reshape (under edition)

A tool for fast time interval (years before present) proxy data analysis for large sediment core databases.

Motivation and scientific goals

This GitHub repository stores all code used for data analysis and visualisation of the stable isotopes and radiocarbon ventilation ages (can be used for any other proxy data) results for the work "Reshaping the Southeast Pacific Water Masses during the Last Glacial-Interglacial transition: Dynamics and Carbon Storage".

We used for published data mining and the organization of our new stable isotope and radiocarbon data the methodology described by Muglia et al., 2023 (https://www.nature.com/articles/s41597-023-02024-2) that consider the organization of depth model, age data raw data and age model and proxy data per sediment core in indivialds folders with notes about the data update and mangment. A soon as the new data is published, it will be submitted to Muglia et al., 2024 (https://zenodo.org/records/11187264). For the most updated versions of the data set, the core information was organised in two .txt files.

Getting started (Generation of proxy data sediment sites input files)

1. Main metadata file: This file (called index) will store all metadata information of the sediment cores that will be analysed. Mandatory information is the location [(longitude (in degrees east), latitude (in degrees north), water depth (in meters below the sea level)] and the ID of the core. The text file is separated by tabs without spaces. About the ID of the core, the first part of the name represents the type of analysis, the second part the name of the core.

• siamrad: represent the cores with results used for d13C and d18O data analysis and visualization.
• siamradven: represent the cores with results used for radiocarbon ventilation ages data analysis and visualisation.

Example of index siamrad

• IDarchive longitude latitude depth
• siamrad_so26_96 -85.84 0.68 2706
• siamrad_so26_127 -85.39 -1.55 2463
• siamrad_so26_131 -85.00 -3.53 3381
• siamrad_gik17747_1 -72.33 -32.74 2464
• siamrad_geob3302_1 -72.09 -33.22 1498

Example of index siamradven

• IDarchive longitude latitude depth
• siamradven_md07_3088 -75.00 -46.00 1536.00
• siamradven_geob7167_6 -73.93 -36.45 2062.00
• siamradven_22sl -73.68 -36.22 1001.00
• siamradven_geob7163_7 -73.60 -36.43 537.00
• siamradven_geob7149_2 -72.00 -31.49 3086.00

2. Main stable isotope data files (siamrad) (each file is one sediment core data organized as the followed) --> A: cm (depth model), B: age in years before present (age model), C: carbon stable isotopes in benthic foraminifera d13C, D: oxygen stable isotope in benthic foraminifera d18O.

Example siamrad files

• cm age d13C d18O
• 7 6500 0.02 2.8
• 10 7543 -0.02 2.92
• 12 8239 -0.09 3.16
• 12 8413 0.09 2.84
• 18 10500 0.01 3.22
• 20 10947 0.07 3.37
• 21 11158 -0.24 3.44
• 21 11290 -0.01 3.46

4. Main radiocarbon data files (siamradven). Each file is one sediment core data organised following Rafter et al., 2022 https://www.science.org/doi/full/10.1126/sciadv.abq5434.

A: depth model in cm (called cm) B: radiocarbon age in years (called age) C: calendar age in years before present (called cal.age) D: error calendar age in years before present (called cal.age.err) E: radiocarbon age benthic foraminifera (called proxy.14C) F: error radiocarbon age benthic foraminifera (called proxy.14C.age.err) G: Delta 14C in permil that was calculated using the equation of Adkins and Boyle., 1997 (called proxy.D14C) H: error Delta 14C in permil that was calculated using the equation of Adkins and Boyle., 1997 (called proxy.D14C.err) I: reference J: planktic foraminifera 14C age (called planktic.14C.age) K: error planktic foraminifera 14C age (called planktic.14C.age.err) L: reservoir age (called Delta.R), M: error reservoir age (called Delta.R.err) N: contemporany atmosphere D14C (atmos.D14C) O: error contemporany atmosphere D14C (atmos.D14C.err) P: atmosphere atmos.14C.age Q: contemporany atmosphere 14C (called atmos.14C.age.err) R: contemporany atmosphere 14C (called D14C.bias.correct) S: (called D14C.bias.correct.err) T: (called DIC.D14C) U: DIC.D14C.err V: DIC.D14C.age W: DIC.D14C.age.err X: DELTA14Cage.atmos.RAW Y: DELTA14Cage.atmos.RAW.err Z: DELTA14Cage.atmos AA: DELTA14Cage.atmos.err

5. Surface sediment data (If you want to include this data)

6. Modern Bottom water hydrological variables (in this case, d13C and d18O equilibrium calcite)

What does each code do?

1. water_mass_plot.py

Several plots using the following variables: latitude, longitude, water depth, versus d13C, d18O,and Radiocarbon ventilation ages

3. (add name).py

4. (add name).py

Run reshape python codes (Generation of output file)

1. Install Python (recommended latest version) https://www.python.org/
2. Check reshape codes 1, 2, 3 (attached)
3. Create on your PC a single folder where you add all input files: index, siamrad core sites, siamradven core sites, surface sediments siamrad core sites (only one file per list), bottom water d13C and d18O (if available)
4. Run the code in your terminal or Spider console

Data management and script developers

• Dharma A. Reyes Macaya - Paleobiogeochemistry working group, Lyell Centre, Heriot-Watt University, Scotland, UK - MARUM, University of Bremen, Germany - [dharmisreyesmacaya@gmail.com] Marine Biogeochemist, Paleoceanographer and Data Scientist
• Francisco Manuel García Araya - [garcicia@gmail.com] Earth Scientist, Numerical Modeller, Python mentor.

reshape Collaborators

• Consuelo Martínez Fontaine - [consuelola.m.f@gmail.com]
• Katya Canal Solis - Paleobiogeochemistry working group, Lyell Centre, Heriot-Watt University, Scotland, UK
• Babette Hoogakker - Paleobiogeochemistry working group, Lyell Centre, Heriot-Watt University, Scotland, UK