rename output dir to docs

jnyaanga · Apr 11, 2022 · fd299a2 · fd299a2
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diff --git a/.Rproj.user/A7880BF4/sources/prop/3C94AC20 b/.Rproj.user/A7880BF4/sources/prop/3C94AC20
@@ -1,6 +1,6 @@
 {
     "source_window_id": "",
     "Source": "Source",
-    "cursorPosition": "4,73",
+    "cursorPosition": "1,17",
     "scrollLine": "0"
 }
diff --git a/_bookdown.yml b/_bookdown.yml
@@ -1,5 +1,5 @@
 book_filename: "bookdown-thesis.Rmd"
-output_dir: "book"
+output_dir: "docs"
 delete_merged_file: true
 always_allow_html: yes
 new_session: true # required for kableExtra to play nicely with bookdown 
diff --git a/book/01_intro.md → docs/01_intro.md b/book/01_intro.md → docs/01_intro.md
diff --git a/book/02_chapter2.md → docs/02_chapter2.md b/book/02_chapter2.md → docs/02_chapter2.md
diff --git a/book/03_chapter3.md → docs/03_chapter3.md b/book/03_chapter3.md → docs/03_chapter3.md
diff --git a/book/04_chapter4.md → docs/04_chapter4.md b/book/04_chapter4.md → docs/04_chapter4.md
@@ -39,8 +39,8 @@ Several functions in the easyXpress package require specific naming conventions
 
 
 ```{=html}
-<div id="htmlwidget-bbd67d006efe78106fc6" style="width:100%;height:auto;" class="datatables html-widget"></div>
-<script type="application/json" data-for="htmlwidget-bbd67d006efe78106fc6">{"x":{"filter":"none","vertical":false,"caption":"<caption>Suggested naming conventions for CellProfiler metadata.<\/caption>","data":[["20191119-growth-p05-m2X_C03.TIF","20191119-growth-p06-m2X_C09.TIF","20191119-growth-p09-m2X_C06.TIF"],["/CellProfiler/example/raw_images","/CellProfiler/example/raw_images","/CellProfiler/example/raw_images"],["20191119","20191119","20191119"],["growth","growth","growth"],["p05","p06","p09"],["m2x","m2x","m2x"],["C03","C09","C06"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>Image_FileName_RawBF<\/th>\n      <th>Image_PathName_RawBF<\/th>\n      <th>Metadata_Date<\/th>\n      <th>Metadata_Experiment<\/th>\n      <th>Metadata_Plate<\/th>\n      <th>Metadata_Magnification<\/th>\n      <th>Metadata_Well<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-c297ecb3459ee125ea46" style="width:100%;height:auto;" class="datatables html-widget"></div>
+<script type="application/json" data-for="htmlwidget-c297ecb3459ee125ea46">{"x":{"filter":"none","vertical":false,"caption":"<caption>Suggested naming conventions for CellProfiler metadata.<\/caption>","data":[["20191119-growth-p05-m2X_C03.TIF","20191119-growth-p06-m2X_C09.TIF","20191119-growth-p09-m2X_C06.TIF"],["/CellProfiler/example/raw_images","/CellProfiler/example/raw_images","/CellProfiler/example/raw_images"],["20191119","20191119","20191119"],["growth","growth","growth"],["p05","p06","p09"],["m2x","m2x","m2x"],["C03","C09","C06"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>Image_FileName_RawBF<\/th>\n      <th>Image_PathName_RawBF<\/th>\n      <th>Metadata_Date<\/th>\n      <th>Metadata_Experiment<\/th>\n      <th>Metadata_Plate<\/th>\n      <th>Metadata_Magnification<\/th>\n      <th>Metadata_Well<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
 ```
 
 The naming of "Metadata_Plate" and "Metadata_Well" are essential to the *setflags()*, *viewPlate()*, *viewWell()*, and *viewDose()* functions. Additionally, "Image_fileName_RawBF" and "Image_PathName_RawBF" are necessary for the proper function of *viewDose()*.

