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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
•  Asian Speleothem Coherency
•  C-iTRACE
•  Coral Sr/Ca calibration
•  Detecting Paleoclimate Transitions with LERM
•  LMR-CMIP6
•  PaleoEnsembles
•  PaleoPCA
•  PrototypeWMG
•  Pyleoclim science
•  geoChronR

Domains

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

Formats

•  Calibration
•  Core Methods
•  Data Manipulation
•  Exploring the Data
•  Extensions
•  Extras
•  Getting Started
•  Lifehacks
•  Loading Data
•  Main Analysis
•  Motivation
•  Paleoclimate Applications
•  Plume Distance
•  Science Bits
•  Temporal Interpretation

Language

•  R
•  python

Packages

•  AWS
•  Great Tables
•  ammonyte
•  arviz
•  basemap
•  cartopy
•  cfr
•  climlab
•  dplyr
•  eofs
•  geoChronR
•  ggplot2
•  intake
•  ipywidgets
•  lipdR
•  matplotlib
•  numpy
•  oxcAAR
•  pandas
•  pens
•  purrr
•  pyLiPD
•  pyleoclim
•  pylipd
•  pymc
•  readr
•  scikit-learn
•  scipy
•  seaborn
•  sqlalchemy
•  statsmodel
•  statsmodels
•  xarray

PaleoBooks

C-iTrace Paleobook C-iTRACE python

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

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

LMR-CMIP6 Paleobook LMR-CMIP6 python

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

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

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

Watermass Geometry Proto exercise PrototypeWMG python

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

data viz, pyleoclim matplotlib ammonyte, Extras Main Analysis

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

Reproducible workflows using the Pyleoclim package Pyleoclim science python

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

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

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

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

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

Investigating interhemispheric precipitation changes over the past millennium PaleoPCA python

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

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

Comparing Paleoclimate Ensembles PaleoEnsembles python

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

https://linked.earth/pens/ug-eg25.html

Regime Shifts in Holocene Paleohydrology as Recorded by Asian Speleothems Asian Speleothem Coherency python

data viz data analysis data wrangling, ammonyte pyLiPD matplotlib pyleoclim basemap pylipd, Main Analysis Exploring the Data Loading Data

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

geoChronR Vignettes (McKay et al., 2021) geoChronR R

correlation spectral analysis visualization PCA regression tidyverse wavelets LiPD calibration data wrangling uncertainty quantification ensemble mapping age uncertainty dimension reduction age modeling, dplyr oxcAAR readr ggplot2 lipdR purrr, Data Manipulation Core Methods Extensions

http://nickmckay.github.io/GeoChronR/articles/Introduction.html

Chapters

ODV style plots with Python C-iTRACE python

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 python

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 python

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 python

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 python

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 python

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 python

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 python

model output, ipywidgets matplotlib, Lifehacks

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

Comparing CMIP6 & LMR LMR-CMIP6 python

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 python

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 python

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

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

Capstone notebook PrototypeWMG python

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 python

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 python

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 python

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 python

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 python

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 python

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 python

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 python

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 python

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 python

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 python

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 python

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 python

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 python

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 python

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

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

Data Exploration Coral Sr/Ca calibration python

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 python

Statistics Calibration Paleocenography, statsmodel Great Tables, Calibration

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

Bayesian Calibration Coral Sr/Ca calibration python

Bayesian Statistics Calibration Paleocenography, pymc arviz, Calibration

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

Model-Data Comparison PaleoPCA python

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

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

motivation PaleoEnsembles python

paleoclimatology data assimilation data viz, matplotlib pens pyleoclim, Motivation

https://linked.earth/pens/notebooks/eg25-Fig1_motivation

Naïve resampling PaleoEnsembles python

data assimilation PaMoDaCo, matplotlib pens, Temporal Interpretation

https://linked.earth/pens/notebooks/eg25-Fig2_naive_resampling

LMRonline PaleoEnsembles python

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

https://linked.earth/pens/notebooks/eg25-Fig3_4_LMRonline

resampling PaleoEnsembles python

data assimilation timeseries modeling, matplotlib pens pyleoclim, Temporal Interpretation

