christen and Perez, 2010). If you want to assign narrower error distributions (more closely resembling the normal distribution), set t.a and t.b at for example 33 and 34 respectively (e.g., for specific dates in your .csv file). For symmetry reasons, t.a must always be equal to t.b-1.

Resolution of the date's distribution. Defaults to date.res=100.

The heights of the distributions of the dates. See also normalise.dists.

Multiplier for the heights of the distributions of dates on the calendar scale. Defaults to calheight=1.

Step size for age units of the distribution. Default agesteps=1.

Avoid plotting very low probabilities of date distributions (default cutoff=0.005).

The colour of the ranges of the date. Default is semi-transparent red: col=rgb(1,0,0,.5).

The colours of the borders of the date. Default is semi-transparent red: border=rgb(1,0,0,0.5).

The default of plotting age on the horizontal axis and event probability on the vertical one can be changed with rotate.axes=TRUE.

Plot the dates as 'blobs'. Set to mirror=FALSE to plot simple distributions.

Directions of distributions if they are plotted non-mirrored. Default up=TRUE.

The calendar scale of graphs is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

The shape of any marker to be added to the date. Defaults to a cross, pch=4. To leave empty, use pch=NA.

Directory where the calibration curves for C14 dates cc are located. By default cc.dir=c().

Detailed information of the current run, stored within this session's memory as variable info.

The calendar scale of graphs and age output-files is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

Units of the depths. Defaults to the one provided in the Bacon() command, depth.unit=set$depth.unit.

Units of the ages. Defaults to age.unit="yr".

Deprecated and replaced by depth.unit.

The labels for the depth axis. Default d.lab="Depth (cm)". See also depth.unit.

The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE).

Deprecated - use age.lab instead

Use kcal BP. Default is kcal=FALSE.

The labels for the accumulation rate plot (top middle). Default d.lab="Acc. rate (yr/cm)" (or whatever units you're using).

The labels for the memory plot (top right). Default d.lab="Memory".

Minimum depth of age-depth model (use this to extrapolate to depths higher than the top dated depth).

Maximum depth of age-depth model (use this to extrapolate to depths below the bottom dated depth).

Depth intervals at which ages are calculated. Default 1. Alternative depth intervals can be provided using, e.g., d.d.by=0.5.

By default, Bacon will calculate the ages for the depths d.min to d.max in steps of d.by. Alternative depths can be provided as, e.g., depths=seq(0, 100, length=500) or as a file, e.g., depths=read.table("CoreDepths.txt". See also depths.file.

By default, Bacon will calculate the ages for the depths d.min to d.max in steps of d.by. If depths.file=TRUE, Bacon will read a file containing the depths for which you require ages. This file, containing the depths in a single column without a header, should be stored within coredir, and its name should start with the core's name and end with '_depths.txt'. Then specify depths.file=TRUE (default FALSE). See also depths.

An experimental option to squeeze and stretch depths below a boundary. Needs 2 parameters: boundary depth and compression ratio, e.g., accordion=c(25,20). Defaults to inactive, accordion=c().

An option to plot ages at different depths (e.g., if a core has been compressed during a run). Use with extreme caution!

Minimum age of the age-depth plot.

Deprecated - use age.min instead.

Maximum age of the age-depth plot.

Deprecated - use age.min instead.

How to calculate accumulation rates and ages for sections with hiatuses. Either extrapolate from surrounding sections (default, hiatus.option=1), use a w-weighted mix between the prior and posterior values for depths below the hiatus and prior information only for above the hiatus (hiatus.option=2), or use the originally calculated slopes (hiatus.option=0).

Darkness of the greyscale age-depth model. By default, the darkest grey value is calculated as 10 times the height of the lowest-precision age estimate dark=c(). Lower values will result in lighter grey but values >1 are not allowed.

Confidence interval to report (between 0 and 1, default 0.95 or 95%).

Rounding of years. Default is to round to single years (1 digit for plum models).

Resolution or amount of greyscale pixels to cover the depth scale of the age-model plot. Default d.res=200.

Resolution or amount of greyscale pixels to cover the age scale of the age-model plot. Default yr.res=200.

Deprecated - use age.res instead.

Date distributions are plotted using date.res=100 points by default.

By default, the age-depth model is plotted with the depths on the horizontal axis and ages on the vertical axis. This can be changed with rotate.axes=TRUE.

The direction of the age axis, which can be reversed using rev.age=TRUE.

Deprecated - use rev.age instead.

The direction of the depth axis, which can be reversed using rev.d=TRUE.

Number of depths to calculate ages for. If this is more than maxcalc=500, a warning will be shown that calculations will take time.

The maximum heights of the distributions of the dates on the plot. See also normalise.dists.

Multiplier for the heights of the distributions of dates on the calendar scale. Defaults to calheight=1.

Plot the dates as 'blobs'. Set to mirror=FALSE to plot simple distributions.

Directions of distributions if they are plotted non-mirrored. Default up=TRUE.

Avoid plotting very low probabilities of date distributions (default cutoff=0.1).

