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Gallery

PaleoBooks is a compendium of digital resources to bridge the gap between paleoclimate observations and models, and between past, present and future. The goal is as much to encourage adoption of open-source, free languages like R and Python by the observational paleoscience community as it is to encourage the modeling community to leverage the unique information coming from paleo archives.

The scholarly objects shown below are of several types:

• Tutorials on how to overcome a particular technical difficulty (“Life Hacks”)

• Tutorials on how to leverage open-source code to achieve easier, more transparent, or more powerful scientific workflows (“Science Bits”)

• Examples of novel paleoscience using the Python ecosystem e.g. as turn-key supplementary material from recent publications (“Papers”)

In the following, “PaleoBooks” refers to curated collections of Jupyter Notebooks organized around various themes. “Chapters” refers to the components of these PaleoBooks. A system of tags allows both PaleoBooks and individual chapters to be associated with one another based on individual themes or methodologies, in addition to their host PaleoBook. These tags enable searching along 3 directions:

• “Domains” refers to scientific themes or methodologies

• “Formats” refers to the type of resource (Life Hacks, Science Bits, or Papers)

• “Packages” refers to the packages being used in each notebook (e.g. Xarray)

The gallery below is a work in progress, and we encourage you to contribute your own analyses if you think they might bring enlightenment to, and/or ease the life of, fellow scientists.

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Book

•  2k Proxy Composite
•  C-iTRACE
•  Coral Sr/Ca calibration
•  Detecting Paleoclimate Transitions with LERM
•  LMR-CMIP6
•  PaleoEnsembles
•  PaleoPCA
•  PrototypeWMG
•  Pyleoclim science

Domains

•  AWS
•  Bayesian Statistics
•  C14
•  CMIP6
•  Calibration
•  Common Era
•  Deglaciation
•  Holocene climate
•  LMR
•  Mystery Interval
•  PCA
•  PMIP
•  PaMoDaCo
•  Paleoceanography
•  Paleocenography
•  Sr/Ca
•  Statistics
•  Volcanic Input
•  age uncertainty
•  calibration
•  cloud-ready data
•  clustering
•  coordinate systems
•  coral
•  correlation
•  cross-wavelet analysis
•  data assimilation
•  data viz
•  eNd
•  endmember mixing
•  insolation
•  machine learning
•  model output
•  model-data comparison
•  modeling
•  oceanography
•  paleoceanography
•  paleoclimate
•  paleoclimatology
•  proxy composite
•  reconstruction
•  spectral analysis
•  statistics
•  temperature
•  timeseries modeling
•  tracers
•  watermass geometry
•  wavelet analysis

Formats

•  Calibration
•  Extras
•  Getting Started
•  Lifehacks
•  Main Analysis
•  Motivation
•  Paleoclimate Applications
•  Plume Distance
•  Science Bits
•  Temporal Interpretation

Packages

•  AWS
•  Great Tables
•  ammonyte
•  arviz
•  basemap
•  cartopy
•  cfr
•  climlab
•  eofs
•  intake
•  ipywidgets
•  matplotlib
•  numpy
•  pandas
•  pens
•  pyleoclim
•  pylipd
•  pymc
•  scikit-learn
•  scipy
•  seaborn
•  sqlalchemy
•  statsmodel
•  statsmodels
•  xarray

PaleoBooks

C-iTrace Paleobook C-iTRACE

C14 model output oceanography Mystery Interval eNd data viz tracers coordinate systems clustering Deglaciation watermass geometry Paleoceanography machine learning, pandas xarray seaborn matplotlib intake cartopy scikit-learn, Science Bits Lifehacks

https://linked.earth/citrace_paleobook/README.html

LMR-CMIP6 Paleobook LMR-CMIP6

cloud-ready data model output Volcanic Input CMIP6 data viz AWS LMR Holocene climate coordinate systems, ipywidgets pyleoclim pandas xarray matplotlib AWS intake cartopy, Science Bits Lifehacks

https://linked.earth/LMR_CMIP_paleobook/README.html

Reproducing the Hockey Stick - Proxy composite over the past 2,000 years using the cfr package 2k Proxy Composite

