Issue115

.Rbuildignore

@@ -0,0 +1,10 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^dev$
+^diagnostics$
+^docs$
+^output$
+^temp$
+^\.github$
+^Crashpad$
+^output$

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

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

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+# 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, beta]
+  pull_request:
+    branches: [main, beta, dev]
+
+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: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - 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
+
+      # - name: Cache
+      #   uses: actions/cache@v3.2.6
+      #   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 dependencies
+      #   run: |
+      #     install.packages('remotes')
+      #     install.packages('testthat')
+      #     remotes::install_github('OHDSI/OhdsiSharing')
+      #     remotes::install_github('OHDSI/OhdsiSharing')
+      #     remotes::install_github('OHDSI/Eunomia')
+      #     remotes::install_github('OHDSI/CohortDiagnostics')
+      #     remotes::install_github('OHDSI/CirceR')
+      #     remotes::install_github('OHDSI/CohortGenerator')
+      #   shell: Rscript {0}

.gitignore

@@ -0,0 +1,7 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+output org
+output
+output.zip

DESCRIPTION

@@ -1,37 +1,49 @@
 Package: TreatmentPatterns
 Type: Package
 Title: A package to analyse real-world treatment patterns of a study population of interest
-Version: 1.0.0
-Author: Aniek F Markus 
-Maintainer: Aniek F Markus <a.markus@erasmusmc.nl>
-Description: This package gives insight in treatment patterns, the following tasks should be performed sequentially:
-    1. Create target/event cohorts of interest
-    2. Optional, only for OMOP-CDM data: Perform baseline characterization of study/target population
-    3. Construct treatment pathways
-    4. Generate output (sunburst plots, Sankey diagrams and more)
-    5. Launch shiny application to visualize the results
+Version: 2.0.0
+Author: Aniek F Markus
+Maintainer: Maarten van Kessel <m.l.vankessel@erasmusmc.nl>
+Description: This package gives insight in treatment patterns, the following
+  tasks should be performed sequentially:
+  1. Construct treatment pathways.
+  2. Generate output (sunburst plots, Sankey diagrams and more).
+  3. Launch shiny application to visualize the results.
 Depends:
-    R (>= 3.6.1)
+  R (>= 4.0)
 Imports: 
-    Andromeda,
-    DatabaseConnector,
+    DatabaseConnector (>= 6.0.0),
+    checkmate,
     data.table,
     dplyr,
     SqlRender,
     stringr,
     stringi,
-    readr,
+    ParallelLogger,
+    fs,
+    glue,
+    utils,
     rjson,
-    reshape2,
-    googleVis,
-    RJSONIO,
-    FeatureExtraction,
-    OhdsiSharing,
-    R.utils
+    googleVis
 Suggests:
-    ROhdsiWebApi
+    tibble,
+    testthat (>= 3.0.0),
+    usethis,
+    knitr,
+    Eunomia,
+    CohortDiagnostics,
+    CohortGenerator,
+    CirceR,
+    rmarkdown
+Remotes:
+    OHDSI/CohortDiagnostics,
+    OHDSI/CohortGenerator,
+    OHDSI/CirceR,
+    OHDSI/Eunomia
 License: Apache License 2.0
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3
 VignetteBuilder: knitr
+Config/testthat/edition: 3
+Additional_repositories: https://OHDSI.github.io/drat

NAMESPACE

@@ -1,17 +1,41 @@
 # Generated by roxygen2: do not edit by hand
 
+export(addPathwayAnalysis)
 export(addPathwaySettings)
-export(cohortCharacterization)
 export(constructPathways)
-export(createCharacterizationSettings)
 export(createCohortSettings)
-export(createCohorts)
 export(createDataSettings)
 export(createPathwaySettings)
+export(createSankeyDiagram)
 export(createSaveSettings)
 export(createSunburstPlot)
 export(executeTreatmentPatterns)
+export(extractFile)
 export(generateOutput)
-export(launchResultsExplorer)
-import(data.table)
-import(magrittr)
+export(getPathways)
+export(loadPathwaySettings)
+export(writeCohortTable)
+import(ParallelLogger)
+import(SqlRender)
+import(checkmate)
+import(dplyr)
+import(fs)
+import(glue)
+import(stringr)
+import(utils)
+importFrom(DatabaseConnector,connect)
+importFrom(DatabaseConnector,disconnect)
+importFrom(DatabaseConnector,querySql)
+importFrom(data.table,":=")
+importFrom(data.table,as.data.table)
+importFrom(data.table,data.table)
+importFrom(data.table,dcast)
+importFrom(data.table,rbindlist)
+importFrom(data.table,rollup)
+importFrom(data.table,shift)
+importFrom(data.table,transpose)
+importFrom(dplyr,filter)
+importFrom(googleVis,gvisSankey)
+importFrom(rjson,toJSON)
+importFrom(stringi,stri_replace_all_fixed)
+importFrom(utils,globalVariables)