                        Changes in version 4.0.1                        

  - depths are now reported correctly when using slumps and
    use.cpp=TRUE.
  - added a version legend to the main age-depth model plot.
  - new option fast, which enables (TRUE; default) or disables (FALSE)
    the use of the fread and fwrite functions within the data.table R
    package to speed up reading/writing to files. Disabling can help
    with issues in reading files in uncommon encoding (e.g. Latin-1).
  - older.than and younger.than dates are now indicated by upward
    respectively downward arrows.

                 Changes in version 4.0.0 (2026-09-16)                  

new features

  - hiatuses are now constrained by a gamma prior (as in the original
    Bacon paper, Blaauw & Christen 2011), no longer by a uniform prior.
    The parameters are hiatus.mean and hiatus.shape. In most cases, the
    data will be dominant steering the hiatus size. If you are very sure
    about the prior size of the hiatus, set hiatus.shape to high values
    such as 10 or 100.
  - calculations of age ranges and age-depth ghost plots are now much
    faster when using the default use.cpp=TRUE in the functions Bacon,
    agedepth, proxy.ghost and ageranges. This option causes the
    underlying calculations to be done in cpp, not R. This feature is
    experimental and can be deactivated using use.cpp=FALSE in the above
    functions.
  - colour gradients (ghost plots) in agedepth can now also be provided
    as from.col and to.col, to choose from one of the >600 colour names
    within R's function colours(). For example,
    agedepth(from.col="papayawhip", to.col="saddlebrown").
  - when there are hiatuses or boundaries, the posterior accumulation
    rates below/above the hiatuses/boundaries are plotted as individual
    histograms - same for hiatuses. Multiple posteriors can also be
    given their colours, e.g., agedepth(acc.post.col=c(rgb(1,0,0,.2),
    rgb(0,1,0,.2))).
  - new option hot.stop in the Bacon function that stops if any provided
    F14C or pMC values are either negative or above 3 or 300,
    respectively. Defaults to TRUE.
  - new function Bacon_runs which lists the cores available in the
    Bacon_runs directory.
  - cleaned up the flux.age.ghost function, adding an option to plot
    ages as BC/AD (the default remains cal BP).
  - any arguments/options that the user provided within the Bacon()
    command can now be retrieved by typing info$command.

improvements

  - accrate.depth and related functions now deal better with slumps.
    Upon invoking a slump, accrate.depth no longer reports NAs for the
    lowermost sections of the piece-wise age-depth model.
  - if a core's .csv file (the one containing the dates) contains
    invisible spaces, quotation marks or spaces preceding commas (e.g.,
    in the headers), these are now removed.
  - greyscales and axis limits in some plotting functions are now more
    robust to the range of values (since it's using quantiles instead of
    max).
  - within the Bacon() command, d.by is now adjusted automatically if it
    is larger than thick. This can be avoided by setting
    adjust.dby=FALSE.
  - even funnier feedback at the end of MCMC runs.
  - rewrote the function flux.age.ghost to make it much faster.
  - the check for cairo capabilities of macOS systems has been updated
    in the Bacon function.
  - add.dates now has options BCAD, is.F and is.pMC.
  - agemodel.it now deals better with hiatuses and slumps.
  - proxy.ghost gains the option to plot the median ages (mean ages were
    already an option).
  - when calculating what proportion of the dates fit within the
    age-depth model, this is now done by checking for each date if any
    of its hpd intervals fall within any of the model's hpds
    (default 95% confidence ranges).
  - if boundaries or hiatuses are set, the acc.rate and (if present)
    hiatus panels of the main agedepth function now show the posteriors
    of the multiple sections separately. They can also be coloured
    separately using for example post.col=c(3,5).
  - supported 210Pb values are now plotted better when ra.case=2.

bug fixes

  - if a depth above/smaller than d.min is provided in 'Bacon.hist',
    this now fails with a more informative error message.
  - cleaned up the function accrate.age.ghost.
  - accrate.age now deals better with hiatuses.
  - now using rice version 2.2.1 and rintcal version 1.4.0.
  - model.dates.hpd and model.Pb.hpd now call rice's hpd.overlap
    function using the option to pad the distributions with 0 at both
    ends. This avoids problems with open-ended distributions.
  - cleaned up 'orphan' variables.
  - some more changes to make the plotting of pdfs more robust on
    different operating systems.