proxy composite temperature, pyleoclim pandas seaborn numpy cfr, Science Bits

https://khider.github.io/DISK-proxyComposite/intro.html

Watermass Geometry Proto exercise PrototypeWMG

clustering endmember mixing watermass geometry tracers, scikit-learn pandas matplotlib sqlalchemy basemap scipy, Science Bits

https://jordanplanders.github.io/past_life_wmg/intro.html

Detecting paleoclimate transitions with Laplacian Eigenmaps of Recurrence Matrices (LERM) Detecting Paleoclimate Transitions with LERM

data viz, matplotlib ammonyte pyleoclim, Extras Main Analysis

https://alexkjames.github.io/Detecting_Paleoclimate_Transitions_with_LERM/intro.html

Reproducible workflows using the Pyleoclim package Pyleoclim science

model output paleoclimate insolation wavelet analysis model-data comparison spectral analysis cross-wavelet analysis age uncertainty paleoceanography correlation, pyleoclim xarray pylipd cartopy climlab, Science Bits

https://linked.earth/PyleoclimPaper/README.html

Coral Sr/Ca Calibration - An Example from Dry Tortugas Coral Sr/Ca calibration

calibration Bayesian Statistics Calibration Paleocenography Statistics Sr/Ca coral paleoceanography, pyleoclim arviz pandas statsmodel matplotlib Great Tables pymc, Calibration Getting Started

https://khider.github.io/dry-tortugas-calibration-fun/intro.html

Investigating interhemispheric precipitation changes over the past millennium PaleoPCA

modeling PCA paleoceanography, eofs pyleoclim pandas xarray matplotlib cartopy, Science Bits

https://projectpythia.org/paleoPCA-cookbook/README.html

Comparing Paleoclimate Ensembles PaleoEnsembles

PMIP statistics data assimilation data viz timeseries modeling PaMoDaCo reconstruction Common Era paleoclimatology, pyleoclim pens pandas seaborn statsmodels matplotlib scipy, Plume Distance Temporal Interpretation Paleoclimate Applications Motivation

https://linked.earth/pens/ug-eg24.html

Chapters

ODV style plots with Python

C-iTRACE

oceanography tracers data viz, xarray matplotlib cartopy pandas seaborn, Lifehacks

https://linked.earth/citrace_paleobook/notebooks/lifehacks/pyODV

Working with data on a model grid

C-iTRACE

model output oceanography coordinate systems, xarray matplotlib cartopy pandas intake, Lifehacks

https://linked.earth/citrace_paleobook/notebooks/lifehacks/working_with_data_on_a_model_grid

eNd model-data comparison (section)

C-iTRACE

model output eNd, xarray matplotlib cartopy pandas, Science Bits

https://linked.earth/citrace_paleobook/notebooks/science_bits/data_scatter_on_pcolor

Paleo watermass geometry using clustering

C-iTRACE

clustering machine learning watermass geometry, xarray matplotlib cartopy scikit-learn, Science Bits

https://linked.earth/citrace_paleobook/notebooks/science_bits/clustering

D14C model-data comparison (downcore)

C-iTRACE

C14 Paleoceanography Deglaciation Mystery Interval, xarray matplotlib cartopy pandas, Science Bits

https://linked.earth/citrace_paleobook/notebooks/science_bits/PaMoDaCo_downcore_D14C

Accessing cloud-hosted CMIP6 output

LMR-CMIP6

AWS cloud-ready data data viz CMIP6, intake AWS xarray pandas, Lifehacks

https://linked.earth/LMR_CMIP_paleobook/notebooks/lifehacks/data_from_esm_cloudcat

Spatiotemporal diagnostics using xarray

LMR-CMIP6

model output CMIP6 coordinate systems, xarray matplotlib cartopy pandas, Lifehacks

https://linked.earth/LMR_CMIP_paleobook/notebooks/lifehacks/spatial_snapshots_xarray_bonuses