Whether or not to plot the curves showing the confidence ranges of the age-model. Defaults to (plot.range=TRUE).

The colour of the curves showing the confidence ranges of the age-model. Defaults to medium grey (range.col=grey(0.5)).

The line type of the curves showing the confidence ranges of the age-model. Defaults to range.lty=12.

Widths of the lines of the ranges of the age-depth model. Default range.lwd=1.

The colour of the mean age-depth model: default mn.col="red".

The line type of the mean age-depth model. Default mn.lty=12.

Width of the line of the mean age-depth model. Default mn.lwd=1.

The colour of the median age-depth model: not drawn by default med.col=NA.

The line type of the median age-depth model. Default med.lty=12.

Width of the line of the median age-depth model. Default med.lwd=1.

The colour of the calibrated ranges of the dates. Default is semi-transparent blue: C14.col=rgb(0,0,1,.35).

The colours of the borders of calibrated 14C dates. Default is semi-transparent dark blue: C14.border=rgb(0, 0, 1, 0.5).

The colour of the non-14C dates. Default is semi-transparent blue-green: cal.col=rgb(0,.5,.5,.35).

The colour of the border of non-14C dates in the age-depth plot: default semi-transparent dark blue-green: cal.border=rgb(0,.5,.5,.5). Not used by default.

As an alternative to colouring dates based on whether they are 14C or not, sets of dates can be coloured as, e.g., dates.col=colours()[2:100].

Probability at which total Pb values are considered to have reached background values, or in other words, that their modelled values are at or below supported + detection limit (Al)). Setting this at 0.5 means that any depth with a Pb measurement, where at least half of the iterations model Pb values reaching background values, is flagged as having reached background. The age-model is not extended to any Pb measurements that have reached background.

Colour of the modelled 210Pb values. Defaults to shades of blue: pbmodelled.col=function(x) rgb(0,0,1,x).

Colour of the measured 210Pb values (default pbmeasured.col="blue"). Draws rectangles of the upper and lower depths as well as the Pb values with 95 percent error ranges.

Axis limits for the Pb-210 data. Calculated automatically by default (pblim=c()).

Colour of supported Pb-210. Defaults to semi-transparent purple, because why not.

Whether or not to remove the tail measurements when plotting. Sometimes automated removal might go wrong, so then this option can be used to avoid removing the tail measurements.

After the MCMC run, if there are more MCMC iterations than requested, only the last 'ssize' iterations will be retained. Defaults to TRUE.

The colour of the depths of any hiatuses. Default hiatus.col=grey(0.5).

The line type of the depths of any hiatuses. Default hiatus.lty=12.

The function to produce a coloured representation of all age-models. Needs 3 values for the intensity of red, green and blue. Defaults to grey-scales: rgb.scale=c(0,0,0), but could also be, say, scales of red (rgb.scale=c(1,0,0)).

Resolution of the colour spectrum depicting the age-depth model. Default rgb.res=100.

Colour of slumps. Defaults to slump.col=grey(0.8).

By default, the distributions of more precise dates will cover less time and will thus peak higher than less precise dates. This can be avoided by specifying normalise.dists=FALSE.

Plot the distributions of the dates all at the same maximum height (default same.height=FALSE).

Calibration curve for 14C dates: cc=1 for IntCal20 (northern hemisphere terrestrial), cc=2 for Marine20 (marine), cc=3 for SHCal20 (southern hemisphere terrestrial). For dates that are already on the cal BP scale use cc=0.

The title of the age-depth model is plotted on the main panel. By default this is the core's name. To leave empty: title="".

Location of the title. Default title.location='topleft'.

Size of the title font. Defaults to title.size=1.5.

Whether or not to plot labels next to the dated depths. Defaults to FALSE.

Add labels to the dates (as given by the first column of the .csv file). FALSE by default.

Position on the age axis of the date labels. By default draws them before the youngest age (1), but can also draw them after the oldest age (2), or above its mean (3).

Size of labels.

Colour of the labels. Defaults to the colour given to the borders of the dates.

Offsets of the positions of the labels, giving the x and y offsets. Defaults to c(0,0).

Justification of the labels. Follows R's adj option: A value of ‘0’ produces left-justified text, ‘0.5’ (the default) centered text and ‘1’ right-justified text.

Rotation of the label. 0 by default (horizontal).

Sets a short section above and below hiatus.depths within which to calculate ages. For internal calculations - do not change.

Type of box to be drawn around plots ("n" for none, and "l" (default), "7", "c", "u", or "o" for correspondingly shaped boxes).

Plot margins for the topleft panel (amount of white space along edges of axes 1-4). Default mar.left=c(3,3,1,1).

Plot margins for the middle panel(s) at the top (amount of white space along edges of axes 1-4). Default mar.middle=c(3,3,1,1).

Plot margins for the topright panel (amount of white space along edges of axes 1-4). Default mar.right=c(3,3,1,1).

Plot margins for the main panel (amount of white space along edges of axes 1-4). Default mar.main=c(3,3,1,1).

Adapt the righthand margins by a certain amount (default 2) to allow a righthand axis to be plotted (for plum)

Axis text margins (where should titles, labels and tick marks be plotted). Defaults to mgp=c(1.7, 0.7, 0.0).

