PCA on proxy and readme info

CITATION.cff

@@ -1,48 +1,13 @@
-cff-version: 1.2.0
+cff-version: 0.0.1
 message: "If you use this cookbook, please cite it as below."
 authors:
-  # add additional entries for each author -- see https://github.com/citation-file-format/citation-file-format/blob/main/schema-guide.md
-  - family-names: Rose
-    given-names: Brian E. J.
-    orcid: https://orcid.org/0000-0002-9961-3821 # optional
-    website: https://github.com/brian-rose # optional
-    affiliation: University at Albany (State University of New York) # optional
-  - family-names: Kent
-    given-names: Julia
-    orcid: https://orcid.org/0000-0002-5611-8986
-    website: https://github.com/jukent
-    affiliation: UCAR/NCAR
-  - family-names: Tyle
-    given-names: Kevin
-    orcid: https://orcid.org/0000-0001-5249-9665
-    website: https://github.com/ktyle
-    affiliation: University at Albany (State University of New York)
-  - family-names: Clyne
-    given-names: John
-    orcid: https://orcid.org/0000-0003-2788-9017
-    website: https://github.com/clyne
-    affiliation: UCAR/NCAR
-  - family-names: Camron
-    given-names: Drew
-    orcid: https://orcid.org/0000-0001-7246-6502
-    website: https://github.com/dcamron
-    affiliation: UCAR/Unidata
-  - family-names: Grover
-    given-names: Maxwell
-    orcid: https://orcid.org/0000-0002-0370-8974
-    website: https://github.com/mgrover1
-    affiliation: Argonne National Laboratory
-  - family-names: Ford
-    given-names: Robert R.
-    orcid: https://orcid.org/0000-0001-5483-4965
-    website: https://github.com/r-ford
-    affiliation: University at Albany (State University of New York)
-  - family-names: Paul
-    given-names: Kevin
-    orcid: https://orcid.org/0000-0001-8155-8038
-    website: https://github.com/kmpaul
-    affiliation: NVIDIA
-  - name: "Cookbook Template contributors" # use the 'name' field to acknowledge organizations
-    website: "https://github.com/ProjectPythia/paleoPCA-Cookbook/graphs/contributors"
-title: "Cookbook Template"
-abstract: "A sample cookbook description."
+  - family-names: "Khider"
+    given-names: "Deborah"
+    orcid: "https://orcid.org/0000-0001-7501-8430"
+    affiliation: "University of Southern California"
+  - family-names: "Sundar"
+    given-names: "Srihari"
+    orcid: " https://orcid.org/0000-0002-0556-3967"
+    affiliation: "National Renewable Energy Lab (NREL)"
+title: "Investigating interhemispheric precipitation changes over the past millennium" 
+url: "https://projectpythia.org/paleoPCA-Cookbook/"

README.md

@@ -1,20 +1,23 @@
 <img src="thumbnail.png" alt="thumbnail" width="300"/>
+<img src="https://github.com/LinkedEarth/Logos/blob/master/LinkedEarth_medium.png?raw=true" alt="LinkedEarth Logo" width="500">
 
-# (Replace_with_your_title) Cookbook
+# Investigating interhemispheric precipitation changes over the past millennium¶
 
 [![nightly-build](https://github.com/ProjectPythia/paleoPCA-Cookbook/actions/workflows/nightly-build.yaml/badge.svg)](https://github.com/ProjectPythia/paleoPCA-Cookbook/actions/workflows/nightly-build.yaml)
 [![Binder](https://binder.projectpythia.org/badge_logo.svg)](https://binder.projectpythia.org/v2/gh/ProjectPythia/paleoPCA-Cookbook/main?labpath=notebooks)
 [![DOI](https://zenodo.org/badge/813352705.svg)](https://zenodo.org/badge/latestdoi/813352705)
 
-This Project Pythia Cookbook covers ... (replace `...` with the main subject of your cookbook ... e.g., _working with radar data in Python_)
+This Project Pythia Cookbook covers paleoclimate model-data comparison using spatio-temporal pattern obtained using Principal Component Analysis (PCA).
 
