SuessR: Calculate Suess and Laws corrections for stable carbon...
In ctclark/SuessR: Suess and Laws Corrections for Marine Stable Carbon Isotope Data

Description Usage Arguments Details Value References Examples

View source: R/SuessR_Package.R

Generates region-specific Suess, Laws, and net (Suess + Laws) corrections for stable carbon isotope data δ¹³C data input by the user. The net correction is then used to calculate the corrected δ¹³C data, which are supplied in the output. This function is specifically for data from regions currently built into SuessR ("Bering", "Aleutians","Gulf of Alaska", and "Subpolar North Atlantic", as of Version 0.1.3). Built-in regions

1	SuessR(data, correct.to = 1850)

`data`	A matrix or data frame including columns containing sample ID ('id'), year of sample collection ('year'), region of sample collection ('region'), and uncorrected δ¹³C data ('d13c').
`correct.to`	The year to which the δ¹³C data will be corrected. Defaults to 1850 (Industrial Revolution).

The SuessR() function uses the year and region of sample collection to calculate Suess, Laws, and net (Suess + Laws) corrections for δ¹³C data from marine organisms. The Suess Correction represents the change in δ¹³C values of dissolved inorganic carbon (DIC) in the surface ocean, and is calculated using an exponential function, calibrated to the global decline DIC δ¹³C values. Surface waters in different regions exhibit varying rates of CO₂ uptake from the atmosphere as a result of differing water mass properties and residence time at the surface. Thus, a region-specific modifier has been calculated from empirical observations of changes in DIC δ¹³C values through time and is applied to each region. The Laws correction accounts for changes in stable carbon isotope fractionation during CO₂ uptake and photosynthesis by phytoplankton, and is impacted by changes in aqueous CO₂ concentrations, temperature, and salinity, as well as community growth rates, average cell diameter, average organic carbon content of phytoplankton cells, permeability of the phytoplankton plasmalemma to CO₂, and the ratio of net diffusional loss of CO₂ to carbon fixation. Historic observations and reconstructions of atmospheric CO₂ concentrations, sea surface temperature, and sea surface salinity are used to make these calculations. See references for more details.

This function allows users to correct their data to a specific year, using the 'correct.to' argument. This argument defaults to AD1850, which represents onset of the Industrial Revolution and the initiation of the large-scale combustion of fossil fuels that created the Suess Effect. Correcting data to 1850 allows them to be compared to data from any samples collected during or before 1850 (including archaeological samples), as well as to any other samples Suess corrected to the year 1850. Users examining contemporary datasets may wish to correct their data to another year. For example, a user examining a dataset of δ¹³C data spanning the years 1970-2010 might choose to correct all their data back to the year 1970, to correct the older samples forward to 2010, or to correct all the samples to 1990, the middle of the time series. In any of these scenarios, corrected data would be comparable to one another. When choosing a value for 'correct.to' consideration should be given to the comparability of the user's data to existing data sets, clarity of presentation of results (i.e., clear statements of the year to which the data were corrected), and reproducibility of results (i.e., presentation of both uncorrected and corrected data so future users can repeat analyses or correct the raw data to another year).

The output of this function is a data frame that includes the sample ID ('id'), year ('year'), uncorrected δ¹³C ('d13c.uncor'), Laws correction ('Laws.cor'), Suess Correction ('Suess.cor'), net correction ('net.cor'), and corrected δ¹³C ('d13c.cor') for each sample. The corrected δ¹³C data is equal to the uncorrected δ¹³C data plus the net correction. The units for all values are the standard 'per mil' used for δ¹³C data.

Clark, C.T., M.R. Cape, M.D. Shapley, F.J. Mueter, B.P. Finney, and N. Misarti. (In Prep) SuessR: Regional Suess and Laws corrections for δ¹³C from marine organisms.

Clark, C.T., L. Horstmann, A. de Vernal, A.M. Jensen, and N. Misarti. (2019) Pacific walrus diet across 4000 years of changing sea ice conditions. Quaternary Research, 1-17.

Misarti, N., B. Finney, H. Maschner, and M.J. Wooller. (2009) Changes in northeast Pacific marine ecosystems over the last 4500 years: evidence from stable isotope analysis of bone collagen from archaeological middens. The Holocene, 19:8. 1139-1151.

example.data <- data.frame(id = c("Sample 1", "Sample 2", "Sample 3", "Sample 4",
                                  "Sample 5", "Sample 6", "Sample 7", "Sample 8"),
                           year = c(2017, 2017, 2017, 2017, 1977, 1977, 1977, 1977),
                           d13c = c(-12, -12, -12, -12, -12, -12, -12, -12),
                           region = c("Bering Sea", "Aleutian Islands",
                                      "Gulf of Alaska", "Subpolar North Atlantic",
                                      "Bering Sea", "Aleutian Islands",
                                      "Gulf of Alaska", "Subpolar North Atlantic"))

SuessR(data = example.data)