Package 'rplum'

Name of the core, given using quotes. Defaults to one of the cores provided with rplum, core="HP1C" also reported by Aquino-Lopez et al. (2018). Also available is LL14, a core kindly provided by Dr Lysanna Anderson (USGS). LL14 has ra-226 data (so can be run with ra.case=1 or ra.case=2, see below), and also has additional C-14 and cal BP data (these can be added using otherdates="LL14_14C.csv"). The original LL14 core has more 14C data than provided here (for reasons of brevity). 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 Plum_runs/MyCore/MyCore.csv. Then run Plum as follows: Plum("MyCore"). Note that for Pb-210 data, the depth in the .csv should be the bottom of the slice, not the mid-point. (For any non-Pb data, depths are the midpoints of their slices). Also make sure that the thickness and density are given correctly for each Pb-210 data point.

Plum will divide the core into sections of equal thickness specified by thick (default thick=1).

Name of (optional) file with radiocarbon dates. This file should have the same format as the one used for rbacon. For example, Bacon("LL14", otherdates="LL14_14C.csv").

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='Plum_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.

Shape parameter of the prior gamma distribution used for the influx of Pb-210 to the sediment, default phi.shape=2.

Mean parameter of the prior gamma distribution used for the influx of Pb-210 to the sediment, default phi.mean=50.

Shape parameter of the prior gamma distribution used for the supported Pb-210 to the sediment, default s.shape=5.

Mean parameter of the prior gamma distribution used for the supported Pb-210 to the sediment, default s.mean=10.

Parameter used to limit the chronologies described in Aquino-Lopez et al. (2018) for the minimum distinguishable unsupported activity; default Al=0.1.

Date (in calendar years, e.g., AD 2023) at which the core was measured for Pb-120. This date will be used as a surface date and is assumed to have no uncertainty. If the date is not provided (in the .csv file or as date.sample), Plum will ask for it.

This value will delete n.supp data points from the deepest part of the core, and these points will then be used exclusively to estimate the supported activity. If this option is used, a constant supported Pb-210 will be assumed, n.supp=-1.

Whether or not to remove the tail measurements when plotting. Sometimes automated removal might go wrong, or additional dates exist further down, so then this option can be used to avoid removing the tail 210Pb measurements. Is set to FALSE if there are non-210Pb data further down the core.

How to use radium-226 measurements if they are provided in the core's .csv file. 1 = assume constant radium, 2 = assume varying radium and use the radium measurements as individual estimates of supported Pb-210. If no radium measurements are present, use ra.case=0.

This variable indicates whether total Pb-210 is expressed in Bq/kg (default; Bqkg=TRUE) or dpm/g if set to FALSE.

Seed used for C++ executions; if it is not assigned then the seed is set by system. Default seed=NA.

Confidence interval to report. This should lie between 0 and 1, default prob=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).

Depth intervals at which ages are calculated. Defaults to d.by=1.

By default, Plum will calculate the ages for the depths d.min to d.max in steps of d.by. If depths.file=TRUE, Plum 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, Plum 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=10 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., Plum(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.

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.

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 Plum 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).

Use an alternative curve (3 columns: cal BP, 14C age, error, separated by white spaces and saved as a plain-text file). See cc.dir.

Directory where the calibration curves for C14 dates cc are located. By default cc.dir="" since they are loaded into R's memory. For example, use cc.dir="." to choose current working directory, or cc.dir="Curves/" to choose sub-folder Curves/. Note that all calibration curves should reside in the same directory. If you want to add a custom-built curve, put it in the directory where the default calibration curves are (probably list.files(paste0(.libPaths(), "/IntCal/extdata/"))). Alternatively produce a new folder, and add your curve as well as the default calibration curves there (cc1, cc2 and cc3; e.g., write.table(copyCalibrationCurve(1), "./3Col_intcal20.14C", sep="\t").)

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

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-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.

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.

By default, Plum 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, Plum will suggest to change the prior. Also, if the length of the core would cause too few or too many sections with the default settings, Plum will suggest an alternative section thickness thick, and it will suggest approaches to estimating supported Pb-120. 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.

Plum 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.

Plum 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 Plum.cleanup().

By default Plum 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 Plum 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.

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 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 upper-left corner of age-model graph) appears problematic.

Starting years for the MCMC iterations.

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

Deprecated - use youngest.age instead.

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

Deprecated - use oldest.age instead.

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

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

Rounding of calendar years. Defaults to 1 decimal.

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

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 (works only for non-210Pb data), 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 'otherdates' .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 (works only for non-210Pb data), 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 'otherdates' .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, ending in "_elbowages.txt".

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

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

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

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