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Scripts used during the first phase of SISAL (Speleothem Isotopes Synthesis and Analyses), a working group under the umbrella of Past Global Changes (PAGES).

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sisal

Scripts used to QC the SISAL workbooks, upload them to the db, query and plot the database. Created by Laia Comas Bru in February 2021.

README

/db_uploads/

Upload_workbooks.py Script uploads workbook to the database. This is executed from the command line as follows:

  • python Upload_workbooks.py input.xlsx

Example_upload_SISAL_agemodels.R Script showing an example on how to upload the SISAL chronology and the date_used fields to the database.

Upload_SISAL_agemodels.R Script with the functions needed to run /DB_uploads/Example_upload_SISAL_agemodels.R

SISAL - documentation for database managers.pdf Documentation for db manager


/csv_extract/

sisalv2_extract_data_csv.R Script to upload and query the sisal database from csv files. Tested with sisalv2. It creates two functions: 1- read.sisal.csv: loads csv sisalv2 files and creates a "sisal object" 2- sisal.time.series: extracts time-series for a time period and region (with references)

/csv_extract/sisalv2_csv/ It contains the csv files downloaded from the UoR repository: https://doi.org/10.17864/1947.256


/sisalv2_example_codes/

SQL, Matlab, Julia, Python and R scripts to access the latest version of the database. These are also available http://dx.doi.org/10.17864/1947.256


/sisal_wokam_plot/

map_sites_count_labels.R Script to produce Figure X in Baker et al., 2021 (ESR accepted). Output saved in /SISAL_sites_wokam_plot/output/map_sites_count_labels_plot.pdf

map_sites_versions.R Scripts to produce Figure 2 in Comas-Bru et al. 2020 (ESSD; https://doi.org/10.5194/essd-12-2579-2020). Output is saved in /SISAL_sites_wokam_plot/output/

/input/wokam/ World Karst Aquifer Map shp data file from Goldscheider, N., Chen, Z., Auler, A.S. et al. Global distribution of carbonate rocks and karst water resources. Hydrogeol J 28, 1661–1677 (2020). https://doi.org/10.1007/s10040-020-02139-5

/input/ne_110m_land/ Coastal shp data file from http://www.naturalearthdata.com/downloads/110m-physical-vectors/


/sisal_regional_map_resolution/

sisalv2_map_resolution_region.R Script to create regional maps with the location of SISAL sites and the number of entities per site (with the World Karst Aquifer map in the background) as well as the “resolution map” for all the sisal entities in that region.

/input/wokam/ World Karst Aquifer Map shp data file from Goldscheider, N., Chen, Z., Auler, A.S. et al. Global distribution of carbonate rocks and karst water resources. Hydrogeol J 28, 1661–1677 (2020). https://doi.org/10.1007/s10040-020-02139-5

/input/ne_110m_land/ Coastal shp data file from http://www.naturalearthdata.com/downloads/110m-physical-vectors/


/sisalv2_paper/

Scripts used to either produce figures or extract information used in Comas-Bru et al., 2020 (ESSD; https://doi.org/10.5194/essd-12-2579-2020).

sisalv2_compare_versions.R Script to extract the information used to create Table 4

sisalv2_regional_coverage_numbers.R Script to obtain numbers in Table 6

sisalv2_uncert_dating_age.R Scripot to produce Figure 6

sisalv2_coverage_period_text.R Script used to extract the numbers mentioned at the end of the conclusions' section


/wb_QC/

wb_check.py Version-controlled script used by SISAL regional coordinators to quality check the submitted workbooks. This is executed from the command line as follows: * python wb_checkv12.py input.xlsx

plot_agemodels_hiatus Version-controlled scripts used by SISAL regional coordinators to quality check the submitted workbooks. Script plot agemodels and their hiatuses from the workbook. The script is to be run in R, changing the path to the input workbook file. PDFs will be generated in the workspace.

README_instructions.txt Instructions to run wb_check.py and plot_agemodels_hiatus

SISAL_workbook.xlsx Latest version of the SISAL workbook.

decimalisation.xls Excel document to automatically convert geographical coordinates from decimal to minutes (and viceversa).

Atomic-Activity-deltaU Calculator.xlsx Excel document to automatically convert ratios to activities.

SISAL_v2_QC_details.pdf Details of automatic and manual checks


Additional documents for wb_QC:


REFERENCES

These scripts work with the latest version of the SISAL database:

Comas-Bru, Laia, Atsawawaranunt, Kamolphat, Harrison, Sandy and SISAL working group members (2020): SISAL (Speleothem Isotopes Synthesis and AnaLysis Working Group) database version 2.0. University of Reading. Dataset. http://dx.doi.org/10.17864/1947.256

Comas-Bru, L., Rehfeld, K., Roesch, C., Amirnezhad-Mozhdehi, S., Harrison, S. P., Atsawawaranunt, K., Ahmad, S. M., Brahim, Y. A., Baker, A., Bosomworth, M., Breitenbach, S. F. M., Burstyn, Y., Columbu, A., Deininger, M., Demény, A., Dixon, B., Fohlmeister, J., Hatvani, I. G., Hu, J., Kaushal, N., Kern, Z., Labuhn, I., Lechleitner, F. A., Lorrey, A., Martrat, B., Novello, V. F., Oster, J., Pérez-Mejías, C., Scholz, D., Scroxton, N., Sinha, N., Ward, B. M., Warken, S., Zhang, H., and SISAL Working Group members: SISALv2: a comprehensive speleothem isotope database with multiple age–depth models, Earth Syst. Sci. Data, 12, 2579–2606, https://doi.org/10.5194/essd-12-2579-2020, 2020.


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Scripts used during the first phase of SISAL (Speleothem Isotopes Synthesis and Analyses), a working group under the umbrella of Past Global Changes (PAGES).

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