 ## Motivation
 
-(Add a few sentences stating why this cookbook will be useful. What skills will you, "the chef", gain once you have reached the end of the cookbook?)
+Paleoclimate observations obtained from tree rings or the geochemical composition of speleothems, ice and sediments provide an out-of-sample validation of climate models. However, comparing the output of climate models directly with the paleoclimate observations is difficult: (1) they are often expressed in different quantities (i.e., temperature vs ring width), (2) paleoclimate observations have large time uncertainties, (3) paleoclimate observations often incorporate more than one environmental signal (i.e., temperature AND moisture).
+
+Recently, [Steinman et al. (2022)](https://www.pnas.org/doi/full/10.1073/pnas.2120015119) used PCA analysis to compare model and data output. Here, we use a similar approach with the [CESM Last Millennium simulation](https://www2.cesm.ucar.edu/models/cesm1.2/) and proxy records stored on the [LiPDverse](https://lipdverse.org). This repository contains paleoclimate datasets that have been curated by the community and are archived in a standard format, facilitating analysis. 
 
 ## Authors
 
-[First Author](@first-author), [Second Author](@second-author), etc. _Acknowledge primary content authors here_
+[Deborah Khider](@khider), [Hari Sundar](@sriharisundar)
 
 ### Contributors
 
@@ -24,15 +27,19 @@ This Project Pythia Cookbook covers ... (replace `...` with the main subject of
 
 ## Structure
 
-(State one or more sections that will comprise the notebook. E.g., _This cookbook is broken up into two main sections - "Foundations" and "Example Workflows."_ Then, describe each section below.)
+This Cookbook is broken down into three main sections. The first section performs the PCA analysis on the output of the CESM LME simulation. The second section performs the same analysis on paleoclimate observations. The last section compares the two analyses.
+
+### PCA analysis on the CESM Last Millennium Analysis¶
 
-### Section 1 ( Replace with the title of this section, e.g. "Foundations" )
+The section walks through fetching the data from JetStream2, calculating the precipitation d18O and running PCA. 
 
-(Add content for this section, e.g., "The foundational content includes ... ")
+### PCA analysis on proxy observations
 
-### Section 2 ( Replace with the title of this section, e.g. "Example workflows" )
+The section shows the query used to obtain relevant proxy datasets from a graphDB mirroring the LiPDverse data, filtering for records that cover at least 1500 of the last 2000 years with a resolution better than 60 years, and running PCA.
 
-(Add content for this section, e.g., "Example workflows include ... ")
+### Model Data Comparison
+
+Visualizing the output of the PCA analyses. 
 
 ## Running the Notebooks
 
@@ -59,22 +66,20 @@ Jupyter](https://foundations.projectpythia.org/foundations/getting-started-jupyt
 
 If you are interested in running this material locally on your computer, you will need to follow this workflow:
 
-(Replace "cookbook-example" with the title of your cookbooks)
-
-1. Clone the `https://github.com/ProjectPythia/cookbook-example` repository:
+1. Clone the `https://github.com/ProjectPythia/paleoPCA-Cookbook` repository:
 
    ```bash
-    git clone https://github.com/ProjectPythia/cookbook-example.git
+    git clone https://github.com/ProjectPythia/paleoPCA-Cookbook.git
    ```
 
-1. Move into the `cookbook-example` directory
+1. Move into the `paleoPCA-Cookbook` directory
    ```bash
-   cd cookbook-example
+   cd paleoPCA-Cookbook
    ```
 1. Create and activate your conda environment from the `environment.yml` file
    ```bash
    conda env create -f environment.yml
-   conda activate cookbook-example
+   conda activate paleoPCA-Cookbook
    ```
 1. Move into the `notebooks` directory and start up Jupyterlab
    ```bash

_toc.yml

@@ -4,6 +4,6 @@ parts:
   - caption: Preamble
     chapters:
       - file: notebooks/how-to-cite
-  - caption: Introduction
+  - caption: Model-Data Comparison
     chapters:
-      - file: notebooks/notebook-template
+      - file: notebooks/paleoPCA

environment.yml

@@ -1,7 +1,20 @@
-name: cookbook-dev
+name: paleoPCA-Cookbook
 channels:
   - conda-forge
 dependencies:
   - jupyter-book
   - jupyterlab
   - sphinx-pythia-theme
+  - pip
+  - pandas
+  - xarray
+  - s3fs
+  - fsspec
+  - numpy
+  - cartopy
+  - matplotlib
+  - pip:
+    - pyleoclim
+    - eofs
+    - nc_time_axis
+