Merge pull request #724 from OHDSI/develop

develop merge for release 1.7.2

.Rbuildignore

@@ -1,3 +1,10 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^.github
+^docs$
+^extras$
+compare_versions
+deploy.sh
+_pkgdown.yml
+^CRAN-SUBMISSION$
+^cran-comments\.md$

.github/workflows/R_CMD_check_Hades.yaml

@@ -0,0 +1,167 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GH_TOKEN }}
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      CDM5_ORACLE_CDM54_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM54_SCHEMA }}
+      CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
+      CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
+      CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
+      CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
+      CDM5_POSTGRESQL_CDM54_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM54_SCHEMA }}
+      CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
+      CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
+      CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
+      CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
+      CDM5_SQL_SERVER_CDM54_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM54_SCHEMA }}
+      CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
+      CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
+      CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
+      CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
+      CDM5_REDSHIFT_CDM54_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM54_SCHEMA }}
+      CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
+      CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
+      CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
+      CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install system requirements
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install -y libssh-dev
+          Rscript -e 'install.packages("remotes")'
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--as-cran")'
+          error-on: '"warning"'
+          check-dir: '"check"'
+
+      - name: Upload source package
+        if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
+        uses: actions/upload-artifact@v2
+        with:
+          name: package_tarball
+          path: check/*.tar.gz
+
+      - name: Install covr
+        if: runner.os == 'macOS'
+        run: |
+          install.packages("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        if: runner.os == 'macOS'
+        run: covr::codecov()
+        shell: Rscript {0}
+
+  Release:
+    needs: R-CMD-Check
+
+    runs-on: macOS-latest
+
+    env:
+      GH_TOKEN: ${{ secrets.GH_TOKEN }}
+
+    if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/main' }}
+
+    steps:
+
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Check if version has increased
+        run: |
+          echo "new_version="$(perl compare_versions --tag) >> $GITHUB_ENV
+
+      - name: Display new version number
+        if: ${{ env.new_version != '' }}
+        run: |
+          echo "${{ env.new_version }}"
+
+      - name: Create release
+        if: ${{ env.new_version != '' }}
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
+        with:
+          tag_name: ${{ env.new_version }}
+          release_name: Release ${{ env.new_version }}
+          body: |
+            See NEWS.md for release notes.
+          draft: false
+          prerelease: false
+
+      - uses: r-lib/actions/setup-r@v2
+        if: ${{ env.new_version != '' }}
+
+      - name: Install drat
+        if: ${{ env.new_version != '' }}
+        run: |
+          install.packages('drat')
+        shell: Rscript {0}
+
+      - name: Remove any tarballs that already exists
+        if: ${{ env.new_version != '' }}
+        run: |
+          rm -f *.tar.gz
+
+      - name: Download package tarball
+        if: ${{ env.new_version != '' }}
+        uses: actions/download-artifact@v2
+        with:
+          name: package_tarball
+
+      - name: Push to drat
+        if: ${{ env.new_version != '' }}
+        run: |
+          bash deploy.sh
+
+      - name: Push to BroadSea
+        if: ${{ env.new_version != '' }}
+        run: |
+          curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/
+

Achilles.Rproj

@@ -13,6 +13,7 @@ RnwWeave: Sweave
 LaTeX: pdfLaTeX
 
 BuildType: Package
+PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageCheckArgs: --no-multiarch
-PackageRoxygenize: rd,collate,namespace,vignette
+PackageRoxygenize: rd,collate,namespace

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.7.2
+Date: 2023-05-11 16:33:58 UTC
+SHA: 7604a7c83bf808b55e4a062c096bdc74e6f7c7bc

