/Aragonite_clumped

Repo containing all the R code to do the data processing and create figures as descibed in the accompanying paper on the clumped isotope composition of lab-grown aragonitic Arctica islandica shells

Primary LanguageRMIT LicenseMIT

Aragonite_clumped

This repository serves as a supplement to the paper titled "Temperature dependence of clumped isotopes (∆47) in aragonite", which is currently in preparation. The paper descibes clumped isotope analyses on aragonitic shells of lab-grown bivalves and discusses the implications for using clumped isotope analyses as a proxy for temperature reconstruction. The repository contains R code to do the data processing and create figures as descibed in the accompanying paper on the clumped isotope composition of lab-grown aragonitic Arctica islandica shells. This repository contains 7 R script files and 1 raw data file.

Dependencies

R files list dependencies required for their operations at the top. The following packages are used in this repository:

Running

Download or git clone the directory and source/load the various R scripts.

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File overview

  • 01_Aragonite_compilation.csv is the raw data file. It contains information about all clumped isotope results (D47) used in the paper. The file contains multiple headers which are used in the scripts to group data and calculate statistics

  • 02_Data_processing.r is the R script file that describes the steps taken to process the raw clumped data in preparation for plotting. The data processing workflow includes:

    • Grouping of the data by specimen ("Aisstats") and per temperature ID ("D47stats").
    • Expandeding uncertainties on measurements by bootstrapping (N = 10^5; see "violin_data")
    • A series of regressions fit through the data.
    • Summarizing statistics of these regressions
    • Calculating the residuals of the data relative to the regressions
    • Calculating the mean D47 and temperature offsets of the full Arctica islandica dataset with reference to pre established clumped isotope regressions

  • 03_Average_error_propagation.r is a script descibing functions used to propagate errors on measurements through calculations of group averages and standard deviations.

  • 04_Temperature_offset.r is a script describing a function for calculating the temperature offset of data from a D47-temperature regression, used to estimate the temperature bias that would result from using the regression.

  • 05_A_islandica_plot.r is a script describing how Figure 1 in the manuscript is created (plotting Arctica islandica data together with regression results)

  • 06_Full_aragonite_plot.r is a script describing the plotting of Figure 2 in the manuscript (showing the full aragonite dataset together with regression results)

  • 07_Aragonite_residual_plot.r is a script describing how Figure 3 in the manuscript is plotted (showing the residuals of the data relative to the regression results)

  • 08_Calibration_offset_plot.r is a script describing the plotting of Figure 4 in the manuscript (showing the offset of the full Arctica islandica dataset from the clumped isotope temperature calibrations of Anderson et al. and Meinicke et al.)