Multi-isotope approaches to Middle Palaeolithic palaeoenvironments - an example from Axlor (Bizkaia, Spain)

This repository contains data, analysis code, and manuscript and supplementary RMarkdown files for:

Pederzani, S., Britton, K., Jones, J., Agudo Pérez, L., Geiling, J. M., Marín-Arroyo, A. B. (2023). Late Pleistocene Neanderthal exploitation of stable, mosaic ecosystems in northern Iberia shown by multi-isotope evidence. Quaternary Research.

An overview of all files can be found below. Variable names are explained in an additional codebook file (AXL_codebook.xls).

The content of this repository was made possible thanks to funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 818299) for the SUBSILIENCE project (https://www.subsilience.eu/).

Prerequisites

In order to be able to run the code, you will need to have an up-to-date version of R and RStudio or pandoc installed on your computer and a few CRAN packages (see below).

All code and analyses were run using R version 4.2.0 (R Core Team 2020) on a Windows 10 operating system.

Install packages

install.packages(c("ggplot2", "dplyr", "tidyr", "cowplot", "captioner", "wesanderson", "knitr", "flextable", "stringr", "officer", "rstatix", "scales", "magick", "patchwork", "ggpubr", "Metrics", "matrixcalc"))

The following versions of these packages were used:

matrixcalc_1.0-5
Metrics_0.1.4
ggpubr_0.4.0
patchwork_1.1.1
magick_2.7.3
scales_1.2.0
rstatix_0.7.0
officer_0.4.2
stringr_1.4.0
flextable_0.7.0
knitr_1.39
wesanderson_0.3.6
captioner_2.2.3
cowplot_1.1.1
tidyr_1.2.0
dplyr_1.0.9
ggplot2_3.3.6

Files and code

The repository contains three folder containing relevant files for conducting the Passey et al. (2005) inverse modelling procedure (run_inverse_model), for producing palaeotemperature estimates (reconstruct_temperature), and for generating the article manuscript and supplementary information and all analyses contained therein (generate_article).

Note that all R scripts and RMarkdown files use relative paths in reference to the location of each file to access data files contained in various repository folders and rely on the folder structure being preserved in the way that it is presented here. To exectute the R scripts, the working directory should be set to the source file location.

In the following each file and its purpose is described. Please refer to the file AXL_codebook.xls for an explanation of the variable names used in the data files.

Inverse modelling

run_inverse_model.r

• R script to execute the inverse modelling procedure. Please refer to the original publications by Passey et al. (2005) and Fraser et al. (2021) for detailed explanations of model equations and parameters. Input parameters need to be changed as needed and the script is run with adjusted parameters once for each specimen of interest. The parameters that were used in this study for each specimen are documented in the model report files contained in run_inverse_model/output.

make_model_report.Rmd

• RMarkdown template called by run_inverse_model.R to print model report html files

run_inverse_model/input

*Tooth Name*_inverse_model_input.csv

• csv files containing sequential d18O data for each analysed tooth, as well as predicted d18Ophos trials from our prediction simulations (see main manuscript methods section for details). These files are structured to serve as the stable isotope input data for run_inverse_model.r.

run_inverse_model/functions

Emeas.R

• R script containing the Emeasfun function called by the run_inverse_model.r script. This is equivalent to the Emeas portion of the codes provided by Passey et al. (2005)

mSolv1.R

• R script containing the PasseyInverse function called by the run_inverse_model.r script. This is equivalent to the mSolv portion of the codes provided by Passey et al. (2005) and has been adapted from the R translation of the the original Passey Matlab codes that has been published by Fraser et al. (2021). The model portions of this code are identical to those provided by Fraser, but have been updated with increased commenting and changed slightly so they can be called by an external script and output can be evaluated in a more automated way.

run_inverse_model/output

AXL_inverse_model_output_all_plot.png

• Plot of the inverse model outcome of all specimens analysed

AXL_inverse_model_out_all.csv

• output of inverse model for all teeth aggregated into a single output file

AXL_inverse_model_output_extrema.csv

• summer peak and winter trough values extracted from the inverse model outcomes for all analysed teeth

*Tooth Name*_inverse_model_output.csv

• inverse model outcome files for all specimens. These files are generated by run_inverse_model.r

*Tooth Name*_inverse_model_report.html

• inverse model report files for all specimens. These files document the input parameters that were used to during the excution of run_inverse_model.r for the relevant specimen. These files are automatically generated by run_inverse_model.r.

AXL66_trials_inverse_model_out_all.csv

• output of inverse model for all predicted d18Ophos time series trials generated in our prediction simulations. Output from all trials is aggregated into a single output file.

AXL66_trials_inverse_model_output_extrema.csv

• summer peak and winter trough values extracted from the inverse model outcomes for all d18Ophos prediction trials.

Palaeotemperature reconstruction

Axlor_Pryor_T_conversion_Layer_*_MAT.xls

• Files conducting d18Odw and palaeotemperature estimates for annual means. Files are labelled with the relevant Layer number. Files use the template published in Pryor et al. (2014) with adapted calibration data. Calibration data is included in the file and separately available in reconstruct_temperature/calibration_data.