diff --git a/book/05_discussion.md → docs/05_discussion.md b/book/05_discussion.md → docs/05_discussion.md
diff --git a/book/06_references.md → docs/06_references.md b/book/06_references.md → docs/06_references.md
diff --git a/book/07_appendix.md → docs/07_appendix.md b/book/07_appendix.md → docs/07_appendix.md
diff --git a/book/404.html → docs/404.html b/book/404.html → docs/404.html
diff --git a/...etch-in-developmental-growth-control.html → ...etch-in-developmental-growth-control.html b/...etch-in-developmental-growth-control.html → ...etch-in-developmental-growth-control.html
diff --git a/...namics-of-c.-elegans-cuticle-mutants.html → ...namics-of-c.-elegans-cuticle-mutants.html b/...namics-of-c.-elegans-cuticle-mutants.html → ...namics-of-c.-elegans-cuticle-mutants.html
diff --git a/book/appendix.html → docs/appendix.html b/book/appendix.html → docs/appendix.html
diff --git a/...-allocation-during-c.-elegans-growth.html → ...-allocation-during-c.-elegans-growth.html b/...-allocation-during-c.-elegans-growth.html → ...-allocation-during-c.-elegans-growth.html
diff --git a/book/dedication.html → docs/dedication.html b/book/dedication.html → docs/dedication.html
diff --git a/book/discussion-2.html → docs/discussion-2.html b/book/discussion-2.html → docs/discussion-2.html
diff --git a/...py-data-generated-using-cellprofiler.html → ...py-data-generated-using-cellprofiler.html b/...py-data-generated-using-cellprofiler.html → ...py-data-generated-using-cellprofiler.html
@@ -275,8 +275,8 @@ <h3><span class="header-section-number">4.4.3</span> Paraquat dose response</h3>
 <div id="naming-conventions" class="section level3" number="4.4.4">
 <h3><span class="header-section-number">4.4.4</span> Naming conventions</h3>
 <p>Several functions in the easyXpress package require specific naming conventions to work properly. For full details regarding essential file naming and directory structure see the package repository (<a href="https://github.com/AndersenLab/easyXpress" class="uri">https://github.com/AndersenLab/easyXpress</a>). Importantly, when using the Metadata module in CellProfiler to extract information describing your images, specific column names are suggested.</p>
-<div id="htmlwidget-bbd67d006efe78106fc6" style="width:100%;height:auto;" class="datatables html-widget"></div>
-<script type="application/json" data-for="htmlwidget-bbd67d006efe78106fc6">{"x":{"filter":"none","vertical":false,"caption":"<caption>Suggested naming conventions for CellProfiler metadata.<\/caption>","data":[["20191119-growth-p05-m2X_C03.TIF","20191119-growth-p06-m2X_C09.TIF","20191119-growth-p09-m2X_C06.TIF"],["/CellProfiler/example/raw_images","/CellProfiler/example/raw_images","/CellProfiler/example/raw_images"],["20191119","20191119","20191119"],["growth","growth","growth"],["p05","p06","p09"],["m2x","m2x","m2x"],["C03","C09","C06"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>Image_FileName_RawBF<\/th>\n      <th>Image_PathName_RawBF<\/th>\n      <th>Metadata_Date<\/th>\n      <th>Metadata_Experiment<\/th>\n      <th>Metadata_Plate<\/th>\n      <th>Metadata_Magnification<\/th>\n      <th>Metadata_Well<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-c297ecb3459ee125ea46" style="width:100%;height:auto;" class="datatables html-widget"></div>
+<script type="application/json" data-for="htmlwidget-c297ecb3459ee125ea46">{"x":{"filter":"none","vertical":false,"caption":"<caption>Suggested naming conventions for CellProfiler metadata.<\/caption>","data":[["20191119-growth-p05-m2X_C03.TIF","20191119-growth-p06-m2X_C09.TIF","20191119-growth-p09-m2X_C06.TIF"],["/CellProfiler/example/raw_images","/CellProfiler/example/raw_images","/CellProfiler/example/raw_images"],["20191119","20191119","20191119"],["growth","growth","growth"],["p05","p06","p09"],["m2x","m2x","m2x"],["C03","C09","C06"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>Image_FileName_RawBF<\/th>\n      <th>Image_PathName_RawBF<\/th>\n      <th>Metadata_Date<\/th>\n      <th>Metadata_Experiment<\/th>\n      <th>Metadata_Plate<\/th>\n      <th>Metadata_Magnification<\/th>\n      <th>Metadata_Well<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"order":[],"autoWidth":false,"orderClasses":false}},"evals":[],"jsHooks":[]}</script>
 <p>The naming of “Metadata_Plate” and “Metadata_Well” are essential to the <em>setflags()</em>, <em>viewPlate()</em>, <em>viewWell()</em>, and <em>viewDose()</em> functions. Additionally, “Image_fileName_RawBF” and “Image_PathName_RawBF” are necessary for the proper function of <em>viewDose()</em>.</p>
 </div>
 <div id="data-availability" class="section level3" number="4.4.5">

diff --git a/book/img/appendixA/fig1.png → docs/img/appendixA/fig1.png b/book/img/appendixA/fig1.png → docs/img/appendixA/fig1.png
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diff --git a/...anchor-sections-1.0.1/anchor-sections.css → ...anchor-sections-1.0.1/anchor-sections.css b/...anchor-sections-1.0.1/anchor-sections.css → ...anchor-sections-1.0.1/anchor-sections.css
diff --git a/.../anchor-sections-1.0.1/anchor-sections.js → .../anchor-sections-1.0.1/anchor-sections.js b/.../anchor-sections-1.0.1/anchor-sections.js → .../anchor-sections-1.0.1/anchor-sections.js
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diff --git a/...ibs/gitbook-2.6.7/css/plugin-bookdown.css → ...ibs/gitbook-2.6.7/css/plugin-bookdown.css b/...ibs/gitbook-2.6.7/css/plugin-bookdown.css → ...ibs/gitbook-2.6.7/css/plugin-bookdown.css
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