                 Changes in version 3.5.2 (2025-05-18)                  

  - removed the ageranges example to avoid the CRAN NOTE about a slow
    example.

                        Changes in version 3.5.1                        

  - reduced the runtime of the ageranges examples to avoid the CRAN
    NOTE.

                        Changes in version 3.5.0                        

  - accrate.age.ghost and accrate.depth.ghost can now be run without
    adding the variable info to the session, e.g. as in: 'mycore <-
    Bacon(save.info=FALSE, ask=FALSE); layout(1);
    accrate.depth.ghost(set=mycore)'.
  - adding delta.R and delta.STD columns to a .csv file was causing an
    occasional error which has been fixed (reported by Najoua
    Gharsalli).
  - a new function ageranges to summarize age estimates of depths.
  - a new function MCMC.diagnostics which calculates the quality of the
    MCMC run (we're looking for a high value of 'effective sample size'
    which indicates good mixing, and a low value of 'z' which indicates
    a stationary run, without drift).

                 Changes in version 3.4.2 (2025-05-04)                  

  - adapted agedepth(), draw.pbmodelled(), PlotPhiPost() and
    PlotSuppost() to make rplum plotting more robust.
  - changes to how greyscales are plotted. The setting use.raster=TRUE
    introduced in rbacon 3.4.0 unfortunately causes unexpected behaviour
    especially between different operation systems (sometimes the images
    are flipped). Therefore the default will be use.raster=FALSE, with
    options to set it to TRUE (the user can unflip the images using the
    'flip.acc', 'flip.d' and 'flip.age' options).
  - within the inst/dev/ folder, there is now a testBaconplots.Rmd
    function which automates plotting and checking many functions. There
    is also a file render-plots.yml which can be used to test many plots
    on a range of github systems (ubuntu, fedora and windows). Produced
    html files can be downloaded and checked locally. To do this, the
    file has to be placed in .github/workflows/.

                 Changes in version 3.4.1 (2025-04-25)                  

  - removed rice:: mentions to functions called from rice, since this
    could cause warnings in the rplum package.

                        Changes in version 3.4.0                        

  - radiocarbon ages can now be entered as F14C or pMC values (e.g. for
    postbomb dates). Please indicate using the F14C or pMC option which
    ones are in F14C/pMC (e.g., Bacon(F14C=2:4) if dates 2 to 4 are in
    F14C). These values will then automatically be rewritten as C14
    ages.
  - the proxy.ghost function now invisibly returns a table of the values
    used in the grid composing the greyscale plot.
  - add.dates now plots additional dates as expected, also when
    rotate.axes=TRUE (although rotate.axes still has to be set to TRUE
    after using the agedepth function with rotate.axes=TRUE).
  - the agedepth function now treats provided values for d.min and d.max
    better.
  - greyscale 'ghost' plots (agedepth, accrate.depth.ghost,
    accrate.age.ghost, proxy.ghost) should now plot with fewer
    disturbances such as lines. This is done by setting useRaster=TRUE
    in image.
  - if available on your system, 'cairo_pdf' will be used to plot pdfs.
  - after a run, the posteriors (for accumulation rate, memory, and if
    present hiatus, phi and supported) are now summarized in a message.
  - the heights of the distributions of the dates can now also be set
    through a variable ex, which could either be of length 1, or have a
    value for each date in the core. This way, some dates can be plotted
    at different heights.
  - when running Bacon as tmp <- Bacon(save.info=FALSE), no additional
    variables beside 'tmp' will be saved in the session. For subsequent
    calculations, provide 'tmp', e.g. as in Bacon.hist(20:40, set=tmp).
    The default remains to save an object 'info' to the session, and
    this object will then be used to make any further calculations using
    set=get('info').

