Handbook v2.5 es

.Rhistory

@@ -1,4 +1,3 @@
-############
 learnr,   # interactive tutorials in RStudio Tutorial pane
 swirl,    # interactive tutorials in R console
 # project and file management
@@ -510,3 +509,4 @@ bookdown::render_book(
 output_format = 'bookdown::bs4_book',
 config_file = "_bookdown.yml")
 renv::status()
+here("data", "linelists", "linelist_raw.xlsx")

.github/workflows/create_pr_on_pr.yml

@@ -14,13 +14,11 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v3
 
-      - name: Set up Git
+
+      - name: Set up Git and Github CLI
         run: |
           git config --global user.name 'ntluong95'
           git config --global user.email 'ph.ntluong95@gmail.com'
-
-      - name: Install GitHub CLI
-        run: |
           sudo apt update
           sudo apt install -y gh
 
@@ -35,97 +33,103 @@ jobs:
 
           for lang in "${LANGS[@]}"; do
             TRANSLATION_BRANCH="handbook_${VERSION_SUFFIX/_en/_$lang}"
+            git fetch --prune
 
-            # Check if the translation branch exists
+            # Ensure we have all history
+            git fetch --all            
+
+            #! Check if the translation branch exists
             if git ls-remote --exit-code --heads origin "${TRANSLATION_BRANCH}"; then
               echo "Branch ${TRANSLATION_BRANCH} exists. Checking out and rebasing with ${EN_BRANCH}"
-              git fetch --prune
               git checkout "${TRANSLATION_BRANCH}"
-
-              echo "${EN_BRANCH#refs/heads/}"
-              echo "${TRANSLATION_BRANCH}"
-
-              git status
               git pull -s recursive -X theirs --no-rebase --no-edit origin "${EN_BRANCH#refs/heads/}" --allow-unrelated-histories
-              git push origin "${TRANSLATION_BRANCH}"
-
             else
               echo "Branch ${TRANSLATION_BRANCH} does not exist. Creating new branch from ${EN_BRANCH}."
               git checkout -b "${TRANSLATION_BRANCH}"
               git pull origin "${EN_BRANCH#refs/heads/}"
             fi
 
-            # Force push the changes to the remote repository
+            #! Force push the changes to the remote repository
             git push origin "${TRANSLATION_BRANCH}" --force
+
+            #! Get the list of changed .qmd files: COMPARED WITH main branch
+            changed_files=$(git diff --name-only origin/main "${TRANSLATION_BRANCH}" | grep -E '\.qmd$' | grep -Ev '\.[a-z]{2}\.qmd$')
+
+            if [ -z "$changed_files" ]; then
+              echo "No .qmd file changes to include in PR for ${TRANSLATION_BRANCH}"
+              continue
+            fi
+
+            echo "Changed files: $changed_files"
 
 
-            # Get the date of the latest commit on the english branch
+            #! Get the date of the latest commit on the english branch
             latest_commit_date=$(git show -s --format=%ci ${EN_BRANCH})
 
             echo "Commits on the English branch that were made after the latest commit on the translation branch at $latest_commit_date"
             latest_commit_en_branch=$(git show --format=%H -s ${EN_BRANCH})
             latest_commit_info=$(git log ${EN_BRANCH} --since="$latest_commit_date" --format="%H %s" --reverse)
             commit_messages=$(echo "$latest_commit_info" | cut -d' ' -f2-)
-            latest_commit_master=$(git show --format=%H -s origin/master)
+            latest_commit_main=$(git show --format=%H -s origin/master)
 
             echo $latest_commit_en_branch
-            echo $latest_commit_master
+            echo $latest_commit_main
             echo $latest_commit_info
 
-            # Check if there are new commits
-            if [ "$latest_commit_en_branch" == "$latest_commit_master" ]; then
+            #! Check if there are new commits
+            if [ "$latest_commit_en_branch" == "$latest_commit_main" ]; then
               echo "No new commits to include in PR for ${TRANSLATION_BRANCH}"
               continue
             fi
 