Axlor_Pryor_T_conversion_Layer_*_Summer.xls

• Files conducting d18Odw and palaeotemperature estimates for the warmest month. File uses the template published in Pryor et al. (2014) with adapted calibration data. Calibration data is included in the file and separately available in reconstruct_temperature/calibration_data.

Axlor_Pryor_T_conversion_Layer_*_Winter.xls

• Files conducting d18Odw and palaeotemperature estimates for the coldest month. File uses the template published in Pryor et al. (2014) with adapted calibration data. Calibration data is included in the file and separately available in reconstruct_temperature/calibration_data.

reconstruct_temperature/calibration_data

GNIP_coldest_month_calibration_data.csv

• Winter d18Oprecip and temperature calibration data used for temperature estimations in Axlor_Pryor_T_conversion_Layer_*_Winter.xls.

GNIP_warmest_month_calibration_data.csv

• Summer d18Oprecip and temperature calibration data used for temperature estimations in Axlor_Pryor_T_conversion_Layer_*_Summer.xls.

GNIP_MAT_month_calibration_data.csv

• Mean annual d18Oprecip and temperature calibration data used for temperature estimations in Axlor_Pryor_T_conversion_Layer_*_MAT.xls.

reconstruct_temperature/output

Axlor_seasonal_T_reconstruction.csv

• Aggregated outputs of d18Odw and palaeotemperature estimates made in the Axlor_Pryor_T_conversion_Layer_*_*.xls files in reconstruct_temperature.

Manuscript and SI

generate_article/common

AXL_librarby.bib

• Bibtex file containing bibliographic information of references cited in the article manuscript and SI.

quaternary_research.csl

• Citation style file used by Rmd files to format citations in the main text and SI correctly.

reference.docx

• style reference file that defines Word formatting styles for the docx output of the main text Rmd file

reference_SI.docx

• style reference file that defines Word formatting styles for the docx output of the Supplementary Information Rmd file

generate_article/data

AXL_carb_phos_d18O.csv

• oxygen isotope data for the carbonate and phosphate moiety of sequential tooth enamel samples. Used for comparing/combining carbonate and phosphate d18O measurements

AXL_carbonate_d13C_d18O.csv

• carbon and oxygen stable isotope data measured from bioapatite carbonates of sequential tooth enamel samples. Includes original measurements in the VPDB scale and conversions to the VSMOW scale

AXL_collagen_C_N_S_data.csv

• all carbon, nitrogen and sulphur stable isotope data measured on collagen samples

AXL_collagen_samples.csv

• overview of sample numbers for collagen d13C, d15N and d34S measurements used in this study, including a breakdown of published and new data points used

AXL_combined_phosphate_times_series.csv

• measured and predicted d18Ophos values and combined d18O time series

AXL_d18O_unmodelled_extrema_and_mean_annual.csv

• tooth enamel phosphate oxygen isotope data for summer peaks, winter troughs, and annual means derived from unmodelled d18Ophos measurement data

AXL_literature_carb_phos_offsite.csv

• a collection of published d18O carbonate and phosphate measurement pairs made on modern (non-archaeological) non-human terrestrial macro-mammals

AXL_stratigraphy_table.csv

• overview of stratigraphic levels of Axlor Cave with age information

AXL_tooth_samples.csv

• list of sample information for all aurochs/bison teeth analysed for d18O

axl66_all_alt_phos_predictions.csv

• 10 variations of d18O time series data made from combining d18Ophos measurements with d18Ophos values predicted from d18Ocarb. Different trials represent possible variations within prediction error of d18phos from d18Ocarb

generate_article/output

markdown_out_documents

Pederzani_Axlor_Main_Text.docx

• Main manuscript file generated by the main text RMarkdown file (Pederzani_Axlor_Main_Text.Rmd)

Pederzani_Axlor_SI.docx

• Supplementary Information file generated by the SI RMarkdown file (Pederzani_Axlor_SI.Rmd)

markdown_out_figures

axl66_inverse-1.png - Figure S4

axl66_model_eval-1.png - Figure S5

carbonates-1.png - Figure S7

carb_v_phos-1.png - Figure 2

collagen_c_n_s-1.png - Figure 5

create_alt_combined_phos-1.png - Figure S3

c_v_o-1.png - Figure S8

d18Odw_plot-1.png - Figure S6

ellipses_cn-1.png - Figure 6

ellipses_cs-1.png - Figure 7

o_extrema-1.png - Figure 3

pred_vs_ms-1.png - Figure S2

temperatures-1.png - Figure 4

generate_article/rmarkdown

Pederzani_Axlor_Main_Text.Rmd

• RMarkdown file that generates the manuscript main text, including figures and directly referenced analyses

Pederzani_Axlor_SI.Rmd

• RMarkdown file that generates the Supplementary Information, including figures and referenced analyses

rmd_images_import

AXL_combined_map.png - image imported for Figure 1

OxA_40151_calibrated.png - image imported for Figure S1