                 Changes in version 3.3.1 (2024-09-28)                  

  - now uses the updated rice package (which loads the data rintcal
    package).
  - new options in the age-depth function to steer the formatting of the
    prior information, such as line width and colour
  - new functions to summarise modelled accumulation rates:
    'accrate.depth.summary()' and 'accrate.age.summary()' to provide
    summaries of single depths and ages, respectively, and
    'accrates.core()' to write these summaries for all depths of a core
    to its folder.

                 Changes in version 3.3.0 (2024-09-06)                  

  - the default file name for cc4 is now "mixed.14C"
  - Bacon can now run without saving the variable 'info' in the session.
    E.g., one can run mycore <- Bacon() and then query 'mycore' as one
    would query 'info'.
  - if the dated depths in the .csv file are not in ascending order,
    this now throws an error (it was a warning, but this caused a
    subsequent more opaque error).
  - new functions to summarise accumulation rates according for a single
    depth or age, or for a sequence of depths: accrate.depth.summary,
    accrate.age.summary and accrates.core().
  - loads the new R package 'rice' to do most of the legwork related to
    plotting, calculating and calibrating radiocarbon ages. The
    'rintcal' package will become a data package with little
    user-oriented functionality.

                 Changes in version 3.2.0 (2023-11-28)                  

  - the overlap function now works better if d.min and/or d.max are set
  - as per CRAN (Kurt Hornik)'s e-mail, added a sentinel "_PACKAGE" file
    to the documentation
  - changed occurrences of %lu in twalk.h to %llu per CRAN (Prof. Brian
    Ripley) request
  - added run puns
  - elbowages are now saved with more relevant information in the file
    name
  - now links to rintcal 0.6.4

                 Changes in version 3.1.1 (2023-07-15)                  

  - repaired a bug related to an upgrade in the rintcal package, which
    caused problems with plotting young radiocarbon dates
  - cleaned up cal.h to remove obsolete references to IntCal13

                 Changes in version 3.1.0 (2023-05-17)                  

  - updated rintcal so that the files containing the NH and SH postbomb
    curves work as expected
  - added an 'accordion' option to squeeze cores with highly irregularly
    dated sections (e.g., with a few cm of high-res Pb-210 data combined
    with much longer but lower-resolution C-14 data). Cores can be
    'squeezed' and 'stretched' - please check the documentation of the
    new 'stretch' function. Use with great care
  - added an option to agedepth called plotatthesedepths, to enable
    plotting alternative depths (e.g., after using the compress
    function), for example agedepth(depths=1:100,
    plotatthesedepths=1.5*(1:100), d.max=200)
  - the upper panels of the accumulation rate, memory, hiatus size, phi
    and supported (where relevant) gain options to adapt their x/y axis
    limits
  - renamed the options MinAge and MaxAge to the hopefully less
    confusing youngest.age and oldest.age
  - added an option save.ages=TRUE to write a file *_elbowages.txt with
    the ages for all elbows
  - added function set.initvals() to allow running with preset initial
    MCMC points
  - replaced sep=paste0(sep, "\t") in read_write.R line 304 with sep=sep
  - new options older.than and younger.than, to use older-than or
    younger-than dates (e.g. for radiocarbon dates at the dating limit)
  - accrate.age and accrate.depth now keep any NA values by default
    (they can be removed using the option na.rm=TRUE)

                 Changes in version 3.0.0 (2022-12-22)                  