Extension of x-axis. By default, add some extra white-space at both extremes (xaxs="r"). See ?par for other options.

Extension of y-axis. By default, add no extra white-space at both extremes (yaxs="i"). See ?par for other options.

Colour of the MCMC output. Defaults to post.col=grey(0.4)).

Colour of the posterior histogram. Defaults to post.col=grey(0.8)).

Colour of the posterior border. Defaults to post.border=grey(0.4)).

Colour of the prior curve. Defaults to light green, prior.col=3).

Line width of the prior curve. Defaults to prior.lwd=2).

Colour of the font accompanying the posterior histograms. Defaults to red, prior.fontcol=2).

Plot tickmarks and values on the vertical axes for the prior and posterior distributions. Defaults to no tick marks (prior.ticks="n"). Set to prior.ticks="s" to plot the tick marks. Note that these values are of little practical use, as they correspond poorly to, e.g., the mean and strength values. All that matters is that the areas of both the prior and the posterior distributions sum to 1; wider distributions tend to give lower peaks, and narrower distributions higher peaks.

Font size of the prior, relative to R's standard size. Defaults to prior.fontsize=0.9.

Font size of the top panels, relative to R's standard size. Defaults to prior.fontsize=0.9.

Font size of values at the tick marks in the main panel, relative to R's standard size. Defaults to mainpanel.tickfontsize=1.

Font size of axis labels in the main panel, relative to R's standard size. Defaults to mainpanel.labelsize=1.

Horizontal axis limits of the accumulation rate panel. Calculated automatically by default.

Vertical axis limits of the accumulation rate panel. Calculated automatically by default.

Horizontal axis limits of the memory panel. Calculated automatically by default.

Vertical axis limits of the memory panel. Calculated automatically by default.

Horizontal axis limits of the hiatus size panel. Calculated automatically by default.

Vertical axis limits of the hiatus size panel. Calculated automatically by default.

Horizontal axis limits of the phi panel. Calculated automatically by default.

Vertical axis limits of the phi panel. Calculated automatically by default.

Horizontal axis limits of the supported-Pb panel. Calculated automatically by default.

Vertical axis limits of the supported-Pb panel. Calculated automatically by default.

Whether or not to plot the x-axis. Can be used to adapt axes after a plot. See ?par for other options.

Whether or not to plot the y-axis. Can be used to adapt axes after a plot. See ?par for other options.

Plot the 210Pb data (if present). Defaults to plot.pb=TRUE.

Line type of measured Pb-210 data.

Produce a pdf file of the age-depth plot.

By default, the age-depth model is plotted on top of the dates. This can be avoided by supplying dates.only=TRUE.

By default, panels showing the MCMC iterations and the priors and posteriors for accumulation rate and memory are plotted above the main age-depth model panel. This can be avoided by supplying model.only=TRUE. Note however that this removes relevant information to evaluate the age-depth model, so we do recommend to present age-models together with these upper panels.

Provide a summary of the age ranges after producing the age-depth model graph; default verbose=FALSE.

By default, a variable called ‘info’ with relevant information about the run (e.g., core name, priors, settings, ages, output) is saved into the working directory. Note that this will overwrite any existing variable with the same name - as an alternative, one could run, e.g., myvar <- Bacon(), followed by supplying the variable myvar in any subsequent commands.

The MCMC iteration of which the age-model should be calculated.

Detailed information of the current run, stored within this session's memory as variable info.

The calendar scale of graphs and age output-files is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

If TRUE, a variable called ‘info’ with relevant information about the run (e.g., core name, priors, settings, ages, output) is saved into the working directory. Note that this will overwrite any existing variable with the same name.

Width of the window.

Step size with which the window moves.

Detailed information of the current run, stored within this session's memory as variable info.

Plot probability values step-wise (defaults to plot.steps=FALSE, which plots smooth curves instead).

The calendar scale of graphs and age output-files is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE).

Deprecated - use age.lab instead

Minimum and maximum calendar age ranges, calculated automatically by default (age.lim=c()).

Deprecated - use age.lim instead

Label of the probability axis (default prob.lab="probability").

Limits of the probability axis (calculated automatically by default).

The default of plotting age on the horizontal axis and event probability on the vertical one can be changed with rotate.axes=TRUE.

The direction of the age axis, which can be reversed using rev.age=TRUE.

Deprecated - use rev.age instead

Extension of the y-axis. Defaults to the exact ranges of the probability values. White space can be added to the vertical axis using yaxs="r".

Type of box to be drawn around plots. Draw a box around the graph ("n" for none, and "l", "7", "c", "u", "]" or "o" for correspondingly shaped boxes).

Detailed information of the current run, stored within this session's memory as variable info.

The detection limit. Default Al=0.1.

