Merge pull request #17 from OHDSI/develop

Release 1.5.1

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 .gitattributes
@@ -7,4 +9,6 @@ extras
 ^\.git
 deploy.sh
 compare_versions
-_pkgdown.yml
+_pkgdown.yml
+work/*
+docs/*

.github/workflows/R_CMD_check_Hades.yaml

@@ -0,0 +1,193 @@
+# 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: windows-latest, r: 'release'}  # Does not appear to have Java 32-bit, hence the --no-multiarch
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_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_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_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_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_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 }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-tinytex@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+          
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |    
+          sudo apt-get install libssh-dev
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch"))
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Install covr
+        if: runner.os == 'macOS'
+        run: |
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Remove check folder if exists
+        if: runner.os == 'macOS'
+        run: unlink("check", recursive = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--no-multiarch"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+
+      - name: Upload source package
+        if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/master'
+        uses: actions/upload-artifact@v2
+        with:
+          name: package_tarball
+          path: check/*.tar.gz
+
+      - 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: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/master' }}
+
+    steps:
+
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0    
+
+      - name: Check if version has increased
+        run: |
+          echo "new_version="$(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@v1
+        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: |
+          perl compare_version --tag && \
+          curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/

.github/workflows/nightly_cleanup_Hades.yml

@@ -0,0 +1,18 @@
+name: 'nightly artifacts cleanup'
+on:
+  schedule:
+    - cron: '0 1 * * *' # every night at 1 am UTC
+
+jobs:
+  remove-old-artifacts:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+    - name: Remove old artifacts
+      uses: c-hive/gha-remove-artifacts@v1
+      with:
+        age: '7 days'
+        # Optional inputs
+        # skip-tags: true
+        skip-recent: 1

.gitignore

@@ -1,3 +1,7 @@
 .Rproj.user
 .Rhistory
 .RData
+renv
+check
+errorReportSql.txt
+.idea

DESCRIPTION

@@ -3,14 +3,15 @@ Type: Package
 Title: Population-level estimation method  that estimates
     incidence rate comparison of exposed/unexposed time within an exposed
     cohort
-Version: 1.5.0
-Date: 2018-11-23
+Version: 1.5.1
+Date: 2021-29-03
 Authors@R: c(
-    person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut", "cre")),
+    person("Jamie", "Gilbert", role = c("aut", "cre")),
+    person("Martijn", "Schuemie", , "schuemie@ohdsi.org", role = c("aut")),
     person("Patrick", "Ryan", role = c("aut"))
     )
-Author: Patrick Ryan, Martijn Schuemie
-Maintainer: Patrick Ryan <ryan@ohdsi.org>
+Author: Patrick Ryan, Martijn Schuemie, James Gilbert
+Maintainer: Jamie Gilbert <jpg@azimov.co.uk>
 Description: This package provides a method to estimate risk by comparing time
     exposed with time unexposed among the exposed cohort.
 URL: https://github.com/OHDSI/SelfControlledCohort
@@ -22,6 +23,13 @@ Imports:
     ParallelLogger,
     rateratio.test
 Suggests:
-    testthat
+    withr,
+    testthat,
+    knitr,
+    rmarkdown,
+    Eunomia,
+    DiagrammeR,
+    dplyr
 License: Apache License 2.0
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1
+VignetteBuilder: knitr

NEWS.md

@@ -0,0 +1,13 @@
+SelfControlledCohort 1.5.1
+==========================
+
+Changes: 
+
+- Added support for github actions and removed travis configuration
+- Added `computeTarDistribution` flag to `runSelfControlledCohort`, which computes the distribution of exposure time
+ windows for subjects experiencing the outcome and average absolute time between exposure and outcome.
+- Added vignette for usage with some examples
+
+Bug Fixes:
+- Fixed issue with DatabaseConnector v 4.0.0 connectionDetails object on osx and linux caused by usage of
+`connectionDetails$conn` for storage of a connection

R/Analyses.R

@@ -1,6 +1,6 @@
 # @file Analyses.R
 #
-# Copyright 2018 Observational Health Data Sciences and Informatics
+# Copyright 2021 Observational Health Data Sciences and Informatics
 #
 # This file is part of SelfControlledCohort
 #

R/CreateArgFunctions.R

@@ -16,7 +16,7 @@
 #' @param studyEndDate                   Date for maximum allowable data for index exposure. Dateformat
 #'                                       is 'yyyymmdd'.
 #' @param addLengthOfExposureExposed     If TRUE, use the duration from drugEraStart -> drugEraEnd
-#'                                       aspart of timeAtRisk.
+#'                                       as part of timeAtRisk.
 #' @param riskWindowStartExposed         Integer of days to add to drugEraStart for start oftimeAtRisk
 #'                                       (0 to include index date, 1 to start the dayafter).
 #' @param riskWindowEndExposed           Additional window to add to end of exposure period
@@ -33,6 +33,10 @@
 #'                                       and unexposed.
 #' @param washoutPeriod                  Integer to define required time observed before exposurestart.
 #' @param followupPeriod                 Integer to define required time observed after exposurestart.
+#' @param computeTarDistribution         If TRUE, computer the distribution of time-at-risk and
+#'                                       average absolute time between treatment and outcome. Note,
+#'                                       may add significant computation time on some database
+#'                                       engines. If set true in one analysis will default to true for all others.
 #'
 #' @export
 createRunSelfControlledCohortArgs <- function(firstExposureOnly = TRUE,
@@ -49,7 +53,8 @@ createRunSelfControlledCohortArgs <- function(firstExposureOnly = TRUE,
                                               riskWindowStartUnexposed = -30,
                                               hasFullTimeAtRisk = FALSE,
                                               washoutPeriod = 0,
-                                              followupPeriod = 0) {
+                                              followupPeriod = 0,
+                                              computeTarDistribution = FALSE) {
   # First: get default values:
   analysis <- list()
   for (name in names(formals(createRunSelfControlledCohortArgs))) {