  - accrates.depth.ghost() and accrate.age.ghost() now invisibly return
    the ranges, medians and means for each depth resp. age for
    subsequent use, e.g., tmp <- accrates.depth.ghost(); head(tmp)
  - MCMC iterations are now stored in the .out files, irrespective of
    whether they were accepted or rejected
  - ssize is now much more predictable (if there are more rows in the
    output file than set by ssize, rbacon keeps only the last n=ssize
    rows)
  - files are read and written faster (assuming that the data.table R
    package is installed and loaded, which can be a problem on Macs)
  - corrected the help description for Bacon.d.Age() with thanks to
    Henningte
  - the length of the ages output of accrate.age() is now the same even
    if there are NAs in the output (with thanks to Henningte)
  - corrected (hopefully) a bug in read.dets related to logical
    comparisons with variable lengths causing errors in R>=4.2 (with
    thanks to Nick McKay for reporting)
  - accrate.age.ghost gains a kcal option
  - repaired warning message about lengths of logical tests
  - now links to rintcal package (renamed from IntCal)
  - better Plum plots
  - runs can now be interrupted by pressing CTRL+c

                 Changes in version 2.5.8 (2022-03-29)                  

  - some minor updates to the vignettes
  - corrected a bug in input.cpp which caused a gcc warning in debian

                 Changes in version 2.5.7 (2021-08-12)                  

  - added an option to agedepth to plot date labels (plot.labels)
  - added vignettes
  - if ask=FALSE, Bacon now does not ask before writing a new folder (if
    so required)

                 Changes in version 2.5.6 (2021-05-28)                  

  - removed closeAllConnections() as requested by Kurt Hornik (CRAN)
  - adapted agedepth() for further Plum corrections
  - corrected the behaviour of the dark option in agedepth(),
    accrate.depth.ghost(), accrate.age.ghost(), flux.age.ghost() and
    proxy.ghost()
  - renamed rplum's option radon.case to ra.case
  - added plot.median to flux.age.ghost() and accrate.age.ghost()
  - repaired BCAD in flux.age.ghost()
  - removed the error message that acc.shape cannot be equal to acc.mean
    (shouldn't be a problem any more)

                 Changes in version 2.5.5 (2021-05-06)                  

  - removed revdep folder which caused issues when submitting to CRAN

                        Changes in version 2.5.4                        

  - further separation of rplum and rbacon
  - the functions thinner and scissors now deal with Plum runs
  - repaired bugs in accrate.age and accrate.age.ghost related to the
    option BCAD

                 Changes in version 2.5.3 (2021-03-29)                  

  - corrected a bug where postbomb dates could not be plotted owing to
    wrong by sign
  - further improvements to how agedepth deals with plot margins
  - corrected error when d.min was set

                 Changes in version 2.5.2 (2021-03-11)                  

  - optimised accrate.age.ghost()
  - added options to modify the margins of the individual panels in the
    agedepth plot: mar.left, mar.middle, mar.right, mar.main
  - added an option to plot the tickmarks and labels on the vertical
    axes of the prior panels: prior.ticks="s" (default "n")
  - removed the panels option in agedepth() as it didn't work as
    expected and is better done outside rbacon functions (e.g.,
    layout(1); agedepth(model.only=T))
  - added median curves for accrate.age.ghost and accrate.depth.ghost
    (as means can be influenced by extreme values)

                 Changes in version 2.5.1 (2021-02-10)                  

  - adapted the default prior for memory to 0.5 (mean) and 10
    (strength), to repair a bug with the original bacon c++ code. This
    default should work with most cores and give similar results to the
    previous settings for the memory prior
  - updated c/c++ code (as used in version 2.4.1 with some minor
    additional updates)
  - pMC.age and other IntCal functions should now load as expected
    (without having to specify, e.g., IntCal::pMC.age)
  - the heights of the calibrated distributions should now scale better
    according to how precise they are
  - the add.dates function now handles postbomb dates. It can also store
    the calibrated information using, e.g., tmp <-
    add.dates(2450,30,20); tmp
  - the greyscale age-depth graph is now more easily exported to
    external graphics editors, because areas with very low probabilities
    are now left empty (instead of plotted as white)
  - corrected a bug where ages above d.min received incorrect ages
  - added an option prior.ticks to show tickmarks and values on the
    vertical axes of the panels that show the prior distributions. These
    are not drawn by default, as they don't provide much information and
    clutter the graphs
  - added new options title.size and prior.fontsize for the size of the
    fonts of the core's title and the red information on settings in the
    top panels, respectively
  - repaired the functions accrate.depth(), accrate.age(),
    accrate.depth.ghost() and accrate.age.ghost()
  - agemodel.it now treats the upper depth of a core as expected