Data exploration with ipywidgets

LMR-CMIP6

model output, ipywidgets matplotlib, Lifehacks

https://linked.earth/LMR_CMIP_paleobook/notebooks/lifehacks/widget_primer

Comparing CMIP6 & LMR

LMR-CMIP6

model output LMR CMIP6, xarray matplotlib cartopy pandas pyleoclim, Science Bits

https://linked.earth/LMR_CMIP_paleobook/notebooks/science_bits/CMIP6_LMR

LMR & Volcanic Aerosols

LMR-CMIP6

Volcanic Input Holocene climate LMR CMIP6, xarray matplotlib cartopy ipywidgets, Science Bits

https://linked.earth/LMR_CMIP_paleobook/notebooks/science_bits/VICS_dashboard

Hockey Stick

2k Proxy Composite

proxy composite temperature, numpy seaborn pandas pyleoclim cfr, Science Bits

https://khider.github.io/DISK-proxyComposite/HockeyStick

Capstone notebook

PrototypeWMG

watermass geometry tracers endmember mixing, basemap scipy matplotlib pandas sqlalchemy, Science Bits

https://jordanplanders.github.io/past_life_wmg/CapstoneProject/jlanders_capstone_fixed

Cluster Centers

PrototypeWMG

clustering watermass geometry, basemap scikit-learn matplotlib, Science Bits

https://jordanplanders.github.io/past_life_wmg/CapstoneProject/clustering_centers_on_raw

Method overview

Detecting Paleoclimate Transitions with LERM

data viz, matplotlib pyleoclim ammonyte, Main Analysis

https://alexkjames.github.io/Detecting_Paleoclimate_Transitions_with_LERM/notebooks/Main_Analysis/Method_Overview

LERM applied to ODP cores

Detecting Paleoclimate Transitions with LERM

data viz, matplotlib pyleoclim ammonyte, Main Analysis

https://alexkjames.github.io/Detecting_Paleoclimate_Transitions_with_LERM/notebooks/Main_Analysis/ODP_LERM

LERM applied to synthetic ODP cores

Detecting Paleoclimate Transitions with LERM

data viz, matplotlib pyleoclim ammonyte, Main Analysis

https://alexkjames.github.io/Detecting_Paleoclimate_Transitions_with_LERM/notebooks/Main_Analysis/Synthetic_ODP_LERM

Sensitivity to resolution

Detecting Paleoclimate Transitions with LERM

data viz, matplotlib pyleoclim ammonyte, Main Analysis

https://alexkjames.github.io/Detecting_Paleoclimate_Transitions_with_LERM/notebooks/Main_Analysis/Resolution_Sensitivity

LERM applied to ice cores

Detecting Paleoclimate Transitions with LERM

data viz, matplotlib pyleoclim ammonyte, Main Analysis

https://alexkjames.github.io/Detecting_Paleoclimate_Transitions_with_LERM/notebooks/Main_Analysis/IceCore_LERM

Sensitivity to events

Detecting Paleoclimate Transitions with LERM

data viz, matplotlib pyleoclim ammonyte, Main Analysis

https://alexkjames.github.io/Detecting_Paleoclimate_Transitions_with_LERM/notebooks/Main_Analysis/Event_Sensitivity

Regime transition probability on synthetic ensembles

Detecting Paleoclimate Transitions with LERM

data viz, matplotlib pyleoclim ammonyte, Main Analysis

https://alexkjames.github.io/Detecting_Paleoclimate_Transitions_with_LERM/Figure_7

Resolution changes on real data

Detecting Paleoclimate Transitions with LERM

data viz, matplotlib pyleoclim ammonyte, Main Analysis

https://alexkjames.github.io/Detecting_Paleoclimate_Transitions_with_LERM/notebooks/Main_Analysis/Resolution_Analysis

Holocene Ice Analysis

Detecting Paleoclimate Transitions with LERM

data viz, matplotlib pyleoclim ammonyte, Extras

https://alexkjames.github.io/Detecting_Paleoclimate_Transitions_with_LERM/notebooks/Extras/Holocene_Ice_Analysis

Holocene Ice Window Increment

Detecting Paleoclimate Transitions with LERM

data viz, matplotlib pyleoclim ammonyte, Extras

https://alexkjames.github.io/Detecting_Paleoclimate_Transitions_with_LERM/notebooks/Extras/Holocene_Ice_Window_Increment

