Quantitative Analysis of Paleomagnetic Sampling Strategies#

Authors: F Sapienza, L. C. Gallo, Y. Zhang, B. Vaes, M. Domeier, N. L. Swanson-Hysell

GitHub

from IPython.display import Markdown, display

display(Markdown("../README.md"))

For a detailed description of the project, take a look at publication at JGR: Solid Earth. This publication was also highlighted in Eos. Take a look to the article Should I Stay or Should I Go…To Another Paleomagnetic Site? by Daniel Pastor-Galán.

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Quantitative Analysis of Paleomagnetic Sampling Strategies

This repository contains all the notebooks and code to reproduce the analysis for the different sampling procedures in order to estimate the precision of different strategies for estimating paleomagnetic poles and paleosecular variation of the magnetic field based on site magnetizations.

You can open a cloud JupyterHub version of all the code in this repository and execute it using the following Binder link:

Binder

Learn more about the Binder project in this link. Note that it will take a very long time to load.

The notebooks in this repository can be directly been access though the following JupyterBook. This link opens a website where all the notebooks can be visualized.

Jupyter Book Badge

Organization

This repository includes a series of tools and code organized in different folders:

  • notebooks: It includes Jupyter Notebooks with examples of different sampling procedures and the code to parallelize the simulations using Dask (Parallel.ipynb).

  • figures: It includes all the Jupyter Notebooks to generate the figures in the paper.

  • outputs: It includes the simulated data from all the simulations used in the figures in csv format.

  • smpsite: Python package to run simulations and estimate poles and dispersion (see Installation for more information).

We also provide an environment.yml and Makefile for setup of the computational environment used for this project.

Installation

All the notebooks inside this notebook can be executed after properly setting the environment. The environment.yml file can be used to install all the required dependencies. Beside some standard Python dependencies, the environment.yml file include the installation of Pmagpy using pip and the extra installation of the module smpsite (included in this repository). The package smpsite includes all the code used to make the simulations and compute the estimated poles.

In order to install the environment, you can use conda or mamba (see Managing Environments for more information) with conda env create -f environment.yml. Once the environment is created, you can create the associated iPython kernel with

python -m ipykernel install --user --name paleostats --display-name "IPython - PaleoStats"

This will allow you to execute this environment directly from Jupyter notebooks.

Alternatively, we included a Makefile that creates the conda environment and installs the associated iPython kernel so this environment can be accessible though Jupyter notebooks all at once. In order to use the Makefile, you need to open a terminal where the repository is located and enter

make env

Alternatively, if you just want to install the smpsite module, you can clone this repository and do

pip install smpsite

or

pip install -e smpsite

if you are working in developer mode.

Makefile

The current repository contains a Makefile that allows the user to run different routines on the code. You can move in a terminal to the path to this repository and use the following commands to trigger their respective actions.

  • make env: Creates the conda environment associated with the environment.yml file and then creates the respective iPython kernel such that the environment can be accessed via Jupyter notebooks.

  • make help: Prints a short description of all available commands and their explanation.

How to cite 📖

If you want to cite this work, please use this BibTex citation from our latest preprint:

@article{sapienza2023quantitative,
  title = {Quantitative Analysis of Paleomagnetic Sampling Strategies},
  author = {Sapienza, Facundo and Gallo, Leandro Cesar and Zhang, Yiming and Vaes, Bram and Domeier, Mathew and Swanson-Hysell, Nicholas L},
  journal = {Authorea Preprints},
  year = {2023},
  publisher = {Authorea}
}

If you want to cite the software in this repository, you can instead use the following DOI in Zenodo:

DOI

or simply use the bibtex format

@software{Sapienza_PaleoSampling,
  author = {Sapienza, Facundo and Gallo, Leandro Cesar and Zhang, Yiming and Vaes, Bram and Domeier, Mathew and Swanson-Hysell, Nick},
  title = {PaleoSampling},
  month = sep,
  year = 2023,
  note = {{Quantitative Analysis of Paleomagnetic Sampling Strategies}},
  publisher = {Zenodo},
  version = {v1.0.0},
  doi = {10.5281/zenodo.8347149},
  url = {https://doi.org/10.5281/zenodo.8347149}
}

Contributors

Facundo Sapienza
Facundo Sapienza
📖 💻 🚇 🎨 🚧		 Leandro Gallo
Leandro Gallo
💻 🐛 🧑‍🏫 🎨 💬		 Nick Swanson-Hysell
Nick Swanson-Hysell
👀 📖 🎨 🧑‍🏫 💻		 matdomeier
matdomeier
🤔 🎨		 Bram Vaes
Bram Vaes
🎨 🤔		 Yiming Zhang
Yiming Zhang
🤔