update

tklammsteiner · tklammsteiner · commit 59822ef5b067 · 2022-10-03T08:35:50.000+02:00
diff --git a/.Rproj.user/A30A3472/sources/prop/INDEX b/.Rproj.user/A30A3472/sources/prop/INDEX
@@ -1,6 +1,10 @@
 ~%2FGithub%2Feggsurfacemicrobiome%2F_site.yml="ED40B1E0"
 ~%2FGithub%2Feggsurfacemicrobiome%2Fdata-analysis-16S.Rmd="0039AD94"
 ~%2FGithub%2Feggsurfacemicrobiome%2Fdata-analysis-16s.Rmd="DA1A8BE7"
+~%2FGithub%2Feggsurfacemicrobiome%2Fdata-analysis-BAC.Rmd="7E527284"
+~%2FGithub%2Feggsurfacemicrobiome%2Fdata-analysis-FUN.Rmd="22702AE3"
+~%2FGithub%2Feggsurfacemicrobiome%2Fdata-analysis-ITS.Rmd="FD1B178A"
+~%2FGithub%2Feggsurfacemicrobiome%2Fdata-analysis.Rmd="43F868D0"
 ~%2FGithub%2Feggsurfacemicrobiome%2Fdata-generation.rmd="B6B2991B"
 ~%2FGithub%2Feggsurfacemicrobiome%2Fdata.Rmd="CE044A0E"
 ~%2FGithub%2Feggsurfacemicrobiome%2Ffigures.Rmd="32EF6EE5"
diff --git a/.Rproj.user/shared/notebooks/paths b/.Rproj.user/shared/notebooks/paths
@@ -1,6 +1,10 @@
 C:/Users/thoma/Documents/Github/eggsurfacemicrobiome/_site.yml="E98F1FB4"
 C:/Users/thoma/Documents/Github/eggsurfacemicrobiome/data-analysis-16S.Rmd="61B1B392"
 C:/Users/thoma/Documents/Github/eggsurfacemicrobiome/data-analysis-16s.Rmd="FC12DF2E"
+C:/Users/thoma/Documents/Github/eggsurfacemicrobiome/data-analysis-BAC.Rmd="CDBA5963"
+C:/Users/thoma/Documents/Github/eggsurfacemicrobiome/data-analysis-FUN.Rmd="349B2BE8"
+C:/Users/thoma/Documents/Github/eggsurfacemicrobiome/data-analysis-ITS.Rmd="45CE665B"
+C:/Users/thoma/Documents/Github/eggsurfacemicrobiome/data-analysis.Rmd="AF202A51"
 C:/Users/thoma/Documents/Github/eggsurfacemicrobiome/data-generation.rmd="4E2105CD"
 C:/Users/thoma/Documents/Github/eggsurfacemicrobiome/data.Rmd="D87DF01B"
 C:/Users/thoma/Documents/Github/eggsurfacemicrobiome/figures.Rmd="6B4945E7"
diff --git a/_site.yml b/_site.yml
@@ -9,7 +9,7 @@ navbar:
         - text: 'Data generation'
           href: data-generation.html
         - text: 'Data analysis'
-          href: data-analysis-16S.html
+          href: data-analysis-BAC.html
         - text: 'Data download'
           href: data.html
     - text: 'Figures'
diff --git a/data-analysis-BAC.Rmd b/data-analysis-BAC.Rmd
diff --git a/data-analysis-FUN.Rmd b/data-analysis-FUN.Rmd
diff --git a/docs/data-analysis-BAC.html b/docs/data-analysis-BAC.html
diff --git a/docs/data-analysis-ITS.html b/docs/data-analysis-ITS.html
diff --git a/docs/data-generation.html b/docs/data-generation.html
@@ -261,7 +261,7 @@
       <a href="data-generation.html">Data generation</a>
     </li>
     <li>
-      <a href="data-analysis-16S.html">Data analysis</a>
+      <a href="data-analysis-BAC.html">Data analysis</a>
     </li>
     <li>
       <a href="data.html">Data download</a>
diff --git a/docs/data.html b/docs/data.html
@@ -267,7 +267,7 @@
       <a href="data-generation.html">Data generation</a>
     </li>
     <li>
-      <a href="data-analysis-16S.html">Data analysis</a>
+      <a href="data-analysis-BAC.html">Data analysis</a>
     </li>
     <li>
       <a href="data.html">Data download</a>
@@ -337,8 +337,8 @@ <h2>Metadata</h2>
 <h2>Explanation of metadata variables</h2>
 <p>This table provides an explanation of the variables presented in the
 metadata table.</p>
-<div id="htmlwidget-0b6a7c614e2751e20f3a" class="reactable html-widget" style="width:auto;height:auto;"></div>