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: Achilles
 Type: Package
-Title: Generates descriptive statistics for an OMOP CDM instance
-Version: 1.7
-Date: 2022-08-02
+Title: Achilles Data Source Characterization
+Version: 1.7.2
+Date: 2023-05-11
 Authors@R: c(
   person("Frank", "DeFalco", email = "fdefalco@ohdsi.org", role = c("aut","cre")),  
   person("Patrick", "Ryan", email = "ryan@ohdsi.org", role = c("aut")),  
@@ -14,33 +14,39 @@ Authors@R: c(
   person("Anthony", "Molinaro", role = c("aut")),
   person("Observational Health Data Science and Informatics", role = c("cph"))
   )
-Maintainer: Frank J DeFalco <fdefalco@ohdsi.org>
+Maintainer: Frank DeFalco <fdefalco@ohdsi.org>
 LazyData: true
-Description: Creates descriptive statistics summary for an entire OMOP CDM
-  instance. Currently supports CDM 5.3 and 5.4.
+Description: Automated Characterization of Health Information at Large-Scale 
+  Longitudinal Evidence Systems. Creates a descriptive statistics summary for 
+  an Observational Medical Outcomes Partnership Common Data Model standardized 
+  data source. This package includes functions for executing summary queries on 
+  the specified data source and exporting reporting content for use across a 
+  variety of Observational Health Data Sciences and Informatics community 
+  applications. 
 Depends:
   DatabaseConnector (>= 2.0.0),
   R (>= 4.0.0)
 Imports:
-    SqlRender (>= 1.6.0),
-    dplyr,
-    rjson,
-    jsonlite,
-    ParallelLogger,
-    readr,
-    data.table,
-    lubridate
+  SqlRender (>= 1.6.0),
+  dplyr,
+  jsonlite,
+  ParallelLogger,
+  readr,
+  data.table,
+  lubridate,
+  tseries,
+  rlang
 Suggests:
   DT,
   magrittr,
   tidyr,
-  knitr, 
+  knitr,
   rmarkdown,
-  Castor
-Remotes:
-  github::OHDSI/Castor
+  testthat (>= 3.0.0),
+  withr
 VignetteBuilder: knitr
 License: Apache License
 Roxygen: list()
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Encoding: UTF-8
+Config/testthat/edition: 3

NAMESPACE

@@ -1,11 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
 export(achilles)
-export(addDataSource)
 export(createIndices)
 export(createTimeSeries)
 export(dropAllScratchTables)
-export(exportAO)
 export(exportConditionEraToJson)
 export(exportConditionToJson)
 export(exportDashboardToJson)
@@ -21,29 +19,38 @@ export(exportPerformanceToJson)
 export(exportPersonToJson)
 export(exportProcedureToJson)
 export(exportResultsToCSV)
+export(exportToAres)
 export(exportToJson)
 export(exportVisitDetailToJson)
 export(exportVisitToJson)
-export(generateDbSummary)
 export(getAnalysisDetails)
+export(getSeasonalityScore)
 export(getTemporalData)
+export(isStationary)
 export(listMissingAnalyses)
 export(optimizeAtlasCache)
 export(performTemporalCharacterization)
 export(runMissingAnalyses)
 export(showReportTypes)
+export(sumAcrossYears)
+export(tsCompleteYears)
 import(DatabaseConnector)
 import(ParallelLogger)
 import(SqlRender)
-import(lubridate)
-import(rjson)
-import(stats)
-import(utils)
+import(dplyr)
 importFrom(data.table,fwrite)
 importFrom(dplyr,desc)
-importFrom(dplyr,left_join)
 importFrom(dplyr,ntile)
+importFrom(rlang,.data)
+importFrom(stats,aggregate)
+importFrom(stats,cycle)
+importFrom(stats,end)
+importFrom(stats,frequency)
+importFrom(stats,start)
+importFrom(stats,ts)
+importFrom(stats,window)
 importFrom(utils,compareVersion)
 importFrom(utils,packageVersion)
 importFrom(utils,read.csv)
+importFrom(utils,write.csv)
 importFrom(utils,zip)

NEWS.md

@@ -0,0 +1,19 @@
+# Achilles 1.7.2
+
+1. Improved test setup management
+
+# Achilles 1.7.1
+
+Changes
+
+1.  Bug fix for Oracle/SqlRender lack of support for 'As' with table alias.
+2.  Improved consistency with version parameters.
+3.  Adherence to HADES requirements.
+
+# Achilles 1.7.0
+
+Changes
+
+Official 1.7 release: Comprehensive updates with over 200 issues closed over the 24 months.
+
+With this release the main branch will now remain in sync with the latest release and ongoing development will be directed to the develop branch.