Name of the core, given using quotes. Defaults to one of the cores provided with rbacon, core="MSB2K". An alternative core provided with this package is RLGH3 (Jones et al., 1989). To run your own core, produce a .csv file with the dates as outlined in the manual, add a folder with the core's name to the default directory for cores (see coredir), and save the .csv file there. For example, the file's location and name could be Bacon_runs/MyCore/MyCore.csv. Then run Bacon as follows: Bacon("MyCore")

Bacon will divide the core into sections of equal thickness specified by thick (default thick=5).

Folder where the core's files core are and/or will be located. This will be a folder with the core's name, within either the folder coredir='Bacon_runs/', or the folder Cores/ if it already exists within R's working directory, or a custom-built folder. For example, use coredir="." to place the core's folder within the current working directory, or coredir="F:" if you want to put the core's folder and files on a USB drive loaded under F:. Thinner (and thus more) sections will result in smoother age-models, but too many sections can cause ‘run-away’ models.

Confidence interval to report. This should lie between 0 and 1, default 0.95 (95 %).

Minimum depth of age-depth model (use this to extrapolate to depths higher than the top dated depth).

Maximum depth of age-depth model (use this to extrapolate to depths below the bottom dated depth).

Add a model section at the bottom of the core, in order to ensure the bottommost date is taken into account. Default add.bottom=TRUE. This is a new option and can cause age-models to differ from previous version. Please re-run the model if in doubt.

Depth intervals at which ages are calculated. Defaults to d.by=1. Please ensure that the value of d.by is smaller than that of 'thick', otherwise plots might turn out wrong.

Seed used for C++ executions. If it is not assigned (seed=NA; default) then the seed is set by system.

By default, Bacon will calculate the ages for the depths d.min to d.max in steps of d.by. If depths.file=TRUE, Bacon will read a file containing the depths for which you require ages. This file, containing the depths in a single column without a header, should be stored within coredir, and its name should start with the core's name and end with ‘_depths.txt’. Then specify depths.file=TRUE (default FALSE). See also depths.

By default, Bacon will calculate the ages for the depths d.min to d.max in steps of d.by. Alternative depths can be provided as, e.g., depths=seq(0, 100, length=500) or as a file, e.g., depths=read.table("CoreDepths.txt". See also depths.file.

Units of the depths. Defaults to depth.unit="cm".

Units of the ages. Defaults to age.unit="yr".

Deprecated and replaced by depth.unit.

The prior for the accumulation rate consists of a gamma distribution with two parameters. Its shape is set by acc.shape (default acc.shape=1.5; higher values result in more peaked shapes).

The accumulation rate prior consists of a gamma distribution with two parameters. Its mean is set by acc.mean (default acc.mean=20 yr/cm (or whatever age or depth units are chosen), which can be changed to, e.g., 5, 10 or 50 for different kinds of deposits). Multiple values can be given in case of hiatuses or boundaries, e.g., Bacon(hiatus.depths=23, acc.mean=c(5,20))

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.strength=10 (higher values result in more peaked shapes) allow for a large range of posterior memory values. Please note that the default memory prior has been updated from rbacon version 2.5.1 on, to repair a bug.

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 mem.mean=0.5 allow for a large range of posterior memory values. Please note that the default memory prior has been updated from rbacon version 2.5.1. on, to repair a bug.

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., acc.mean=c(5, 20). See also hiatus.depths, mem.mean, acc.mean and acc.shape. Setting many boundaries might not work, and having more than one boundary per model section (see 'thick') might not work either.

The assumed depths for any hiatus should be provided as, e.g., hiatus.depths=20 for one at 20cm depth, and hiatus.depths=c(20,40) for two hiatuses at 20 and 40 cm depth.

The prior for the maximum length of the hiatus. Hiatus length is a uniform distribution, with equal probabilities between 0 and hiatus.max yr (or whatever other age.unit is chosen).

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.

Sets a short section above and below hiatus.depths within which to calculate ages. For internal calculations - do not change.

Calibration curve for C-14 dates: cc=1 for IntCal20 (northern hemisphere terrestrial), cc=2 for Marine20 (marine), cc=3 for SHCal20 (southern hemisphere terrestrial). For dates that are already on the cal BP scale use cc=0.

For northern hemisphere terrestrial 14C dates (IntCal20).

For marine 14C dates (Marine20).

For southern hemisphere 14C dates (SHCal20).

Provide the name of an alternative curve (3 columns: cal BP, 14C age, error, separated by white spaces and saved as a plain-text file). It is important here to first produce a tailor-made folder for your and the default calibration curves to live in. See cc.dir. Defaults to cc4="mixed.14C".

Directory where the calibration curves for C14 dates cc are located. By default uses the location of the rintcal package which provides the calibration curves. If you want to use custom-made calibration curves, first set up a new folder using the function new.ccdir() in the rintcal package, e.g., new.ccdir="MyCurves", then place the custom curve in that folder using rintcal::mix.ccurves(, cc.dir="MyCurves", save=TRUE).

Use a postbomb curve for negative (i.e. postbomb) 14C ages. 0 = none, 1 = NH1, 2 = NH2, 3 = NH3, 4 = SH1-2, 5 = SH3

Radiocarbon ages can be provided as F14C values. If doing so, please indicate here which dates were entered as F14C (e.g., if the first 4 dates are in F14C, write F14C=1:4). The F14C values in your .csv file will then be replaced by their corresponding C14 ages.

