Merge pull request #9 from ohdsi-studies/develop

Develop fixes tested on IPCI and RMD

.Rbuildignore

@@ -0,0 +1,12 @@
+^renv$
+^renv\.lock$
+^.*\.Rproj$
+^\.Rproj\.user$
+^CodeToRunSynthea\.R
+^CodeToRunIPCI\.R
+^results$
+^errorReportSql\.txt$
+^badgesMarkdownCode\.md$
+^LICENSE\.md$
+^\.github$
+^README\.Rmd$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,47 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, develop]
+  pull_request:
+    branches: [main, develop]
+
+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'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.gitignore

@@ -0,0 +1,13 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+
+errorReport*
+Results/*
+
+.DS_Store
+CodeToRunSynthea.R
+CodeToRunSnowflake.R
+CodeToRunIPCI.R
+errorReportSql.txt

DESCRIPTION

@@ -1,4 +1,5 @@
-Package: EhdenAlopecia 
+Package: EhdenAlopecia
+Title: Analytic software to perform large-scale distributed analysis of patients with Alopecia as part of the EHDEN study-athon
 Version: 1.1.1
 Authors@R: person("Ross", "Williams", , "r.williams@derasmusmc.nl", role = c("aut", "cre"))
 Description: This package creates the cohorts for this EHDEN Alopecia study study. Based on this cohort diagnostics, incidence and prevalence rates and treatment patterns are analysis are performed.
@@ -9,19 +10,29 @@ RoxygenNote: 7.2.3
 Depends:
     R (>= 3.6.1)
 Imports:
-    DBI,
     dplyr,
-    glue,
-    zip,
     magrittr,
-    checkmate,
-    log4r,
-    lubridate,
-    rlang,
-    readr
+    readr,
+    TreatmentPatterns (>= 2.6.0),
+    CohortDiagnostics,
+    CirceR,
+    CohortGenerator
 Suggests: 
     testthat (>= 3.0.0),
+    here,
     rmarkdown,
     checkmate,
+    SqlRender,
     duckdb,
+    ParallelLogger,
+    DBI,
+    glue,
+    zip,
+    lubridate,
+    rlang,
+    jsonlite
+Remotes:
+  ohdsi/CohortDiagnostics,
+  ohdsi/CirceR,
+  ohdsi/CohortGenerator
 Config/testthat/edition: 3