Merge branch 'main' into linters

.Rbuildignore

@@ -7,4 +7,5 @@
 .lintr
 ^cran-comments\.md$
 ^README\.Rmd$
+^data-raw$
 .vscode

.github/sync.yaml

@@ -0,0 +1,32 @@
+ssi-dk/diseasystore:
+  - .github/workflows/synchronise-files.yaml
+  - .github/sync.yaml
+
+  - R/0_linters.R
+  - tests/testthat/test-0_linters.R
+
+  - R/0_R6_utils.R
+  - tests/testthat/test-0_R6_utils.R
+
+  - R/0_documentation.R
+  - tests/testthat/test-0_documentation.R
+
+  - tests/testthat/test-0_return.R
+  - tests/testthat/test-0_examples.R
+
+
+ssi-dk/diseasy:
+  - .github/workflows/synchronise-files.yaml
+  - .github/sync.yaml
+
+  - R/0_linters.R
+  - tests/testthat/test-0_linters.R
+
+  - R/0_R6_utils.R
+  - tests/testthat/test-0_R6_utils.R
+
+  - R/0_documentation.R
+  - tests/testthat/test-0_documentation.R
+
+  - tests/testthat/test-0_return.R
+  - tests/testthat/test-0_examples.R

.github/workflows/synchronise-files.yaml

@@ -0,0 +1,21 @@
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  sync:
+    name: 🔄 Sync diseasyverse files
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@master
+      - name: Run GitHub File Sync
+        uses: BetaHuhn/repo-file-sync-action@v1
+        with:
+          GH_PAT: ${{ secrets.GH_PAT }}
+          CONFIG_PATH: .github/sync.yaml
+          COMMIT_PREFIX: "chore: "
+          PR_BODY: Automatically synchronise files between diseasyverse repositories

DESCRIPTION

@@ -17,8 +17,10 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Language: en-GB
+LazyData: TRUE
 Depends:
-    diseasystore
+    diseasystore,
+    R (>= 3.5.0)
 Imports:
     checkmate,
     digest,

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export("%.%")
+export(DiseasyActivity)
 export(DiseasyBaseModule)
 export(DiseasyObservables)
 export(DiseasySeason)

R/0_documentation.R

@@ -1,3 +1,11 @@
+rd_activity_units <- function(type = "param") {
+  checkmate::assert_choice(type, c("param", "field"))
+  paste("(`list(list())`)\\cr",
+        "A nested list of all possible 'units' of activity that can be opened or closed.",
+        ifelse(type == "field", " Read only.", ""))
+}
+
+
 rd_stratification <- function(type = "param") {
   checkmate::assert_choice(type, c("param", "field"))
   paste("(`list`(`quosures`))\\cr",
@@ -15,6 +23,22 @@ rd_diseasystore <- function(type = "param") {
 }
 
 
+rd_contact_basis <- function(type = "param") {
+  checkmate::assert_choice(type, c("param", "field"))
+  paste("(`list(list())`)\\cr",
+        "A nested list with all the needed information for the contact_basis\\cr",
+        "* `counts` contains the age stratified contact counts across the arenas of the basis",
+        "  (e.g. 'work', 'home', 'school', 'other')\\cr",
+        "* `proportion` contains a list of the proportion of population in each age-group\\cr",
+        "* `demography` contains a `data.frame` with the columns\\cr",
+        "  * `age` (`integer()`) 1-year age group\\cr",
+        "  * `population` (`numeric()`) size of population in age group\\cr",
+        "  * `proportion` (`numeric()`) proportion of total population in age group\\cr",
+        "* `description` contains information about the source of the contact basis.",
+        ifelse(type == "field", " Read only.", ""))
+}
+
+
 rd_observable <- function(type = "param") {
   checkmate::assert_choice(type, c("param", "field"))
   paste("(`character`)\\cr",
@@ -154,3 +178,18 @@ rd_training_length <- paste(
   "(`numeric`)\\cr",
   "The number of days that should be included in the training of the model."
 )
+
+
+rd_side_effects <- "NULL (called for side effects)"
+
+
+
+rd_age_cuts_lower <- paste(
+  "(`numeric`)\\cr",
+  "vector of ages defining the lower bound for each age group. If NULL (default), age groups of contact_basis is used."
+)
+
+rd_activity_weights <- paste(
+  "(`numeric(4)`)\\cr",
+  "vector of weights for the four types of contacts. If NULL (default), no weighting is done."
+)