Analysis

Open source software

The LinkedEarth team currently maintain the following open source packages:

• Utilities that enable users to open, manipulate, and write files using the Linked Paleo Data (LiPD) format.

  • For R: lipdR

  • For Python: PyLiPD

• GeoChronR: an integrated framework in R that allows scientists to generate state-of-the-art age models for their records, create time-uncertain ensembles of their data, analyze those ensembles with a number of commonly-used techniques, and visualize their results in an intuitive way.GeoChronR is meant to work directly with files formatted in the LiPD format.

• Pyleoclim: a Python package designed for the analysis of paleoclimate data. Pyleoclim leverages various data science libraries (numpy, pandas, scikit-learn) for time series analysis, as well as and Matplotlib and Cartopy for the creation of publication-quality figures. The package is designed around object-oriented Series, which can be directly manipulated for plotting, spectral and wavelet analysis, and other time series-appropriate operations. Pyleoclim is meant to work with data in numpy arrays or Pandas DataFrame. The PyLiPD utilities can convert LiPD files to Pandas Dataframe for direct integration.

Computational Narratives

• We have a library of Jupyter Notebooks illustrating the use of Pyleoclim in paleoclimate research.

• We maintain a a compendium of digital resources called PaleoBooks to bridge the gap between tutorials and using software in practice.

• R vignettes are available from the GeoChronR Github repository.

• autoTS: an automated system for time series analysis.

• ClimateDISK: a framework to test and revise hypotheses based on automatic analysis of scientific data as it becomes available over time.

See our Gallery for examples of fully executable notebooks.