https://linked.earth/pens/notebooks/eg25-Fig5_resampling

Definition & Properties PaleoEnsembles python

statistics PaMoDaCo, matplotlib pens seaborn, Plume Distance

https://linked.earth/pens/notebooks/eg25-Fig6_8_plume_distance

Schematic PaleoEnsembles python

statistics PaMoDaCo, matplotlib pens seaborn, Plume Distance

https://linked.earth/pens/notebooks/eg25-Fig9_plume_distance-schematic

PAGES 2k (2019) ensemble PaleoEnsembles python

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

https://linked.earth/pens/notebooks/eg25-Fig10_compare_PAGES2k2019_recons

Büntgen et al (2021) PaleoEnsembles python

reconstruction statistics Common Era, matplotlib pens, Paleoclimate Applications

https://linked.earth/pens/notebooks/eg25-Fig11_12_compare_LMRvsB21

PMIP3 PaleoEnsembles python

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

https://linked.earth/pens/notebooks/eg25-Tab1_LMR_PMIP3_proximity_table

Getting data into LiPD Asian Speleothem Coherency python

data wrangling, pyLiPD, Loading Data

https://alexkjames.github.io/AsianSpeleothemCoherency/notebooks/Loading_Data/Getting_data_into_LiPD

Loading Data Asian Speleothem Coherency python

data wrangling, pylipd pyleoclim, Loading Data

https://alexkjames.github.io/AsianSpeleothemCoherency/notebooks/Loading_Data/Load_Data_Pyleoclim

Detrended Stackplot Asian Speleothem Coherency python

data viz data analysis, pyleoclim matplotlib, Exploring the Data

https://alexkjames.github.io/AsianSpeleothemCoherency/notebooks/Exploring_the_Data/DetrendedStack_Figure

Mapping Data Asian Speleothem Coherency python

data viz data analysis, pyleoclim basemap, Exploring the Data

https://alexkjames.github.io/AsianSpeleothemCoherency/notebooks/Exploring_the_Data/Map_Data

Synthetic Data Asian Speleothem Coherency python

data viz data analysis, pyleoclim matplotlib, Main Analysis

https://alexkjames.github.io/AsianSpeleothemCoherency/notebooks/Main_Analysis/Synthetic_Data

Kernel Density Estimation Asian Speleothem Coherency python

data analysis data viz, matplotlib pyleoclim, Main Analysis

https://alexkjames.github.io/AsianSpeleothemCoherency/notebooks/Main_Analysis/KDE_Plots

Detecting Regime Shifts Asian Speleothem Coherency python

data viz data analysis, pyleoclim ammonyte matplotlib, Main Analysis

https://alexkjames.github.io/AsianSpeleothemCoherency/notebooks/Main_Analysis/LERM_Plot

MC PCA Analysis Asian Speleothem Coherency python

data viz data analysis, pyleoclim matplotlib, Main Analysis

https://alexkjames.github.io/AsianSpeleothemCoherency/notebooks/Main_Analysis/MC_PCA_Analysis

Introduction geoChronR R

age modeling uncertainty quantification, geoChronR lipdR, Core Methods

https://nickmckay.github.io/GeoChronR/articles/Introduction

Ensemble Correlation geoChronR R

correlation age uncertainty, geoChronR ggplot2, Core Methods

https://nickmckay.github.io/GeoChronR/articles/correlation

Regression & Calibration-in-Time geoChronR R

regression calibration, geoChronR readr ggplot2, Core Methods

https://nickmckay.github.io/GeoChronR/articles/regression

Spectral Analysis geoChronR R

spectral analysis wavelets, geoChronR, Core Methods

https://nickmckay.github.io/GeoChronR/articles/spectral_analysis

Ensemble PCA geoChronR R

PCA dimension reduction, geoChronR, Core Methods

https://nickmckay.github.io/GeoChronR/articles/PCA

Plot Timeseries Stack geoChronR R

visualization, geoChronR ggplot2, Data Manipulation

https://nickmckay.github.io/GeoChronR/articles/PlotTimeseriesStack

Filtering & Mapping geoChronR R

data wrangling mapping, geoChronR, Data Manipulation

https://nickmckay.github.io/GeoChronR/articles/TsFilteringAndMapping

Tidy Filtering & Mapping geoChronR R

data wrangling tidyverse, geoChronR dplyr purrr, Data Manipulation

https://nickmckay.github.io/GeoChronR/articles/tidyIso2k

OxCal Integration geoChronR R

age modeling, geoChronR oxcAAR, Extensions

https://nickmckay.github.io/GeoChronR/articles/oxCal

Add Ensemble to LiPD geoChronR R

LiPD ensemble, geoChronR, Extensions

https://nickmckay.github.io/GeoChronR/articles/AddEnsemble