Holocene Ice Window Size

Detecting Paleoclimate Transitions with LERM

data viz, matplotlib pyleoclim ammonyte, Extras

https://alexkjames.github.io/Detecting_Paleoclimate_Transitions_with_LERM/notebooks/Extras/Holocene_Ice_Window_Size

Chasing cyclicities

Pyleoclim science

spectral analysis wavelet analysis cross-wavelet analysis insolation paleoceanography, xarray pyleoclim pylipd climlab, Science Bits

https://linked.earth/PyleoclimPaper/OrbitalCycles/Chasing_orbital_cyclicities

Model-Data Confrontation

Pyleoclim science

model output spectral analysis model-data comparison paleoclimate, xarray pyleoclim, Science Bits

https://linked.earth/PyleoclimPaper/MDConfrontation/Model_data_confrontation

Correlations at Sea

Pyleoclim science

paleoclimate correlation age uncertainty, xarray pyleoclim cartopy pylipd, Science Bits

https://linked.earth/PyleoclimPaper/CrystalCorrelations/CrystalCorrelations

Data Exploration

Coral Sr/Ca calibration

paleoceanography Sr/Ca coral calibration, matplotlib pyleoclim pandas, Getting Started

https://khider.github.io/dry-tortugas-calibration-fun/DataExploration

Frequentist Calibration

Coral Sr/Ca calibration

Statistics Calibration Paleocenography, statsmodel Great Tables, Calibration

https://khider.github.io/dry-tortugas-calibration-fun/FrequentistCalibration

Bayesian Calibration

Coral Sr/Ca calibration

Bayesian Statistics Calibration Paleocenography, pymc arviz, Calibration

https://khider.github.io/dry-tortugas-calibration-fun/BayesianCalibration

Model-Data Comparison

PaleoPCA

paleoceanography PCA modeling, xarray pyleoclim cartopy matplotlib pandas eofs, Science Bits

https://projectpythia.org/paleoPCA-cookbook/notebooks/paleoPCA

motivation

PaleoEnsembles

paleoclimatology data assimilation data viz, matplotlib pens pyleoclim, Motivation

https://linked.earth/pens/notebooks/eg24-Fig1_motivation

Naïve resampling

PaleoEnsembles

data assimilation PaMoDaCo, matplotlib pens, Temporal Interpretation

https://linked.earth/pens/notebooks/eg24-Fig2_naive_resampling

LMRonline

PaleoEnsembles

data assimilation timeseries modeling, matplotlib pens statsmodels seaborn, Temporal Interpretation

https://linked.earth/pens/notebooks/eg24-Fig3_4_LMRonline

resampling

PaleoEnsembles

data assimilation timeseries modeling, matplotlib pens pyleoclim, Temporal Interpretation

https://linked.earth/pens/notebooks/eg24-Fig5_resampling

Definition & Properties

PaleoEnsembles

statistics PaMoDaCo, matplotlib pens seaborn, Plume Distance

https://linked.earth/pens/notebooks/eg24-Fig6_8_plume_distance

Schematic

PaleoEnsembles

statistics PaMoDaCo, matplotlib pens seaborn, Plume Distance

https://linked.earth/pens/notebooks/eg24-Fig9_plume_distance-schematic

PAGES 2k (2019) ensemble

PaleoEnsembles

reconstruction statistics Common Era, matplotlib seaborn pens scipy, Paleoclimate Applications

https://linked.earth/pens/notebooks/eg24-Fig10_compare_PAGES2k2019_recons

Büntgen et al (2021)

PaleoEnsembles

reconstruction statistics Common Era, matplotlib pens, Paleoclimate Applications

https://linked.earth/pens/notebooks/eg24-Fig11_12_compare_LMRvsB21

PMIP3

PaleoEnsembles

data assimilation PaMoDaCo PMIP, matplotlib pens pyleoclim pandas, Paleoclimate Applications

https://linked.earth/pens/notebooks/eg24-Tab1_LMR_PMIP3_proximity_table