Radiocarbon ages can be provided as pMC values. If doing so, please indicate here which dates were entered as pMC (e.g., if the first 4 dates are in pMC, write pMC=1:4). The pMC values in your .csv file will then be replaced by their corresponding C14 ages.

Mean of core-wide age offsets (e.g., regional marine offsets).

Error of core-wide age offsets (e.g., regional marine offsets).

The dates are treated using the t distribution (Christen and Perez 2009) by default (normal=FALSE). This t-distribution has two parameters, t.a and t.b, set at 3 and 4 by default (see Christen and Perez, 2010). If you want to assign narrower error distributions (more closely resembling the normal distribution), set t.a and t.b at for example 33 and 34 respectively (e.g., for specific dates in your .csv file). For symmetry reasons, t.a must always be equal to t.b-1.

The dates are treated using t distribution by default (normal=FALSE). The t-distribution has two parameters, t.a and t.b, set at 3 and 4 by default (see Christen and Perez, 2009). If you want to assign narrower error distributions (more closely resembling the normal distribution), set t.a and t.b at for example 33 and 34 respectively (e.g., for specific dates in your .csv file). For symmetry reasons, t.a must always be equal to t.b-1.

By default, Bacon uses the t-distribution to treat the dates. Use normal=TRUE to use the normal/Gaussian distribution. This will generally give higher weight to the dates.

If initial analysis of the data indicates abnormally slow or fast accumulation rates, Bacon will suggest to change the prior.

Automatically accept the suggested values. Use with care. Default accept.suggestions=FALSE. Also, if the length of the core would cause too few or too many sections with the default settings, Bacon will suggest an alternative section thickness thick. Accept these suggested alternative settings by typing "y" (or "yes please" if you prefer to be polite), or leave as is by typing "n" (or anything else, really). To get rid of these suggestions, use suggest=FALSE.

Bacon will warn you if the number of sections lies outside the safe range (default between 10 and 200 sections; reswarn=c(10,200)). Too few sections could lead to an ‘elbowy’ model while with too many sections the modelling process can get lost, resulting in age-models far away from the dated depths.

Bacon will try to remember which settings you have applied to your cores (default remember=TRUE). If you run into inconsistencies or other problems, try running your core again with remember=FALSE, or, start cleanly by typing Bacon.cleanup().

By default Bacon will ask you to confirm that you want to run the core with the provided settings. Disable this using ask=FALSE (e.g., for batch runs).

In order to load an existing Bacon run instead of producing a new one, you can use run=FALSE.

Name of the file containing settings for the core. For internal use only - do not change.

Separator between the fields of the plain text file containing the dating information. Default sep=",".

Character for decimal points. Default to dec=".".

Text to add to the corename for specific runs, e.g., runname="MyCore_Test1".

Upper and lower depths of any sections of assumed abrupt accumulation, that require excising before age-modelling (and adding after age-modelling). Requires pairs of depths, e.g., slump=c(10,15,60,67) for slumps at 67-60 and 15-10 cm core depth.

Whether or not to remove depths within slumps. Defaults to remove=FALSE.

The calendar scale of graphs and age output-files 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 BCAD=TRUE.

The amount of iterations to store at the end of the MCMC run. Default 4000; decrease for faster (but less reliable) runs or increase for cores where the MCMC mixing (panel at upper-left corner of age-model graph) appears problematic.

Starting years for the MCMC iterations. These are randomly chosen by default.

Amount of initial, likely sub-optimal MCMC iterations that will be removed.

Minimum age limit for Bacon runs, default at current year in cal BP. To set plot limits, use age.min instead.

Maximum age limit for Bacon runs, default at 1,000,000 cal BP. To set plot limits, use age.max instead.

Deprecated - use youngest.age instead.

Deprecated - use oldest.age instead.

Avoid plotting very low probabilities of date distributions (default cutoff=0.001).

Produce a pdf file of the age-depth plot. Defaults to plot.pdf=TRUE after a Bacon run.

Darkness of the greyscale age-depth model. The darkest grey value is dark=1 by default. Lower values will result in lighter grey but values >1 are not allowed.

Date distributions are plotted using date.res=100 segments by default.

Resolution or amount of greyscale pixels to cover the age scale of the age-model plot. Default yr.res=200.

Deprecated - use age.res instead

Internal option to close connections after a run. Default close.connections=TRUE.

By default, a variable called ‘info’ with relevant information about the run (e.g., core name, priors, settings, ages, output) is saved into the working directory. Note that this will overwrite any existing variable with the same name - as an alternative, one could run, e.g., myvar <- Bacon(), followed by supplying the variable myvar in any subsequent commands.

an option to enable dates at the limit of C-14 dating. If there are older.than dates, they tell us that the core should be older than a certain age at that depth. For example, if the 7th and 8th dates in the core's .csv file are older-than dates, use as older.than=c(7,8). The MCMC run could be problematic if the older-than ages do not fit with the other information.

an option to provide younger-than ages, for example a historical pollen marker. If there are younger-than dates, they tell us that the core should be younger than a certain age at that depth. For example, if the 7th and 8th dates in the core's .csv file are younger.than dates, use as younger.than=c(7,8). The MCMC run could be problematic if the younger.than ages do not fit with the other information.