                 Changes in version 2.5.0 (2020-10-28)                  

  - updated src/kernel.cpp and src/twalk.h, to repair a bug in one of
    the moves ('hop'). This means we can now add the updated MCMC code
    of version 2.4.0 again and accommodate code to run 210Pb-dated cores
    (via the package rplum)
  - radiocarbon calibration curves are now loaded from the imported
    IntCal R package, and have been removed from the rbacon package to
    save space and remove duplication
  - added option rgb.scale to draw shades of other colours than grey,
    e.g. red: rgb.scales(1,0,0), for the functions agedepth,
    accrate.depth.ghost, accrate.age.ghost, proxy.ghost and
    flux.age.ghost (based on an idea kindly provided by Oliver Wilson).
  - related to rgb.scale, the resolution of the colours has been renamed
    from grey.res to rgb.res
  - added option 'add' to add proxy.ghost graphs to existing plots
    (based on an idea by Oliver Wilson)
  - repaired bug with greyscales accrate.age.ghost
  - if the file with the dates has been modified more recently than a
    loaded run (e.g., dates could have been added, removed or changed),
    then a warning is now given that Bacon.cleanup should be ran
  - added a new function Bacon.d.Age to provide the depths belonging to
    a specific modelled age (kindly contributed by Timon Netzel)
  - depth units are now handled better by the agedepth function
  - new option accept.suggestions, which automatically accepts
    suggestions regarding acc.rate and thick. Use with caution (this
    option was kindly suggested by Quinn Asena)
  - by default, a section is now added below the bottom-most dated
    depth, in order to ensure that the this depth is always taken into
    account. Defaults to add.bottom=TRUE.
  - the calibrated distributions should now be of the same size again,
    so that more precise dates peak more than less precise ones
    (suggested by Tiffany Napier).

                 Changes in version 2.4.3 (2020-08-10)                  

  - replaced 'cat' with 'message' or 'warning' where possible
  - updated to the IntCal20 calibration curves (Reimer et al., 2020)

                 Changes in version 2.4.2 (2020-04-21)                  

  - reverted the c/c++ code back to that of version 2.3.9.1, owing to
    problems with the code introduced in version 2.4.0 (posteriors of
    memory and age-model are apparently too wide)
  - repaired bug that caused an error when using slumps or boundaries
  - enhanced behaviour of rotate.axes option

                 Changes in version 2.4.1 (2020-03-15)                  

  - updated the code to deal with changes in how base-R deals with c()
    in loops, as suggested by Martin Maechler's e-mail 29 February 2020

                 Changes in version 2.4.0 (2020-02-07)                  

  - the MCMC code has been updated to remove bugs and to accommodate
    runs with the upcoming 'rplum' package for 210Pb dating
  - added functions which are required to run the 'rplum' package
    (although 'rbacon' does not require 'rplum' to be installed)

                Changes in version 2.3.9.1 (2019-07-03)                 

  - added a new option calheight, which acts as a multiplier for the
    relative height of non-14C dates
  - set default for y-axis to have no space added after the extreme
    values (yaxs="i"); x-axis has some space added by default (xaxs="r")
  - added a bit of space to d.max and d.min in the main age-depth graph,
    to accommodate age blobs
  - new option kcal, which gives tick marks every 1,000 cal years
    (default kcal=FALSE)
  - corrected an error when running a core with 4 columns in the .csv
    file and cc=0
  - depth.unit and age.unit now work correctly when provided as options
    in Bacon or agedepth
  - corrected a bug where thickness (dC) was sometimes internally set to
    wrong values
  - redid hiatuses: If a core has one or more hiatuses, then variables
    slopes.above and slopes.below are made for each hiatus, and used
    internally to adapt ages and accumulation rates for each depth below
    and above a hiatus within a section containing a hiatus.
  - slumps, hiatuses and boundaries have gone through a thorough check
    and should now work better than they did before. Reports of weird
    behaviour welcome!
  - renamed info$d to info$elbows (internal; for better consistency with
    the naming of parameters within the Bacon paper)

