101: Create hex logo for simIDM and prepare for CRAN release [skip …

…vbump] (#102) Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
insightsengineering · Dec 11, 2023 · a883751 · a883751
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diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
@@ -3,13 +3,16 @@ name: Check 🛠
 
 on:
   pull_request:
+    types:
+      - opened
+      - synchronize
+      - ready_for_review
     branches:
       - main
-      - pre-release
   push:
     branches:
       - main
-      - pre-release
+  workflow_dispatch:
 
 jobs:
   audit:
@@ -28,29 +31,30 @@ jobs:
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
   linter:
-    if: github.event_name != 'push'
+    if: github.event_name == 'pull_request'
     name: SuperLinter 🦸‍♀️
     uses: insightsengineering/r.pkg.template/.github/workflows/linter.yaml@main
   roxygen:
     name: Roxygen 🅾
     uses: insightsengineering/r.pkg.template/.github/workflows/roxygen.yaml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+    with:
+      auto-update: true
   gitleaks:
     name: gitleaks 💧
     uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main
   spelling:
+    if: github.event_name == 'pull_request'
     name: Spell Check 🆎
     uses: insightsengineering/r.pkg.template/.github/workflows/spelling.yaml@main
-    secrets:
-      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
   links:
-    if: github.event_name != 'push'
+    if: github.event_name == 'pull_request'
     name: Check URLs 🌐
     uses: insightsengineering/r.pkg.template/.github/workflows/links.yaml@main
   vbump:
     name: Version Bump 🤜🤛
-    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    if: github.event_name == 'push'
     uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
@@ -61,12 +65,8 @@ jobs:
     name: License Check 🃏
     uses: insightsengineering/r.pkg.template/.github/workflows/licenses.yaml@main
   style:
-    if: github.event_name != 'push'
+    if: github.event_name == 'pull_request'
     name: Style Check 👗
     uses: insightsengineering/r.pkg.template/.github/workflows/style.yaml@main
     with:
       auto-update: true
-  grammar:
-    if: github.event_name != 'push'
-    name: Grammar Check 🔤
-    uses: insightsengineering/r.pkg.template/.github/workflows/grammar.yaml@main
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
@@ -5,32 +5,17 @@ on:
   push:
     branches:
       - main
-    paths:
-      - inst/templates/**
-      - _pkgdown.*
-      - DESCRIPTION
-      - '**.md'
-      - man/**
-      - LICENSE.*
-      - NAMESPACE
   pull_request:
     branches:
       - main
-      - pre-release
-    paths:
-      - inst/templates/**
-      - _pkgdown.*
-      - DESCRIPTION
-      - '**.md'
-      - man/**
-      - LICENSE.*
-      - NAMESPACE
+  workflow_dispatch:
 
 jobs:
   docs:
     name: Pkgdown Docs 📚
     uses: insightsengineering/r.pkg.template/.github/workflows/pkgdown.yaml@main
-    secrets:
-      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
+      refs-order: c("latest-tag", "main")
       default-landing-page: latest-tag
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/post-release.yaml b/.github/workflows/post-release.yaml
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -5,24 +5,43 @@ on:
   push:
     tags:
       - "v*"
+  workflow_dispatch:
 