-            # Check if a PR already exists for this branch
+            #! Check if a PR already exists for this branch
             PR_EXISTS=$(gh pr list --head "${TRANSLATION_BRANCH}" --state open --json number --jq length)
             if [ "$PR_EXISTS" -eq 0 ]; then
               echo "Creating new PR for ${TRANSLATION_BRANCH}"
               PR_URL=$(gh pr create --base deploy-preview --head "$TRANSLATION_BRANCH" --title "Handbook ${VERSION_SUFFIX/_en/} $lang" --body "Automated pull request for $lang handbook version ${VERSION_SUFFIX/_en/}")
               PR_NUMBER=$(echo "$PR_URL" | grep -oE '[0-9]+$')
             else
-              # Get the PR number for the translation branch
+              #! Get the PR number for the translation branch
               echo "PR already exists for ${TRANSLATION_BRANCH}"
               PR_NUMBER=$(gh pr list --head "${TRANSLATION_BRANCH}" --state open --json number --jq ".[0].number")
             fi
 
             echo "Pull Request Number: $PR_NUMBER"
+
+            #! Initialize new PR body
+            new_pr_body="# Automated pull request for $lang handbook version ${VERSION_SUFFIX/_en/}"$'\n\n'
+
+            #! Mention a user in the PR description
+            case "$lang" in
+              "vn") new_pr_body+="@ntluong95, please review changes and check the box when you finish"$'\n' ;;
+              "fr") new_pr_body+="@oliviabboyd, please review changes and check the box when you finish"$'\n' ;;
+              "es") new_pr_body+="@amateo250, please review changes and check the box when you finish"$'\n' ;;
+              "jp") new_pr_body+="@hitomik723, please review changes and check the box when you finish"$'\n' ;;
+              "tr") new_pr_body+="@ntluong95, please review changes and check the box when you finish"$'\n' ;;
+              "pt") new_pr_body+="@Luccan97, please review changes and check the box when you finish"$'\n' ;;
+              "ru") new_pr_body+="@ntluong95, please review changes and check the box when you finish"$'\n' ;;
+            esac
 
-            # Add new commits as checkboxes to the PR description
+            #! Add new commits as checkboxes to the PR description
+            IFS=$'\n' # Change the Internal Field Separator to newline for correct iteration over lines
             checkboxes=""
-            for commit in $latest_commit_en_branch; do
-              checkboxes="$checkboxes- [ ] [$commit_messages](https://github.com/${{ github.repository }}/commit/$commit)"
+            for file in $changed_files; do
+              #! List only new commits compared with the main branch, tail -n +2 to skip the first line of output from git log, the latest commit will not be added into the message
+              list_commits=$(git log origin/main..${TRANSLATION_BRANCH} --follow --pretty=format:"%H" -- $file | tail -n +2 | paste -sd, - | sed 's/,/, /g')
+              for commit in $latest_commit_en_branch; do
+                checkboxes="$checkboxes- [ ] Chapter [\`$file\`](https://github.com/${{ github.repository }}/pull/$PR_NUMBER/files?file-filters%5B%5D=.qmd&show-viewed-files=true) has changes in the following commit(s): $list_commits. "
+                checkboxes="$checkboxes"$'\n'"$checkbox"
+
+              done
             done
 
-
-            # Mention a user in the PR description
-            if [ "$lang" = "vn" ]; then
-              checkboxes="$checkboxes @ntluong95, please check the box when you finish"
-            elif [ "$lang" = "fr" ]; then
-              checkboxes="$checkboxes @nsbatra, please check the box when you finish"
-            elif [ "$lang" = "es" ]; then
-              checkboxes="$checkboxes @robcrystalornelas, please check the box when you finish"
-            elif [ "$lang" = "jp" ]; then
-              checkboxes="$checkboxes @ntluong95, please check the box when you finish"
-            elif [ "$lang" = "tr" ]; then
-              checkboxes="$checkboxes @ntluong95, please check the box when you finish"
-            elif [ "$lang" = "pt" ]; then
-              checkboxes="$checkboxes @ntluong95, please check the box when you finish"
-            elif [ "$lang" = "ru" ]; then
-              checkboxes="$checkboxes @ntluong95, please check the box when you finish"
+            if [ -n "$checkboxes" ]; then
+              # Append the checkboxes to the new PR body
+              new_pr_body="$new_pr_body"$'\n'"$checkboxes"
             fi
 
