git push origin masterMerge branch 'bookdown'

Author: dlebauer

README.md

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+rmd_subdir: true
+rmd_files: ["index.Rmd", "Intro.Rmd", "data-sources.Rmd", 
+"software.Rmd", "scientific-objectives-and-experimental-design/README.Rmd",
+"scientific-objectives-and-experimental-design/protocols/README.Rmd",
+"scientific-objectives-and-experimental-design/protocols/controlled-environment-protocols.Rmd",
+"scientific-objectives-and-experimental-design/protocols/manual-field-data-protocols.Rmd",
+"scientific-objectives-and-experimental-design/protocols/phenotractor-protocols.Rmd",
+"scientific-objectives-and-experimental-design/protocols/sensor-calibration.Rmd",
+"scientific-objectives-and-experimental-design/protocols/template-protocol.Rmd",
+"scientific-objectives-and-experimental-design/protocols/uav-protocols.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/README.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-danforth/README.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-danforth/sorghum-lines-danforth.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/README.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-1.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-1-continued.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-genomics/sorghum-lines-genomics-year-2.Rmd",
+"scientific-objectives-and-experimental-design/experimental-design/experimental-design-mac.Rmd",
+"user-manual/README.Rmd",
+"user-manual/what-data-is-available.Rmd",
+"user-manual/data-products/README.Rmd",
+"user-manual/data-products/environmental-conditions.Rmd",
+"user-manual/data-products/fluorescence-intensity-imaging.Rmd",
+"user-manual/data-products/genomics-data.Rmd",
+"user-manual/data-products/geospatial-information.Rmd",
+"user-manual/data-products/hyperspectral-imaging-data.Rmd",
+"user-manual/data-products/infrared-heat-imaging-data.Rmd",
+"user-manual/data-products/multispectral-imaging-data.Rmd",
+"user-manual/data-products/meteorological-data.Rmd",
+"user-manual/data-products/plantcv-trait-data.Rmd", 
+"user-manual/data-products/point-cloud-data.Rmd",
+"user-manual/how-to-access-data/README.Rmd",
+"user-manual/how-to-access-data/using-clowder-sensor-and-genoomics-data.Rmd",
+"user-manual/how-to-access-data/using-globus-sensor-and-genomics-data.Rmd",
+"user-manual/how-to-access-data/using-betydb-trait-data-experimental-metadata/README.Rmd",
+"user-manual/how-to-access-data/using-betydb-trait-data-experimental-metadata/accessing-betydb-via-arcmap-and-other-gis-software.Rmd",
+"user-manual/how-to-access-data/using-coge-genomics.Rmd",
+"user-manual/how-to-access-data/using-cyverse-genomics.Rmd",
+"user-manual/how-to-access-data/using-analysis-workbench-all-data.Rmd",
+"user-manual/data-use-policy.Rmd",
+"user-manual/manuscripts-and-authorship-guidelines.Rmd",
+"user-manual/release-reprocessing-schedule.Rmd",
+"technical-documentation/README.Rmd",
+"technical-documentation/data-standards/README.Rmd",
+"technical-documentation/data-standards/existing-data-standards.Rmd",
+"technical-documentation/data-standards/agronomic-and-phenotype-data-standards.Rmd",
+"technical-documentation/data-standards/genomic-data-standards.Rmd",
+"technical-documentation/data-standards/sensor-data-standards.Rmd",
+"technical-documentation/data-standards/data-standards-committee.Rmd",
+"technical-documentation/directory-structure.Rmd",
+"technical-documentation/data-storage.Rmd",
+"technical-documentation/data-transfer.Rmd",
+"technical-documentation/data-processing-pipeline/README.Rmd",
+"technical-documentation/data-processing-pipeline/geospatial-time-series-structure.Rmd",
+"technical-documentation/data-backup.Rmd",
+"technical-documentation/data-collection.Rmd",
+"technical-documentation/data-product-creation/README.Rmd",
+"technical-documentation/data-product-creation/genomic-data.Rmd",
+"technical-documentation/data-product-creation/hyperspectral-data.Rmd",
+"technical-documentation/quality-assurance-and-quality-control.Rmd",
+"developer-manual/README.Rmd",
+"developer-manual/submitting-data-to-clowder.Rmd",
+"developer-manual/submitting-data-to-betydb.Rmd",
+"developer-manual/submitting-data-to-coge.Rmd",
+"developer-manual/developing-clowder-extractors.Rmd",
+"tutorials.Rmd",
+"appendix/README.Rmd",
+"appendix/code-of-conduct.Rmd",
+"appendix/collaboration-tools.Rmd",
+"appendix/glossary.Rmd"]

_bookdown.yml

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+bookdown::gitbook:
+  split_by: chapter

_output.yml

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+---
+title: "TERRA REF"
+---

appendix/README.md renamed to appendix/README.Rmd

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+# Introduction
+
+## About this book
+
+This book describes the TERRA-REF data collection, computing, and analysis pipelines. The following links provide quick access to:
+
+* [Available Data](user-manual/what-data-is-available.md)
+* [How to access data](user-manual/how-to-access-data/)
+* [Hands on tutorials](tutorials.md)
+
+## About TERRA-REF
+
+The ARPA-E-funded Transportation Energy Resources from Renewable Agriculture Phenotyping Reference Platform \(TERRA-REF\) program aims to transform plant breeding by using remote sensing to quantify plant traits such as plant architecture, carbon uptake, tissue chemistry, water use, and other features to predict the yield potential and stress resistance of 300+ diverse Sorghum lines.
+
+The data storage and computing system provides researchers with access to the reference phenotyping data and analytics resources using a high performance computing environment. The reference phenotyping data includes direct measurements and sensor observations, derived plant phenotypes, and genetic and genomic data.
+
+Our objectives are to ensure that the software and data in the reference data and computing pipeline are interoperable, reusable, extensible, and understandable. Providing clear definitions of common formats will make it easier to analyze and exchange data and results.
+
+## Versions
+
+* The first edition \(alpha release\) was published **November 2016**.
+* The second edition \(beta release\) will be published **November 2018** 
+* The third edition \(version 1.0\) will be published **November 2019**
+