AccumC: Accum(ulate) C(arbon)

In bogfossil/AccumC-package: A package for estimating carbon accumulation in peatlands

Description

AccumC is a method for estimating the rate of carbon accumulation in peatlands, especially those where many reworked macrofossils have been dated.

Usage

AccumC(corename = NA, bin_size = NA, age_bw = NA, kernel = "r", calcurve = intcal13, it_power = 17, pct_C = 0.48)

Arguments

x	a data.frame where names(x) == c("labcode", "depth", "bp", "std", "afbd")
corename	The case-sensitive name of the directory and filenames i.e. "corename/corename.dat" and "corename/corename.afbd"
bin_size	size of age bandwith in years. If NA (default), it is set automatically.
age_bw	size of age bandwith in years. If NA (default), it is set automatically.
kernel	kernel shape for PDF smoothing, as in stats::density()
calcurve	The radiocarbon calibration curve to be used. Built-in choices are intcal13 or shcal13, but any data.frame with columns cal and bp can be used.
it_power	The Monte Carlo simulation of accumulation rates will be run 2^it_power times.
pct_C	Fraction carbon in ash-free bulk density. A default value of 0.48 is used. Replace this value with 1 if fraction carbon is used instead of ash-free bulk density.

Details

If x is used, corename is merely a text string that is used as the name of the core, but if x is not specified, corename is assumed to be the name of a folder inside R's working directory that contains a comma-separated file called "corename.dat".

Value

A list is returned with the following components:

$metadata	settings and descriptive information about the dataset
$calibrations	a data.frame with columns labcodes, depths, and maxLikeAge
$rates	a data.frame with the age of the midpoint, top, and bottom of each depth bin, its sediment accumulation rate,
$total_prob	a list of two vectors describing the PDF of the age of sediment in the core
$age_mid_quantiles	Quantiles of the probable age of depth bin midpoints, where p = c(0, 0.25, 0.5, 0.75, 1)
$age_test	an array with the results of the Monte Carlo simulation of the age of the top and bottom of each depth bin.
$rate_test	an array with the results of the Monte Carlo simulation of the sedimentation rate of each depth bin.
$crate_test	an array with the results of the Monte Carlo simulation of the carbon accumulation rate of each depth bin.
$all_pdfs	a list containing the PDF of the calibrated age of each radiocarbon date
$age_quantiles	Quantiles of the probable age of depth ends, where p = c(0, 0.25, 0.5, 0.75, 1)
$rate_quantiles	Quantiles of the probable carbon accumulation rate of each depth bin, where p = c(0, 0.25, 0.5, 0.75, 1)
$binned_pdfs	the PDF of the age of each depth bin

Author(s)

Jonathan E. Nichols
Lamont-Doherty Earth Observatory
Columbia University

[e-mail]

References

Nichols et al., 2016

See Also

plot.AccumC

Examples

data(imv)
x <- AccumC(imv)
plot(x, bigplot = F)

bogfossil/AccumC-package documentation built on May 12, 2019, 11:32 p.m.