-<script type="application/json" data-for="htmlwidget-0b6a7c614e2751e20f3a">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"Variable":["SampleID","Replicate","Group","Label","Condition","Stage","Tissue","Time","Temperature","Target","Primer_set","Forward_primer","Reverse_primer","Forward_reads","Reverse_reads","Reads","Extraction_date","Biomass"],"Description":["Unique sample identifier","Number of replicate","Sample group","Explanation of SampleID","Information about the sterilization of samples","Developmental stage from which the sample was taken","Tissue from which the sample was obtained","Days after the larvae of the first cycle hatched","Rearing temperature","Targeted hypervariable region on the 16S/ITS gene","Primer set used to target the respective hypervariable region on the 16S/ITS gene","Sequence of forward primer","Sequence of reverse primer","File name of forward reads","File name of reverse reads","Number of generated raw reads","Date on which the DNA was extracted","Biomass of the sample from which the DNA was extracted"],"Format":["","","","","","","","[days]","[°C]","","","","","","","","[yyyy-mm-dd]","[g]"]},"columns":[{"accessor":"Variable","name":"Variable","type":"character","maxWidth":170},{"accessor":"Description","name":"Description","type":"character","maxWidth":550},{"accessor":"Format","name":"Format","type":"character","maxWidth":100}],"pagination":false,"defaultPageSize":10,"paginationType":"numbers","showPageInfo":true,"minRows":1,"borderless":true,"compact":true,"dataKey":"d32e20691980d52bebe6916c2d3dfa94"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script>
+<div id="htmlwidget-44e61e9b87b66ae81fab" class="reactable html-widget" style="width:auto;height:auto;"></div>
+<script type="application/json" data-for="htmlwidget-44e61e9b87b66ae81fab">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"Variable":["SampleID","Replicate","Group","Label","Condition","Stage","Tissue","Time","Temperature","Target","Primer_set","Forward_primer","Reverse_primer","Forward_reads","Reverse_reads","Reads","Extraction_date","Biomass"],"Description":["Unique sample identifier","Number of replicate","Sample group","Explanation of SampleID","Information about the sterilization of samples","Developmental stage from which the sample was taken","Tissue from which the sample was obtained","Days after the larvae of the first cycle hatched","Rearing temperature","Targeted hypervariable region on the 16S/ITS gene","Primer set used to target the respective hypervariable region on the 16S/ITS gene","Sequence of forward primer","Sequence of reverse primer","File name of forward reads","File name of reverse reads","Number of generated raw reads","Date on which the DNA was extracted","Biomass of the sample from which the DNA was extracted"],"Format":["","","","","","","","[days]","[°C]","","","","","","","","[yyyy-mm-dd]","[g]"]},"columns":[{"accessor":"Variable","name":"Variable","type":"character","maxWidth":170},{"accessor":"Description","name":"Description","type":"character","maxWidth":550},{"accessor":"Format","name":"Format","type":"character","maxWidth":100}],"pagination":false,"defaultPageSize":10,"paginationType":"numbers","showPageInfo":true,"minRows":1,"borderless":true,"compact":true,"dataKey":"d32e20691980d52bebe6916c2d3dfa94"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script>
 </div>
 
 
diff --git a/docs/figures.html b/docs/figures.html
@@ -261,7 +261,7 @@
       <a href="data-generation.html">Data generation</a>
     </li>
     <li>
-      <a href="data-analysis-16S.html">Data analysis</a>
+      <a href="data-analysis-BAC.html">Data analysis</a>
     </li>
     <li>
       <a href="data.html">Data download</a>
diff --git a/docs/index.html b/docs/index.html
@@ -261,7 +261,7 @@
       <a href="data-generation.html">Data generation</a>
     </li>
     <li>
-      <a href="data-analysis-16S.html">Data analysis</a>
+      <a href="data-analysis-BAC.html">Data analysis</a>
     </li>
     <li>
       <a href="data.html">Data download</a>
diff --git a/docs/sterilization.html b/docs/sterilization.html
@@ -261,7 +261,7 @@
       <a href="data-generation.html">Data generation</a>
     </li>
     <li>
-      <a href="data-analysis-16S.html">Data analysis</a>
+      <a href="data-analysis-BAC.html">Data analysis</a>
     </li>
     <li>
       <a href="data.html">Data download</a>