                 Changes in version 2.3.8 (2019-05-25)                  

  - repaired a bug in cal.h which prevented the postbomb curve
    postbomb_SH3 from being used
  - repaired bug where the prior for the accumulation rate would not
    always be drawn entirely
  - Bacon.hist now takes alternative values for prob into account (e.g.,
    prob=.68)
  - the agedepth function now deals better with d.min and d.max values
  - colours of cal BP dates now as expected when cc=0 is provided as
    Bacon option
  - the fit of the dates to the age-model is now reported correctly also
    when BCAD=TRUE
  - date distributions should now plot as expected over a wider range of
    values
  - new option acc.lab to provide alternative label for the accumulation
    rate axis (top-middle panel of the main agedepth graph)
  - when provided, d.max or d.min are now dealt with better if extra
    columns are provided for dR/dSTD and/or t.a/t.b in the core's .csv
    file
  - new options depth.unit (default 'cm') and age.unit (default 'yr'),
    deprecating the previous poorly named option 'unit' which defaulted
    to 'cm'. So can now also deal with, e.g., 'Ma' and 'km'
  - replaced occurrences of yr with the more generic unit of age
    (deprecate yr.min, yr.max, MinYr, MaxYr)
  - when Bacon asks for confirmation to run a core (Y/n), the user can
    now simply press Enter instead of having to type y first. Similarly,
    by default suggestions to adapt the prior accumulation rate are not
    accepted (y/N)
  - enhanced drawing of very precise ages (e.g., 1 yr)
  - Bacon now stops if there are less than 2 sections between
    neighbouring hiatuses
  - a warning is now given if acc.shape <1 (since this results in
    weirdly shaped gamma prior distributions)
  - an error is thrown when the core's .csv file has 'orphan' commas
    (can happen if the file was made in a spreadsheet program - check in
    a plain-text editor)
  - add.dates now plots better when mirror=FALSE
  - more consistent error messages

                 Changes in version 2.3.7 (2019-02-13)                  

  - adapted cpp code to allow for more than 10 hiatuses/boundaries (now
    limited to 50)
  - corrected bug causing a warning when a hiatus was set with multiple
    acc.mean priors provided
  - now ensures that hiatus or boundary depths are in the correct order
    (ascending in depth)

                 Changes in version 2.3.6 (2019-01-17)                  

  - further enhancements to memory usage in MCMC calculations (bacon.h)

                 Changes in version 2.3.5 (2018-12-19)                  

  - added function agemodel.it to extract single iterations of a Bacon
    age-depth model
  - added functions clam2bacon and bacon2clam to translate Bacon dates
    files into clam files et vice versa (inspired by a suggestion from
    Dewey Dunnington)
  - corrected behaviour of boundary and hiatus (especially if together
    with slumps)
  - iterations with age reversals across a hiatus are now removed
  - removed closeAllConnections (suggested by Dewey Dunnington)
  - added option to change the field separator to mix.curves (suggested
    by Thomas Dye)
  - MinYr now defaults to the current year (1950 -
    as.integer(format(Sys.time(), "%Y")))
  - added option in the scissors function to remove a specific range of
    iterations (e.g., iterations 400 to 800, or the first/last 300)
  - produced separate R files for groups of functions
  - Bacon now stops if it finds 6 columns with unexpected names in the
    .csv file. If provided with a delta.R column, Bacon expects a
    delta.STD column as well.
  - added an option dates.col to colour sets of dates (suggestion by
    Greg Cooper)
  - enhancements in bacon.h of MCMC calculations and memory usage

                 Changes in version 2.3.4 (2018-04-15)                  