 jobs:
+  release:
+    name: Create release 🎉
+    uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main
+    permissions:
+      contents: write
+  r-cmd:
+    name: R CMD Check 🧬
+    needs: [release, docs]
+    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    with:
+      additional-r-cmd-check-params: --as-cran
+  coverage:
+    name: Coverage 📔
+    needs: [release, docs]
+    uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   build:
     name: Build package 🎁
     needs: release
     uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
     secrets:
-      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    with:
+      skip-r-cmd-check: true
+      skip-r-cmd-install: true
   docs:
     name: Pkgdown Docs 📚
     needs: release
     uses: insightsengineering/r.pkg.template/.github/workflows/pkgdown.yaml@main
-    secrets:
-      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
+      refs-order: c("latest-tag", "main")
       default-landing-page: latest-tag
-  release:
-    name: Create release 🎉
-    uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main
     secrets:
-      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+      REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml
@@ -0,0 +1,14 @@
+---
+name: Scheduled 🕰️
+
+on:
+  schedule:
+    - cron: '45 3 * * 0'
+  workflow_dispatch:
+
+jobs:
+  cran-status:
+    name: CRAN Status Monitor 📺
+    uses: insightsengineering/r.pkg.template/.github/workflows/cran-status.yaml@main
+    with:
+      issue-assignees: "niessl,danielinteractive"
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,12 +1,12 @@
 Type: Package
 Package: simIDM
 Title: Simulating Oncology Trials using an Illness-Death Model
-Version: 0.0.5.9026
+Version: 0.1.0
 Authors@R: c(
     person("Alexandra", "Erdmann", , "[email protected]", role = c("aut", "cre")),
     person("Kaspar", "Rufibach", , "[email protected]", role = "aut"),
-    person("Holger", "Loewe", , "holger.loewe@roche.com", role = "aut"),
-    person("Daniel", "Sabanes Bove", , "[email protected]", role = "aut"),
+    person("Holger", "Löwe", , "hbj.loewe@gmail.com", role = "aut"),
+    person("Daniel", "Sabanés Bové", , "[email protected]", role = "aut"),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")),
     person("University of Ulm", role = c("cph", "fnd"))
   )
@@ -17,7 +17,7 @@ Description: Based on the illness-death model a large number of clinical
     for random and event-driven censoring, an arbitrary number of
     treatment arms, staggered study entry and drop-out.  Exponentially,
     Weibull and piecewise exponentially distributed survival times can be
-    generated.
+    generated. The correlation between PFS and OS can be calculated.
 License: Apache License 2.0
 URL: https://github.com/insightsengineering/simIDM/
 BugReports: https://github.com/insightsengineering/simIDM/issues

diff --git a/NEWS.md b/NEWS.md
@@ -1,22 +1,21 @@
-# simIDM 0.0.5.9026
+# simIDM 0.1.0
 
 ### New Features
 
--   `prepareData` allows formatting of trial data for log-likelihood computation.
--   `estimateParams` estimates parameters of exponential and Weibull transition hazards for a given data set.
+-   `estimateParams` estimates parameters of exponential and Weibull transition hazards using maximum likelihood for a given data set after using `prepareData`.
+-   `corTrans` calculates the correlation between PFS and OS for a given set of transition hazards, and `corPFSOS` estimates this correlation for a given data set, optionally with a bootstrap based confidence interval.
 
 ### Bug Fixes
 
 -   `ExpSurvOS` now returns 0 instead of NaN for large values of t.
 -   `WeibSurvOS` now does not return an error for large values of t.
--   `PWCSurvOS` now does not return an error for large values of t.
--   `PWCSurvOS` no longer returns values larger than 1, and is significantly faster, based on a closed form calculation instead of numerical integration.
+-   `PWCSurvOS` now does not return an error for large values of t. It also no longer returns values larger than 1. It is significantly faster, based on a closed form calculation instead of numerical integration.
 -   `getSimulatedData` now also works when there are no transitions from progression to death, similarly for `getOneClinicalTrial` (which now warns if there are no such transitions at all).
 
 ### Miscellaneous
 
--   Renamed piecewise constant hazards function to `getPWCHazard` (previously `getPCWHazard`).
 -   `PwcOSInt`, `integrateVector`, `WeibOSInteg` are no longer exported, and only used internally.
+-   Renamed piecewise constant hazards function to `getPWCHazard` (previously `getPCWHazard`).
 
 # simIDM 0.0.5
 

diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 <!-- markdownlint-disable-file -->
 <!-- README.md needs to be generated from README.Rmd. Please edit that file -->
 
-# simIDM
+# simIDM <img src="man/figures/logo.png" align="right" height="139" />
 
 <!-- badges: start -->
 
@@ -32,13 +32,16 @@ illness-death model, which can be used for trail planning, for example.
 The simulation set-up allows random and event-driven censoring, an
 arbitrary number of treatment arms, staggered study entry and drop-out.
 Exponentially, Weibull and piecewise exponentially distributed survival
-times can be generated.
+times can be generated. In addition, the correlation between PFS and OS
+can be calculated based on the simulation scenario, or estimated from a
+given data set.
 