If you want to have a file with the MCMC-derived ages for all the age-depth model's elbows, set save.elbowages=TRUE and a file with the ages will be saved in the core's folder, starting with the core name, followed by its number of sections, d.min, and section thickness, and ending in "_elbowages.txt".

Provide feedback on what is happening (default verbose=TRUE).

options for the age-depth graph. See agedepth and calib.plot

The depth of which Bacon age estimates are to be returned. Has to be a single depth.

Detailed information of the current run, stored within this session's memory as variable info.

The set of MCMC iterations to be used. Defaults to the entire MCMC output, its=set$output.

The calendar scale of graphs and age output-files is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

Whether or not to remove NA values (ages within slumps)

Detailed information of the current run, stored within this session's memory as variable info.

The age estimate for which depths are to be returned. Has to be a single age.

Detailed information of the current run, stored within this session's memory as variable info.

The calendar scale of graphs and age output-files is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

The set of MCMC iterations to be used. Defaults to the entire MCMC output, its=set$output.

Whether or not to remove NA values (ages within slumps)

The depth or depths for which a histogram and age ranges should be provided. If multiple depths are given, then just the age ranges, median and means (no graphs) are provided for each depth.

Detailed information of the current run, stored within this session's memory as variable info.

The calendar scale of graphs and age output-files is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE).

Minimum and maximum calendar age ranges, calculated automatically by default (age.lim=c()).

The y-axis is labelled ylab="Frequency" by default.

Calculate ranges? Takes time so can be left out

Limits of the y-axis.

Draw a plot or not. Defaults to draw=TRUE, however no plots are made if more than one depth d is provided. If draw=FALSE, then the age ranges, median and mean are given for each depth (as four columns).

Age ranges are given as quantiles, e.g., 2.5% and 97.5% for the default of 95% confidence limits (prob=0.95)).

Colour of the histogram. Default grey, hist.col=grey(0.5).

Colour of the histogram's outline. Default dark grey, hist.border=grey(0.2).

Colour of confidence ranges. Defaults to range.col="blue".

Colour of the median. Defaults to med.col="green".

Colour of the mean. Defaults to mn.col="red".

Provide feedback on what is happening (default verbose=TRUE).

A variable called ‘info’ with relevant information about the run (e.g., core name, priors, settings, ages, output) can be saved into the working directory. Note that this will overwrite any existing variable with the same name - as an alternative, one could run, e.g., myvar <- Bacon(), followed by supplying the variable myvar in any subsequent commands.

The name of the core for which a Bacon .csv.file needs to be translated into a clam .csv file

The directory where the Bacon runs reside. Defaults to coredir="Bacon_runs".

The directory where the clam runs reside. Defaults to coredir="clam_runs".

The separator for the .csv files. Defaults to sep=",".

Name of the core, given using quotes. Defaults to one of the cores provided with rbacon, core="MSB2K".

Amount of runs to test for mixing. Default runs=5.

If initial analysis of the data indicates abnormally slow or fast accumulation rates, Bacon will suggest to change the prior.

Provide feedback on what is happening (default verbose=TRUE).

additional options that can be given to the Bacon function.

Detailed information of the current run, stored within this session's memory as variable info.

The set of determinations to be plotted.

If depths have to be squeezed/stretched, the parameters can be set here. Defaults to being empty, but requires 2 parameters if active, e.g., accordion=c(10,20).

The calendar scale of graphs is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

Calibration curve to be used (defaults to info$cc)

The default of plotting age on the horizontal axis and event probability on the vertical one can be changed with rotate.axes=TRUE.

The direction of the depth axis can be reversed from the default (rev.d=TRUE).

The direction of the calendar age axis can be reversed from the default (rev.age=TRUE)

Deprecated - use rev.age instead

Minimum and maximum calendar age ranges, calculated automatically by default (age.lim=c()).

Deprecated - use age.lim instead

Date distributions are plotted using date.res=100 points by default.

The labels for the depth axis. Default d.lab="Depth (cm)".

The labels for the calendar axis (default yr.lab="cal BP" or "BC/AD" if BCAD=TRUE).

Deprecated - use age.lab instead

The heights of the distributions of the dates. See also normalise.dists.

Multiplier for the heights of the distributions of dates on the calendar scale. Defaults to calheight=1.

Plot the dates as 'blobs'. Set to mirror=FALSE to plot simple distributions.

Directions of distributions if they are plotted non-mirrored. Default up=TRUE.

Avoid plotting very low probabilities of date distributions (default cutoff=0.1).

Colour of the calibrated distributions of the dates. Default is semi-transparent blue: rgb(0,0,1,.35).

Colours of the borders of calibrated 14C dates. Default is transparent dark blue: cal.col

Colour of the non-14C dates in the age-depth plot: default semi-transparent blue-green: rgb(0,.5,.5,.35).

