Release 4.0.0 (Part 3)

OHDSI · Jul 19, 2024 · f1cdd1f · f1cdd1f
2 parents d63136a + b8d1234
commit f1cdd1f
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Showing 36 changed files with 139 additions and 100 deletions.
diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml
@@ -134,7 +134,7 @@ jobs:
     env:
       GH_TOKEN: ${{ secrets.GH_TOKEN }}
 
-    if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/master' }}
+    if: ${{ github.event_name != 'pull_request' && github.ref_name == github.event.repository.default_branch }}
 
     steps:
 
@@ -194,3 +194,9 @@ jobs:
         run: |
           curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/
           
+      - name: Synchronize main
+        if: ${{ env.new_version != '' }}
+        run: |
+          git update-ref refs/heads/main ${{ env.new_version }}
+          git push origin +main
+
diff --git a/R/Classes.R b/R/Classes.R
@@ -47,7 +47,7 @@ IncidenceDesign <- R6::R6Class("IncidenceDesign",
     .studyWindow=NA
   ),
   active = list(
-    #' @field cohortDefs A list of cohort definitions.  Must be a list of class "CohortDefinition"
+    #' @field cohortDefs A list of cohort definitions.  Must be a list of \link[=CohortDefinition]{CohortDefinition}
     cohortDefs = function(cohortDefs) {
       if (missing(cohortDefs)) {
         private$.cohortDefs
@@ -69,7 +69,7 @@ IncidenceDesign <- R6::R6Class("IncidenceDesign",
         self
       }
     },
-    #' @field targetDefs A list of cohort references to be used as target cohorts.  Must be a list of class "CohortReference"
+    #' @field targetDefs A list of cohort references to be used as target cohorts.  Must be a list of \link[=CohortReference]{CohortReference}
     targetDefs = function(targetDefs) {
       if (missing(targetDefs)) {
         private$.targetDefs
@@ -80,7 +80,7 @@ IncidenceDesign <- R6::R6Class("IncidenceDesign",
         self
       }
     },
-    #' @field outcomeDefs A list of cohort references to be used as target cohorts.  Must be a list of class "CohortReference"
+    #' @field outcomeDefs A list of outcome definitions.  Must be a list of \link[=Outcome]{Outcome}
     outcomeDefs = function(outcomeDefs) {
       if (missing(outcomeDefs)) {
         private$.outcomeDefs
@@ -91,7 +91,7 @@ IncidenceDesign <- R6::R6Class("IncidenceDesign",
         self
       }
     },
-    #' @field timeAtRiskDefs A list of cohort references to be used as target cohorts.  Must be a list of class "CohortReference"
+    #' @field timeAtRiskDefs A list of time-at-risk definitions.  Must be a list of \link[=TimeAtRisk]{TimeAtRisk}
     timeAtRiskDefs = function(timeAtRiskDefs) {
       if (missing(timeAtRiskDefs)) {
         private$.timeAtRiskDefs
@@ -102,7 +102,7 @@ IncidenceDesign <- R6::R6Class("IncidenceDesign",
         self
       }
     },
-    #' @field analysisList A list of cohort references to be used as target cohorts.  Must be a list of class "CohortReference"
+    #' @field analysisList A list of analyses, containing the T-O-TAR combinations to perform.  Must be a list of \link[=IncidenceAnalysis]{IncidenceAnalysis}
     analysisList = function(analysisList) {
       if (missing(analysisList)) {
         private$.analysisList
@@ -113,7 +113,7 @@ IncidenceDesign <- R6::R6Class("IncidenceDesign",
         self
       }
     },
-    #' @field subgroups A list of cohort references to be used as target cohorts.  Must be a list of class "CohortReference"
+    #' @field subgroups A list of subgroups.  Must be a list of \link[=CohortSubgroup]{CohortSubgroup}
     subgroups = function(subgroups) {
       if (missing(subgroups)) {
         private$.subgroups
@@ -124,7 +124,7 @@ IncidenceDesign <- R6::R6Class("IncidenceDesign",
         self
       }
     },
-    #' @field strataSettings The strata settings for this design.  Must be a class "StrataSettings"
+    #' @field strataSettings The strata settings for this design.  Must be a class \link[=StrataSettings]{StrataSettings}
     strataSettings = function(strataSettings) {
       if (missing(strataSettings)) {
         private$.strataSettings
@@ -135,7 +135,7 @@ IncidenceDesign <- R6::R6Class("IncidenceDesign",
         self
       }
     },
-    #' @field studyWindow a study window for this design.  Must be a list of class "DateRange"
+    #' @field studyWindow a study window for this design.  Must be a list of class \link[=DateRange]{DateRange}
     studyWindow = function(studyWindow) {
       if (missing(studyWindow)) {
         private$.studyWindow

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -14,3 +14,24 @@ navbar:
     hades:
       text: hadesLogo
       href: https://ohdsi.github.io/Hades
+
+reference:
+  - title: "R6 Classes"
+  - contents:
+    - CohortDefinition
+    - CohortReference
+    - CohortSubgroup
+    - DateRange
+    - IncidenceAnalysis
+    - IncidenceDesign
+    - Outcome
+    - StrataSettings
+    - TimeAtRisk
+  - title: "R6 Class Factory Functions"
+  - contents: 
+    - starts_with("create")
+  - title: "Other Functions"
+  - contents: 
+    - starts_with("build")
+    - starts_with("execute")
+    - starts_with("get")
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/using-cohortincidence.html b/docs/articles/using-cohortincidence.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 2.0.9
 pkgdown_sha: ~
 articles:
   using-cohortincidence: using-cohortincidence.html
-last_built: 2024-07-08T17:23Z
+last_built: 2024-07-19T13:34Z
 
diff --git a/docs/reference/CohortDefinition.html b/docs/reference/CohortDefinition.html
diff --git a/docs/reference/CohortIncidence-package.html b/docs/reference/CohortIncidence-package.html
diff --git a/docs/reference/CohortReference.html b/docs/reference/CohortReference.html
diff --git a/docs/reference/CohortSubgroup.html b/docs/reference/CohortSubgroup.html
diff --git a/docs/reference/DateRange.html b/docs/reference/DateRange.html
diff --git a/docs/reference/IncidenceAnalysis.html b/docs/reference/IncidenceAnalysis.html
diff --git a/docs/reference/IncidenceDesign.html b/docs/reference/IncidenceDesign.html
diff --git a/docs/reference/Outcome.html b/docs/reference/Outcome.html
diff --git a/docs/reference/StrataSettings.html b/docs/reference/StrataSettings.html
diff --git a/docs/reference/TimeAtRisk.html b/docs/reference/TimeAtRisk.html
diff --git a/docs/reference/buildOptions.html b/docs/reference/buildOptions.html
diff --git a/docs/reference/buildQuery.html b/docs/reference/buildQuery.html
diff --git a/docs/reference/createCohortRef.html b/docs/reference/createCohortRef.html
diff --git a/docs/reference/createCohortSubgroup.html b/docs/reference/createCohortSubgroup.html
diff --git a/docs/reference/createDateRange.html b/docs/reference/createDateRange.html
diff --git a/docs/reference/createIncidenceAnalysis.html b/docs/reference/createIncidenceAnalysis.html
diff --git a/docs/reference/createIncidenceDesign.html b/docs/reference/createIncidenceDesign.html
diff --git a/docs/reference/createOutcomeDef.html b/docs/reference/createOutcomeDef.html