  - faster drawing of greyscale plots (though still slower yet better
    than in version 2.3.1.1 and before)
  - added progress bar to functions that can be slow
  - repaired a bug in calculating how many dates fall within the model
    range
  - delta.R is now accepted as a header for the dates file

                 Changes in version 2.3.3 (2018-02-20)                  

  - added an option to include slumps (sort of - more testing still
    welcome). Example: Bacon(slump=c(50, 52, 60, 70)) for two slumps
    between 50-52 and 60-70 cm depth
  - date-files with .csv.txt extensions are now renamed to .csv (and
    informing us that it did so)
  - default darkness of age-depth greyscale now adapts to a ratio
    between most and least precise sections (so that very imprecise
    sections still show some grey)
  - repaired option depths (e.g., Bacon(depths=0:100))
  - repaired height of prior distribution axes
  - repaired Baconvergence()
  - added a commentary after each run, mentioning the proportion of
    dates that lie within the age-depth model's range (some sort of
    'agreement')

                 Changes in version 2.3.2 (2018-02-04)                  

  - added option boundary, which sets hiatus length to (close to) 0.
    This leaves the hiatus functionality more or less unchanged, and
    should cause less confusion with setting hiatus.depths even if no
    hiatus is desired.
  - enhanced plotting and age calculation of depths close to hiatuses or
    boundaries.
  - ensured more predictable behaviour if R is started in a non-writable
    directory (e.g. plain, non-Rstudio R on Windows).
  - added confidence ranges to accrate.age.ghost and
    accrate.depth.ghost.
  - enhanced calculation of mean and median (now based on age
    distribution, not on a derived histogram).
  - corrected behaviour of title.location.
  - corrected many sundry bugs related to plotting, especially with
    hiatuses or with BCAD=TRUE.
  - added a NEWS.md file to track changes to the package.

                Changes in version 2.3.1.1 (2017-12-15)                 

  - now a CRAN R package (not called bacon since that name was already
    taken).
  - default core directory now Bacon_runs. Other directories can be
    given, for more flexibility in workflows of users.
  - calibration curves can be put in a user-specified directory ccdir
    (hidden by default).
  - new function copyCalibrationCurve() to copy calibration curves into
    an R's session.
  - renamed several options to be more consistent, d.R and d.STD now
    named delta.R and delta.STD.
  - can now provide depths to be calculated as a variable, as
    alternative to using a file with depths.
  - added option to not plot x or y axis (xaxt, yaxt).
  - added option to not plot the date distributions mirrored.
  - new function Baconvergence() to test for good mixing of MCMC runs.
  - renamed weighted means of age estimates to means.
  - updated documentation.
  - renamed functions flux.age, plot.accrate.age and plot.accrate.depth
    to flux.age.ghost, accrate.age.ghost and accrate.depth.ghost,
    respectively.
  - BCAD dealt with more correctly.
  - repaired many sundry bugs.

                         Changes in version 2.2                         

  - updated to 14C calibration curves IntCal13, Marine13 and SHCal13.
  - changed .hpd to _ages.txt since many users get tricked by the
    extension.
  - changed from .dat files to .csv files as these are more documented
    and easier to open and edit by users.
  - separator for .csv file can be adapted.
  - renamed res to hopefully more intuitive thick (thickness of
    sections)
  - added d.R and d.STD
  - Bacon.hist gives 95% ranges, mid and wmean, and reads from a file
    instead of from the command line.
  - added options to change axis limits, orientation and rotation.
  - BCAD introduced, though not yet working entirely as expected.
  - different prior for acc.mean suggested if initial estimates indicate
    that this would be beneficial.
  - introduced a settings file.
  - removed calc.every (gave problems with long cores).
  - killed hist bug that assumed integers.
  - language cleanup of cpp files.
  - added option to remove unnecessary files after a run.
  - added option in agedepth to only plot the age-model (so not the
    upper panels).
  - many bug fixes in the Bacon.R and underlying C/C++ codes