 **Scope:**
 
 - Simulation of the illness-death model with constant, Weibull or
   piecewise constant transition hazards.
 - Conversion of the transition times to PFS and OS survival times.
+- Correlation between PFS and OS survival times can be calculated.
 
 **Main Features:**
 
@@ -49,18 +52,21 @@ times can be generated.
 - Arbitrary number of treatment arms and flexible randomization ratio.
 - Staggered study entry.
 - Derivation of PFS and OS survival functions from transition hazards.
+- Correlation between PFS and OS can be estimated from a given data set.
 
 ## Installation
 
-<!-- **CRAN** -->
-<!-- You can install the current stable version from CRAN with: -->
-<!-- ```{r cran-installation, eval = FALSE} -->
-<!-- install.packages("mmrm") -->
-<!-- ``` -->
+### Release
 
-**GitHub**
+You can install the current release version from *CRAN* with:
 
-You can install the current development version from GitHub with:
+``` r
+install.packages("simIDM")
+```
+
+### Development
+
+You can install the current development version from *GitHub* with:
 
 ``` r
 if (!require("remotes")) {
@@ -71,8 +77,9 @@ remotes::install_github("insightsengineering/simIDM")
 
 ## Getting Started
 
-See also the `quickstart` vignette or get started by trying out the
-example:
+See also the [quick
+start](https://insightsengineering.github.io/simIDM/latest-tag/articles/quickstart.html)
+vignette or get started by trying out this example:
 
 ``` r
 library(simIDM)

diff --git a/README.rmd b/README.rmd
@@ -5,7 +5,7 @@ output: github_document
 <!-- markdownlint-disable-file -->
 <!-- README.md needs to be generated from README.Rmd. Please edit that file -->
 
-# simIDM
+# simIDM <img src="man/figures/logo.png" align="right" height="139" />
 
 ```{r, echo = FALSE}
 knitr::opts_chunk$set(
@@ -33,11 +33,13 @@ assumption of proportional hazards. This package provides the tools to simulate
 endpoints OS and PFS based on the illness-death model, which can be used for trail planning, for example. The simulation 
 set-up allows random and event-driven censoring, an arbitrary number of treatment arms, staggered study entry and drop-out.
 Exponentially, Weibull and piecewise exponentially distributed survival times can be generated.
+In addition, the correlation between PFS and OS can be calculated based on the simulation scenario, or estimated from a given data set.
 
 **Scope:**
 
 * Simulation of the illness-death model with constant, Weibull or piecewise constant transition hazards.
 * Conversion of the transition times to PFS and OS survival times.
+* Correlation between PFS and OS survival times can be calculated.
 
 **Main Features:**
 
@@ -46,20 +48,21 @@ Exponentially, Weibull and piecewise exponentially distributed survival times ca
 * Arbitrary number of treatment arms and flexible randomization ratio.
 * Staggered study entry.
 * Derivation of PFS and OS survival functions from transition hazards.
+* Correlation between PFS and OS can be estimated from a given data set.
 
 ## Installation
 
-<!-- **CRAN** -->
+### Release
 
-<!-- You can install the current stable version from CRAN with: -->
+You can install the current release version from *CRAN* with:
 
-<!-- ```{r cran-installation, eval = FALSE} -->
-<!-- install.packages("mmrm") -->
-<!-- ``` -->
+```{r cran-installation, eval = FALSE}
+install.packages("simIDM")
+```
 
-**GitHub**
+### Development
 
-You can install the current development version from GitHub with:
+You can install the current development version from *GitHub* with:
 
 ```{r gh-installation, eval = FALSE}
 if (!require("remotes")) {
@@ -70,9 +73,9 @@ remotes::install_github("insightsengineering/simIDM")
 
 ## Getting Started
 
-See also the `quickstart` vignette or get started by trying out the example:
+See also the [quick start](https://insightsengineering.github.io/simIDM/latest-tag/articles/quickstart.html) vignette or get started by trying out this example:
 
-```{r getting-started}
+```{r getting-started, results = 'hide'}
 library(simIDM)
 transitionGroup1 <- exponential_transition(h01 = 1.2, h02 = 1.5, h12 = 1.6)
 transitionGroup2 <- exponential_transition(h01 = 1, h02 = 1.3, h12 = 1.7)