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Merge develop and publish (#112)
* Removed Python requirement * Add rough outline, objective, and title for synthesis vignette * changed path for traits github installation * removed references to private key * changed season 2 to season 6 * made revisions according to issue #101 * Combine data and set up model for weather/trait synthesis * Run and plot models for all cultivars, get histogram of inflection points * Add draft of text explaining the weather/trait synthesis and analysis * made more edits in reference to issue #101 * Calculate greenness metric for single image file and plot with canopy cover * Add draft of text explaining the image/trait synthesis * '=' --> '<-' * Updated vignette * Change <- back to = to resolve compile error * Updated for local file name and leaf position in image * Added tags to code blocks * remove type * removed typo * Adjust weather/trait model parameters * make .yml easier to read * add relevant R history to gitignore * fix chunk name to knit book * fix headers, style issues * header formatting * Fix inflection point calculation by using analytical solution * fixing headers and turning off chunks that don't work * make syntax more clear * don't need to install this every time * collapse to section in output * override default gitbook presets * add some files to gitignore * fix headers * Improve image metric text Co-Authored-By: KristinaRiemer <reamy316@aim.com> * Redo weather/trait model using nest and map method * condense top level headers in the Overview * restructure first vignette * Edit weather vignette (#107) * Move API and database details from vignette to tutorial * Keep only one time series plot of a weather variable * Add additional plot with all variables time series * Move chunk-level commands to index.Rmd * Fix all markdown formatting * Edit heading in weather tutorial Co-Authored-By: KristinaRiemer <reamy316@aim.com> * Specify Clowder link to TERRA REF Co-Authored-By: KristinaRiemer <reamy316@aim.com> * Fix piping format * Update vignettes/02-get-weather-data-R.Rmd * Switch back to loop method for runnning models * Updated to minimalist vignette to reflect actual data conditions * Remove API key * Updated style and format to suggested standard * Update index.Rmd Co-Authored-By: jeanetteclark <jclark@nceas.ucsb.edu> * Update index.Rmd - whitespace Co-Authored-By: jeanetteclark <jclark@nceas.ucsb.edu> * change F to FALSE Co-Authored-By: jeanetteclark <jclark@nceas.ucsb.edu> * change F to False Co-Authored-By: jeanetteclark <jclark@nceas.ucsb.edu> * Fixed up images vignettes. Still needs where to get zip from * Fixed a logic problem * Made some David recommended changes * Updated to successful compile * Changed some variable names to be consistent in naming convention * Fix section headers * Corrected greeness algorithm * Added greenness citation * Added .gitignore * remove API key call * update gitignore * update gitignore again * Added information on finding gdal * add a hidden chunk to get paths correct for bookdown structure * rendered book materials
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‎.gitignore‎

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‎_bookdown.yml‎

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book_filename: "terraref-tutorials"
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delete_merged_file: true
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output_dir: "docs"
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language:
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ui:
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chapter_name: "Chapter "
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rmd_files: ["index.Rmd", "vignettes/00-introduction.Rmd", "vignettes/01-get-trait-data-R.Rmd", "vignettes/02-get-weather-data-R.Rmd",
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"vignettes/03-get-images-python.Rmd", "vignettes/04-synthesis-data.Rmd", "traits/03-access-r-traits.Rmd","sensors/01-meteorological-data.Rmd",
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rmd_files: ["index.Rmd",
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"vignettes/00-introduction.Rmd",
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"vignettes/01-get-trait-data-R.Rmd",
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"vignettes/02-get-weather-data-R.Rmd",
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‎_output.yml‎

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config:
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toc:
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