Colour of the of the border of non-14C dates in the age-depth plot: default semi-transparent dark blue-green: rgb(0,.5,.5,.5).

As an alternative to colouring dates based on whether they are 14C or not, sets of dates can be coloured as, e.g., dates.col=colours()[2:100].

Colour of slumps. Defaults to slump.col=grey(0.8).

Start a new plot (new.plot=TRUE) or plot over an existing plot (new.plot=FALSE).

Plot the distributions of the dates (default plot.dists=TRUE).

Plot the distributions of the dates all at the same maximum height (default same.height=FALSE), which instead normalises the distributions (all have an area of 1).

The name of the core for which a clam .csv.file needs to be translated into a Bacon .csv file

The directory where the clam runs reside. Defaults to coredir="clam_runs".

The directory where the Bacon runs reside. Defaults to coredir="Bacon_runs".

The separator for the .csv files. Defaults to sep=",".

Calibration curve for C-14 dates: cc=1 for IntCal20 (northern hemisphere terrestrial), cc=2 for Marine20 (marine),

Detailed information of the current run, stored within this session's memory as variable info.

The default of plotting age on the horizontal axis and event probability on the vertical one can be changed with rotate.axes=TRUE.

The direction of the depth axis can be reversed from the default (rev.d=TRUE).

The direction of the calendar age axis can be reversed from the default (rev.age=TRUE)

The calendar scale of graphs and age output-files 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 BCAD=TRUE.

Minimum and maximum of the 210Pb axis ranges, calculated automatically by default (pb.lim=c()).

Minimum and maximum of the age ranges to be used to plot 210Pb values. Calculated automatically by default (age.lim=c()).

Minimum and maximum depths to plot; calculated automatically by default (d.lim=c()).

The labels for the depth axis. Default d.lab="Depth (cm)".

The label for the 210Pb axis (default pb.lab="210Pb (Bq/kg)" or "210Pb (dpm/g)").

The label for the measured 210Pb data. pbmeasured.col="blue".

Line type of the measured 210Pb data. Defaults to continuous lines.

Use a log scale for the 210Pb-axis (default pb.log=FALSE).

Colour of the supported 210Pb data. Defaults to red: supp.col="red".

make new plot (default TRUE)

Plot the Pb-210 on the cal BP scale. Defaults to FALSE.

Detailed information of the current run, stored within this session's memory as variable info.

The calendar scale of graphs is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

The default of plotting age on the horizontal axis and event probability on the vertical one can be changed with rotate.axes=TRUE.

The direction of the depth axis can be reversed from the default (rev.d=TRUE).

The direction of the calendar age axis can be reversed from the default (rev.age=TRUE)

Minimum and maximum of the 210Pb axis ranges, calculated automatically by default (pb.lim=c()).

Minimum and maximum depths to plot; calculated automatically by default (d.lim=c()).

The labels for the depth axis. Default d.lab="Depth (cm)".

The label for the 210Pb axis (default pb.lab="210Pb (Bq/kg)" or "210Pb (dpm/g)").

Colour of the modelled 210Pb values. Defaults to scales of blue: pbmodelled.col=function(x) rgb(0,0,1,x).

Colour of the measured 210Pb values. Defaults to blue.

Colour of the supported 210Pb data. Defaults to red: supp.col="red".

Plot the measured 210Pb values (default plot.measured=TRUE).

values of the age axis. Used to calculate where to plot the pb values on the secondary axis

Axis text margins (where should titles, labels and tick marks be plotted). Defaults to mgp=c(1.7, .7, .0).

Line type of measured Pb-210 data.

Which proxy to use (counting from the column number in the .csv file after the depths column).

Minimum and maximum calendar age ranges, calculated automatically by default (age.lim=c()).

Deprecated - use age.lim instead

Resolution or amount of greyscale pixels to cover the age scale of the plot. Default age.res=200.

Deprecated - use age.res instead

Detailed information of the current run, stored within this session's memory as variable info.

Define a flux variable within the R session (consisting of depths and their proxy concentrations in two columns) and provide the name of this variable, e.g.: flux.age.ghost(flux=flux1). If left empty (flux=c()), a flux file is expected (see proxy).

Plot curves that indicate a probability range, at resolution of yr.res.

Probability range, defaults to prob=0.8 (10 % at each side).

Red seems nice.

Line type of the confidence ranges.

Plot the mean fluxes.

Red seems nice.

Line type of the means.

Plot the median fluxes.

Blue seems nice.

Line type of the medians.

Limits of the flux axes.

Axis labels. Defaults to flux.lab="flux".

Maximum flux rates to plot. Defaults to the upper 99%; upper=0.99.

The function to produce a coloured representation of all age-models. Needs 3 values for the intensity of red, green and blue. Defaults to grey-scales: rgb.scale=c(0,0,0), but could also be, say, scales of red (rgb.scale=c(1,0,0)).

Resolution of the colour spectrum depicting the age-depth model. Default rgb.res=100.

The darkest grey value is dark=1 by default; lower values will result in lighter grey but values >1 are not allowed.

