COMPYCALC is a R script for EC yield extrapolation and charring correction. The script uses the the raw data output from a thermo-optical OC/EC analyzer (Model 5L, Sunset Laboratory Inc., OR, United States) running the Swiss_3S protocol for OC/EC separation developed by Zhang et al. (2012) for EC yield and charring calculation. Using F14C(EC) values measured by accelerator mass spectrometry (AMS) and calculated F14OC values, the script performs the EC yield extrapolation to 100% EC yield and a charring correction to 0% charring for F14C(EC) values.
To use the run COMPYCALC program, follow the steps written in the comment section of the compycalc.R file. This is the file you want to run, the other files in the subfolder (zsrc) are linked to this script.
In the first section, you are asked to set the working directory, either with the command setwd() or by going to Session → Set Working Directory → To Source File Location if you are using R Studio.
In the second step, you are ask to add your Sunset raw files in folders to the working directory folder. Obviously, you can also do it the other way around by adding the compycalc.R script to the folder where your data is. Please be aware that the script will take the last digit of each folder for naming, so make sure that you name your folders accordingly.
OPTION: add a EC, TC or Swiss_4S run raw data file recorded with the same Sunset OC/EC analyzer oven conditions than your samples. Add the file into the zsrc folder and rename it to custom_cooldown.csv. This is to correct for the opacity of the Sunset OC/EC analyzer to accurately calcualte the EC yield. This option is highly recommended. Otherwise, the default custom_cooldown.csv file will be used, which is a generic cooldown file reflecting a new analyzer oven.
Note: delete all unnecessary files (including hidden files) in the folder you want to run COMPYCALC. Keep only the Sunset raw file folders as described above, the compycalc.R script, the zsrc folder containing additional scripts and the cooldown data.
Last but not least you have to add the F14C(EC) and F14C(OC) raw data with uncertainties as separate csv files. F14C(EC) contains the measured F14C(EC) values in the first column and measurement uncertainties in the second column. For OC you do the same: F14C(OC) contains the calculated F14C(OC) values in the first column and uncertainties in the second column. Note that the files need to be in sample order. The csv files must be in the working directory, i.e. the folder where your compycalc.R file is.
Finally, you are ready to run the COMPYCALC script.
As an output, you will get:
- Each folder with Sunset measurement files will get five output files:
- calc-summary-plots.pdf
- clean-results.csv
- mean-results.csv
- raw-results.csv
- stats.csv
- The working directory folder will get two files:
- mean-summary-with-F14C.csv
- F14C-and-EC-yield-and-charring-summary.pdf
COMPYCALC (COMprehensive Yield CALCulation) consists of three subscripts for data input and output, EC yield and charring, as well as an extrapolation of the F14C(EC) values to 100% EC yield. For each sample, the OC/EC analyzer raw data files containing the laser transmission signal for each OC removal run need to be in a designated subfolder. Additionally, the script requires the uncorrected F14C(EC) and F14C(OC) data in separate files (csv format) in the main folder. The data input and output script loads the OC/EC analyzer raw data files for each sample folder and initiates the calculation with the EC yield and charring script. The results written in each sample folder is then read by the main script and forwarded to the second calculation script for the extrapolation to 100% EC yield. Finally, the F14C(EC) value extrapolated to 100% EC yield is corrected for charring in the main script, as this should be regarded as an OC contamination of the measured EC. After all calculations, a summary data file (csv) with overall EC yield, the charring contribution for each OC removal step (S1, S2, S3), the total charring contribution as well as the raw F14C(EC), F14C(EC) extrapolated to 100% EC yield, and F14C(EC) extrapolated to 100% EC yield and corrected for charring is generated as an output. Additionally, a summary pdf is generated with plots for all F14C results, EC yields, and charring for each step (S1, S2, S3).
This tool was written by Martin Rauber and Gary Salazar for LARA, the Laboratory for the Analysis of Radiocarbon with AMS at the University of Bern. Please get in touch for any bug fixes and suggestions!
COMPYCALC is released under the MIT License.