Merge pull request #5 from khider/info

Book setup

.gitignore

@@ -1,6 +1,7 @@
 
 .ipynb_checkpoints/Coral_thermometer_calibration-checkpoint.ipynb
-./virtual_documents
+/.virtual_documents
 .ipynb_checkpoints/DataExploration-checkpoint.ipynb
 .DS_Store
 /.ipynb_checkpoints
+/paleobook/_build

paleobook/_config.yml

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+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: Coral Sr/Ca Calibration - An Example from Dry Tortugas 
+author: Deborah Khider
+logo: coral_logo.jpg
+
+# Patterns to skip when building the book. Can be glob-style (e.g. "*skip.ipynb")
+exclude_patterns            : [_build, Thumbs.db, .DS_Store, "**.ipynb_checkpoints"]
+# Auto-exclude files not in the toc
+only_build_toc_files        : true
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: off
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/khider/dry-tortugas-calibration-fun  # Online location of your book
+  branch: main  # Which branch of the repository should be used when creating links (optional)
+
+# Add GitHub buttons to your book
+# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+html:
+  use_issues_button: true
+  use_repository_button: true
+  use_multitoc_numbering    : true   # Continuous numbering across parts/chapters

paleobook/_toc.yml

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+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: intro
+parts:
+  - caption: Getting Started
+    chapters:
+      - file: DataExploration.ipynb
+  - caption: Calibration
+    chapters:
+      - file: Calibration.ipynb
+      - file: BayesianCalibration.ipynb

paleobook/intro.md

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+[![PyPI](https://img.shields.io/badge/python-3.11-yellow.svg)]()
+[![license](https://img.shields.io/github/license/khider/dry-tortugas-calibration-fun.svg)]()
+
+
+# Coral Sr/Ca calibration - An example from Dry Tortugas
+
+
+This Jupyter Book covers the calibration of coral Sr/Ca to sea surface temperature using data from Dry Tortugas (DeLong et al., 2011). The book illustrates the frequentist and Bayesian approach to the task. 
+
+## Author
+
+[Deborah Khider](https://github.com/khider)
+
+## Contributor
+
+<a href="https://github.com/khider/dry-tortugas-calibration-fun/graphs/contributors">
+  <img src="https://contrib.rocks/image?repo=khider/dry-tortugas-calibration-fun" />
+</a>
+
+## Structure
+
+This Book is broken down into three chapters:
+- Data exploration of the Sr/Ca data from three cores and nearby sea surface temperature data
+- Calibration uses ordinary and weighted least square regression
+- Bayesian calibration presents a Bayesian alternative to OLS. 
+
+## Data Reference
+DeLong, K.L., J.A. Flannery, C.R. Maupin, R.Z. Poore, and T.M. Quinn. 2011. A coral Sr/Ca calibration and replication study of two massive corals from the Gulf of Mexico. Palaeogeography, Palaeoclimatology, Palaeoecology, 307(1-4), 117-128. doi: 10.1016/j.palaeo.2011.05.005
+
+Dataset citation: DeLong, K.L.; Flannery, J.A.; Maupin, C.R.; Poore, R.Z.; Quinn, T.M. (2011-09-14): NOAA/WDS Paleoclimatology - Dry Tortugas Siderastrea and Montastraea Coral Sr/Ca Data, 1992-2008. [indicate subset used]. NOAA National Centers for Environmental Information. https://doi.org/10.25921/n674-8145. Accessed 2024-09-05. 
+
+## License
+
+All notebooks herein are provided under an [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0) license.
+
+## Citation
+
+We needn't tell you that making research tools accessible requires time and effort. If you find any of these resources useful and use them in your own research, please do us the kindness of one or more citations. Notebooks in this collection are registered on Zenodo, and associated with a digital object identifier (DOI).  A ready-to-use citation is provided in this GitHub repository in APA and BibTex (in the About section on the right panel, click on "Cite this repository"). If you use Pyleoclim, please cite them as well. It will make us (and NSF!) very happy to hear that these investments spawned more research.

paleobook/meta_data/chapter_meta.yaml

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+shortname: calibration
+type: Paleobook
+thumbnail: coral_logo.jpg
+parts:
+  - caption: Getting Started
+    chapters:
+      - shortname: Data Exploration
+        filename: DataExploration
+        thumbnail: dataexp.png
+        tags:
+          domains:
+            - paleoceanography
+            - Sr/Ca
+            - coral
+            - calibration
+          packages:
+            - matplotlib
+            - pyleoclim
+            - pandas
+  - caption: Science Bits - Calibration
+    chapters:
+      - shortname: Calibration - OLS
+        filename: Calibration
+        thumbnail: table.png
+        tags:
+          domains:
+            - Statistics
+            - Calibration
+            - Paleocenography
+          packages:
+            - statsmodel
+            - Great Tables
+      - shortname: Bayesian Calibration
+        filename: BayesianCalibration
+        thumbnail: bayes.png
+        tags:
+          domains:
+            - Bayesian Statistics
+            - Calibration
+            - Paleocenography
+          packages:
+            - pymc
+            - arviz