Point below which colours will no longer be printed. Default cutoff=0.001.

The calendar scale of graphs and age output-files is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE).

Deprecated - use age.lab instead

The default of plotting calendar year on the horizontal axis and fluxes on the vertical one can be changed with rotate.axes=TRUE.

The flux axis can be reversed with rev.flux=TRUE.

The direction of the age axis can be reversed using rev.age=TRUE.

Deprecated - use rev.age instead

Which proxy to use (counting from the column number in the .csv file after the depths column).

Label of the proxy axis. Default names are taken from the csv file.

Greyscale pixels are calculated for proxy.res=250 proxy values by default, as a compromise between image quality and calculation speed. If the output looks very pixel-like (e.g., when choosing to plot only part of the record using proxy.lim), set this option to higher values.

Resolution or amount of greyscale pixels to cover the age scale of the age-model plot. Default age.res=250 as a compromise between image quality and calculation speed. If the output looks very pixel-like (e.g., when choosing to plot only part of the record using age.lim), set this option to higher values.

Deprecated - use age.res instead

The function to produce a coloured representation of all age-models. Needs 3 values for the intensity of red, green and blue. Defaults to grey-scales: rgb.scale=c(0,0,0), but could also be, say, scales of red (rgb.scale=c(1,0,0)).

Resolution of the colour spectrum depicting the age-depth model. Default rgb.res=100.

Detailed information of the current run, stored within this session's memory as variable info.

Point below which colours will no longer be printed. Default cutoff=0.001.

By default, the darkest grey value is assigned to the most likely value within the entire core (normalised to 1; dark=1). By setting dark to, e.g., dark=.8, all values of and above 0.8 will be darkest (and values below that threshold will be lighter grey the lower their probabilities).

Darkness of the most likely value. Is black by default (darkest=1); lower values will result in lighter grey.

The default is to plot the calendar horizontally, however the plot can be rotated (rotate.axes=TRUE).

The proxy axis can be reversed if proxy.rev=TRUE.

The calendar axis can be reversed using yr.rev=TRUE.

Deprecated - use age.rev instead

The mean ages of the proxy values can be added using plot.mean=TRUE.

Colour of the weighted mean ages of the proxy values.

Minimum and maximum calendar age ranges, calculated automatically by default (yr.lim=NULL).

Deprecated - use age.lim instead

Ranges of the proxy axis, calculated automatically by default (proxy.lim=NULL).

Separator between the fields of the plain text file containing the depth and proxy data.

Extension of x-axis. By default, no white-space will be added at the axis extremes (xaxs="i"). See ?par for other options.

Extension of y-axis. By default, no white-space will be added at the axis extremes (xaxs="i"). See ?par for other options.

The x-axis is plotted by default, but this can be switched off using xaxt="n".

The y-axis is plotted by default, but this can be switched off using yaxt="n".

Type of box to be drawn around the plot ("n" for none, and "l" (default), "7", "c", "u", or "o" for correspondingly shaped boxes).

The calendar scale of graphs and age output-files is in cal BP by default, but can be changed to BC/AD using BCAD=TRUE.

The labels for the calendar axis (default age.lab="cal BP" or "BC/AD" if BCAD=TRUE).

Deprecated - use age.lab instead

Provide feedback on what is happening (default verbose=TRUE).

Add to an existing graph (default add=FALSE).

Number of iterations to remove of the iterative time series. If this value is higher than the amount of remaining iterations, a warning is given and the iterations are not removed. If the provided number is negative, the iterations will be removed from the end of the run, not from the start. If a range is given, this range of iterations is removed.

Detailed information of the current run, stored within this session's memory as variable info.

Whether or not to write the changes to the output file. Defaults to TRUE.

By default, a variable called ‘info’ with relevant information about the run (e.g., core name, priors, settings, ages, output) is saved into the working directory. Note that this will overwrite any existing variable with the same name - as an alternative, one could run, e.g., myvar <- Bacon(), followed by supplying the variable myvar in any subsequent commands.

Detailed information of the current run, stored within this session's memory as variable info.

The name of the core for which a bacon.init file needs to be made

use this if you wish to provide the values (2 rows with starting age, accumulation rates for each model section, and memory parameter w).

use this if you wish to use the cursor to manually select age-depth points from the current graphic device. This is the default option. Right click once you have selected all datapoints, or provide the number of expected datapoints as a value (e.g., click=5).

The depth(s) to be squeezed

The depth below which depths should be squeezed

The factor by which the depths should be squeezed

The depth(s) to be stretched

The depth below which depths should be stretched

The factor by which the depths should be stretched

Proportion of iterations to remove. Should be between 0 and 1. Default proportion=0.1.

Detailed information of the current run, stored within this session's memory as variable info.

Whether or not to write the changes to the output file. Defaults to TRUE.

By default, a variable called ‘info’ with relevant information about the run (e.g., core name, priors, settings, ages, output) is saved into the working directory. Note that this will overwrite any existing variable with the same name - as an alternative, one could run, e.g., myvar <- Bacon(), followed by supplying the variable myvar in any subsequent commands.

options for the Bacon command. See Bacon