-
-            # Retrieve the current PR description
-            current_pr_body=$(gh pr view $PR_NUMBER --json body --jq '.body')
-
-            # Append checkboxes to the current PR description
-            new_pr_body=$(printf "%s\n%s" "$current_pr_body" "$checkboxes")
-
-            # gh api repos/${{ github.repository }}/issues/$PR_NUMBER --method PATCH --field body="$checkboxes"
             gh api repos/${{ github.repository }}/issues/$PR_NUMBER --method PATCH --field body="$new_pr_body"
 
           done
         env:
-          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

_quarto.yml

@@ -66,7 +66,7 @@ book:
       - icon: twitter
         href: "https://twitter.com/appliedepi"
       - icon: linkedin
-        href: "https://www.linkedin.com/company/appliedepi/"
+        href: "https://www.linkedin.com/company/appliedepi"
       # - icon: github
       #   menu:
       #     - text: Source Code
@@ -206,6 +206,7 @@ book:
     - new_pages/reportfactory.qmd #done
     - new_pages/flexdashboard.qmd #done
     - new_pages/shiny_basics.qmd #done
+    - new_pages/quarto.qmd #done
 
   # MISCELLANEOUS
   - part: "Miscellaneous"

data/quarto/outbreak_dashboard.qmd

@@ -0,0 +1,90 @@
+---
+title: "Outbreak dashboard"
+output: 
+  flexdashboard::flex_dashboard:
+    orientation: columns
+    vertical_layout: fill
+---
+
+```{r setup, echo=FALSE}
+pacman::p_load(rio, here, tidyverse, flexdashboard,       # load packages
+               flextable, incidence2, epicontacts, DT, janitor)
+
+linelist <- import(here("data", "case_linelists", "linelist_cleaned.rds")) # import data
+```
+
+## Column 1 {data-width=500}
+### Summary and action items 
+
+This report is for the Incident Command team of the fictional outbreak of Ebola cases. **As of `r format(max(linelist$date_hospitalisation, na.rm=T), "%d %B")` there have been `r nrow(linelist)` cases reported as hospitalized.**  
+
+* Several previously-unaffected areas to the West are now reporting cases  
+* Internal reviews suggest that better communication is needed between district and provincial level data management teams  
+* Safe and dignified burial teams are reporting difficulties  
+
+### Review data
+#### Cases by hospital
+```{r}
+linelist %>%
+  count(hospital) %>%
+  adorn_totals() %>%
+  rename("Hospital" = hospital,
+         "Cases" = n) %>% 
+  knitr::kable()
+```
+
+
+## Column 2 {data-width=500}
+### Epidemic curve by age
+
+```{r}
+age_outbreak <- incidence(linelist, "date_onset", "week", groups = "age_cat")
+plot(age_outbreak, fill = "age_cat", col_pal = muted, title = "") %>% 
+  plotly::ggplotly()
+```
+
+### Transmission chain (select cases)
+```{r}
+# load package
+pacman::p_load(epicontacts)
+
+## generate contacts
+contacts <- linelist %>%
+  transmute(
+    infector = infector,
+    case_id = case_id,
+    location = sample(c("Community", "Nosocomial"), n(), TRUE),
+    duration = sample.int(10, n(), TRUE)
+  ) %>%
+  drop_na(infector)
+
+## generate epicontacts object
+epic <- make_epicontacts(
+  linelist = linelist,
+  contacts = contacts,
+  id = "case_id",
+  from = "infector",
+  to = "case_id",
+  directed = TRUE
+)
+
+## subset epicontacts object
+sub <- epic %>%
+  subset(
+    node_attribute = list(date_onset = c(as.Date(c("2014-06-30", "2014-06-01"))))
+  ) %>%
+ thin("contacts")
+
+# temporal plot
+plot(
+  sub,
+  x_axis = "date_onset",
+  node_color = "outcome",
+  col_pal = c(Death = "firebrick", Recover = "green"),
+  arrow_size = 0.5,
+  node_size = 13,
+  label = FALSE,
+  height = 700,
+  width = 700
+)
+```