Merge pull request #17 from ecohealthalliance/dev

shift to quarto; fix #12; fix #13; fix #14; fix #15
ecohealthalliance · Nov 30, 2024 · 12eb698 · 12eb698
2 parents 8f83623 + c1b8da1
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diff --git a/.Rprofile b/.Rprofile
@@ -0,0 +1 @@
+source("renv/activate.R")
diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,6 @@
 .Rhistory
 .RData
 .Ruserdata
+
+/.quarto/
+
diff --git a/02-tools.Rmd → 01-tools.qmd b/02-tools.Rmd → 01-tools.qmd
diff --git a/03-database.Rmd → 02-database.qmd b/03-database.Rmd → 02-database.qmd
@@ -1,3 +1,15 @@
+```{r setup, include = FALSE}
+library(airtabler)
+
+for (f in list.files(here::here("R"), full.names = TRUE)) source (f)
+
+airtable_metadata <- airtable(
+  base = "appAL7fJUpBPYtOq4", 
+  tables = "Meta Data"
+)$`Meta Data`$select()
+```
+
+
 # Database {#database}
 
 The current database is built using [Airtable](https://airtable.com). The current database has the following schema:

diff --git a/04-sources.Rmd → 03-sources.qmd b/04-sources.Rmd → 03-sources.qmd
diff --git a/05-updates.Rmd → 04-updates.qmd b/05-updates.Rmd → 04-updates.qmd
diff --git a/06-survey.Rmd → 05-survey.qmd b/06-survey.Rmd → 05-survey.qmd
diff --git a/07-references.Rmd → 06-references.qmd b/07-references.Rmd → 06-references.qmd
diff --git a/_bookdown.yml b/_bookdown.yml
diff --git a/_bookdown_files/_main_files/figure-html/actions diagram-1.png b/_bookdown_files/_main_files/figure-html/actions diagram-1.png
diff --git a/_bookdown_files/_main_files/figure-latex/actions diagram-1.pdf b/_bookdown_files/_main_files/figure-latex/actions diagram-1.pdf
diff --git a/_output.yml b/_output.yml
diff --git a/_quarto.yml b/_quarto.yml
@@ -0,0 +1,55 @@
+project:
+  type: book
+  output-dir: docs
+
+book:
+  title: Africa CDC Database
+  subtitle: Technical Handbook
+  author:
+    - name: Dr Jonathan Epstein
+      orcid: 0000-0002-1373-9301
+      email: [email protected]
+      affiliation: 
+        - name: EcoHealth Alliance
+          city: New York
+    - name: Ava Sullivan
+      orcid: 0000-0003-4339-2430
+      email: [email protected]
+      affiliation:
+        - name: EcoHealth Alliance
+          city: New York
+    - name: Shannon Ball
+      orcid: 0000-0001-8306-3493
+      email: [email protected]
+      affiliation:
+        - name: EcoHealth Alliance
+          city: New York
+  date: last-modified
+  date-format: "DD MMMM YYYY"
+  chapters:
+    - index.qmd
+    - 01-tools.qmd
+    - 02-database.qmd
+    - 03-sources.qmd
+    - 04-updates.qmd
+    - 05-survey.qmd
+    - 06-references.qmd
+  cover-image: images/AfricaCDC_Logo.png
+  search: true
+  repo-url: https://github.com/ecohealthalliance/acdc-db-handbook/
+  repo-actions: [edit]
+  downloads: [pdf, epub]
+  sharing: [twitter, facebook]
+
+bibliography: book.bib
+
+format:
+  html:
+    theme: lumen
+    highlight-style: breeze
+  pdf:
+    documentclass: scrreprt
+    highlight-style: breeze
+  epub:
+    cover-image: images/AfricaCDC_Logo.png
+    highlight-style: breeze
diff --git a/rig-handbook.Rproj → acdc-db-handbook.Rproj b/rig-handbook.Rproj → acdc-db-handbook.Rproj
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/_main.epub b/docs/_main.epub
diff --git a/docs/_main.pdf b/docs/_main.pdf
diff --git a/docs/_main.tex b/docs/_main.tex
diff --git a/docs/_main_files/figure-html/actions diagram-1.png b/docs/_main_files/figure-html/actions diagram-1.png
diff --git a/docs/database.html b/docs/database.html
diff --git a/docs/images/airtable_Weekly Digest.png b/docs/images/airtable_Weekly Digest.png
diff --git a/docs/images/clinicaltrial1.png b/docs/images/clinicaltrial1.png
diff --git a/docs/images/clinicaltrial2.png b/docs/images/clinicaltrial2.png
diff --git a/docs/images/clinicaltrial3.png b/docs/images/clinicaltrial3.png
diff --git a/docs/images/clinicaltrial4.png b/docs/images/clinicaltrial4.png
diff --git a/docs/images/clinicaltrial5.png b/docs/images/clinicaltrial5.png
diff --git a/docs/images/clinicaltrial6.png b/docs/images/clinicaltrial6.png
diff --git a/docs/images/clinicaltrial7.png b/docs/images/clinicaltrial7.png
diff --git a/docs/images/clinicaltrial8.png b/docs/images/clinicaltrial8.png
diff --git a/docs/images/database_schema.png b/docs/images/database_schema.png
diff --git a/docs/images/edctp1.png b/docs/images/edctp1.png
diff --git a/docs/images/edctp2.png b/docs/images/edctp2.png
diff --git a/docs/images/gepris1.png b/docs/images/gepris1.png
diff --git a/docs/images/gepris2.png b/docs/images/gepris2.png
diff --git a/docs/images/initial-acdc-db-search_NK.png b/docs/images/initial-acdc-db-search_NK.png
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/introduction.html b/docs/introduction.html
diff --git a/docs/libs/anchor-sections-1.1.0/anchor-sections-hash.css b/docs/libs/anchor-sections-1.1.0/anchor-sections-hash.css
diff --git a/docs/libs/anchor-sections-1.1.0/anchor-sections.css b/docs/libs/anchor-sections-1.1.0/anchor-sections.css
diff --git a/docs/libs/anchor-sections-1.1.0/anchor-sections.js b/docs/libs/anchor-sections-1.1.0/anchor-sections.js
diff --git a/docs/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf b/docs/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf
diff --git a/docs/libs/gitbook-2.6.7/css/plugin-bookdown.css b/docs/libs/gitbook-2.6.7/css/plugin-bookdown.css
diff --git a/docs/libs/gitbook-2.6.7/css/plugin-clipboard.css b/docs/libs/gitbook-2.6.7/css/plugin-clipboard.css