Merge pull request #1 from Novartis/gh-actions

.github/.gitignore

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

.github/workflows/build-book.yaml

@@ -0,0 +1,53 @@
+# 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, pull_request]
+
+name: build-book
+
+jobs:
+  build-book:
+    runs-on: ubuntu-latest
+
+    name: build-book
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: 'release'
+
+      - name: Repos
+        run: |
+          cat("\noptions(repos=c(stan='https://mc-stan.org/r-packages/',CRAN ='https://cloud.r-project.org'))\n", file = "~/.Rprofile", append = TRUE)
+        shell: Rscript {0}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+
+      - name: Install CmdStan
+        shell: Rscript {0}
+        run: |
+          cmdstanr::check_cmdstan_toolchain(fix = TRUE)
+          cmdstanr::install_cmdstan()
+
+      - uses: quarto-dev/quarto-actions/setup@v2
+
+      # - uses: quarto-dev/quarto-actions/render@v2
+      #   with:
+      #     to: html # If set, it will be equivalent to `quarto render --to html`
+
+      - name: build BAMDD book
+        run: make website QUARTO_PROFILE=public
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs/public

DESCRIPTION

@@ -0,0 +1,65 @@
+Package: bamdd
+Title: (Bayesian) Applied Modelling in Drug Development
+Version: 0.0.0.9000
+Authors@R: 
+    c(
+        person("Sebastian", "Weber", , "sebastian.weber@novartis.com", role = c("aut", "cre")),
+        person("Björn", "Holzhauer", , "bjorn.holzhauer@novartis.com", role = "aut"),
+        person("Lukas", "Widmer", , "lukas.widmer@novartis.com", role = "aut"),
+        person("Andrew", "Bean", , "andrew.bean@novartis.com", role = "aut")
+    )
+Description: Applied modelling in drug development: flexible Bayesian regression modelling in Stan via brms
+License: `use_gpl3_license()`
+Encoding: UTF-8
+Imports:
+  bayesplot,
+  BOIN,
+  brms, 
+  checkmate, 
+  clustermq, 
+  cmdstanr, 
+  digest, 
+  directlabels, 
+  dplyr, 
+  dqrng, 
+  emmeans, 
+  future, 
+  GGally, 
+  ggfortify,
+  ggplot2, 
+  ggpubr, 
+  ggrepel, 
+  gt, 
+  here, 
+  knitr, 
+  lme4, 
+  MASS, 
+  Matrix,
+  meta, 
+  mmrm, 
+  multinma, 
+  mvtnorm, 
+  nlme, 
+  OncoBayes2, 
+  parallel, 
+  parallelly, 
+  patchwork, 
+  posterior, 
+  prettyunits,
+  purrr, 
+  RBesT, 
+  readr, 
+  rlang, 
+  rmarkdown, 
+  rstan, 
+  scales, 
+  simsurv, 
+  stringr, 
+  survival, 
+  survminer, 
+  tidybayes, 
+  tidyr, 
+  tidyverse, 
+  utils, 
+  vctrs, 
+  viridis

README.md

@@ -16,4 +16,14 @@ with the `brms` package.
 
 - quarto 
 - cmdstanr and cmdstan (`cmdstanr::install_cmdstan()`)
-- other R package dependencies `src/install_dependencies.R`
+- other R package dependencies (see Imports under the dummy `DESCRIPTION` file)
+
+## License
+
+### Code 
+
+The code is licensed under GPL-2 ([LICENSE])
+
+### Materials
+
+The book itself is licensed under CC BY 4.0 ([docs/public/LICENSE])

_quarto-public.yml

@@ -3,7 +3,7 @@ project:
   post-render: src/move_videos.R # workaround for Quarto issue https://github.com/quarto-dev/quarto-cli/issues/3892
 
 book:
-  repo-url: https://github.com/Novartis/RBesT/ # TO BE REPLACED
+  repo-url: https://github.com/Novartis/bamdd/
   site-url: https://opensource.nibr.com/RBesT/ # TO BE REPLACED
   chapters:
     - index.qmd

_quarto.yml

@@ -34,6 +34,9 @@ bibliography:
 format:
   html:
     theme: cosmo
+# embedding of resources would be desirable to avoid using google fonts, but deno does not
+# work nice with the company SSL certificate setup
+    embed-resources: false
 #    code-fold: true
     code-tools: true
 #    code-summary: "Show the code"

bamdd_public.Rproj → bamdd.Rproj

@@ -12,4 +12,4 @@ Encoding: UTF-8
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
 
-BuildType: Makefile
+BuildType: Makefile

docs/public/LICENSE

@@ -0,0 +1,80 @@
+Copyright 2023 Novartis Pharma AG 
+
+Attribution 4.0 International
+By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions.
+
+Section 1 – Definitions.
+Adapted Material means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. For purposes of this Public License, where the Licensed Material is a musical work, performance, or sound recording, Adapted Material is always produced where the Licensed Material is synched in timed relation with a moving image.
+Adapter's License means the license You apply to Your Copyright and Similar Rights in Your contributions to Adapted Material in accordance with the terms and conditions of this Public License.
+Copyright and Similar Rights means copyright and/or similar rights closely related to copyright including, without limitation, performance, broadcast, sound recording, and Sui Generis Database Rights, without regard to how the rights are labeled or categorized. For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights.
+Effective Technological Measures means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements.
+Exceptions and Limitations means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material.
+Licensed Material means the artistic or literary work, database, or other material to which the Licensor applied this Public License.
+Licensed Rights means the rights granted to You subject to the terms and conditions of this Public License, which are limited to all Copyright and Similar Rights that apply to Your use of the Licensed Material and that the Licensor has authority to license.
+Licensor means the individual(s) or entity(ies) granting rights under this Public License.
+Share means to provide material to the public by any means or process that requires permission under the Licensed Rights, such as reproduction, public display, public performance, distribution, dissemination, communication, or importation, and to make material available to the public including in ways that members of the public may access the material from a place and at a time individually chosen by them.
+Sui Generis Database Rights means rights other than copyright resulting from Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, as amended and/or succeeded, as well as other essentially equivalent rights anywhere in the world.
+You means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning.
+Section 2 – Scope.
+License grant .
+Subject to the terms and conditions of this Public License, the Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-exclusive, irrevocable license to exercise the Licensed Rights in the Licensed Material to:
+reproduce and Share the Licensed Material, in whole or in part; and
+produce, reproduce, and Share Adapted Material.
+Exceptions and Limitations . For the avoidance of doubt, where Exceptions and Limitations apply to Your use, this Public License does not apply, and You do not need to comply with its terms and conditions.
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+No downstream restrictions . You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, the Licensed Material if doing so restricts exercise of the Licensed Rights by any recipient of the Licensed Material.
+No endorsement . Nothing in this Public License constitutes or may be construed as permission to assert or imply that You are, or that Your use of the Licensed Material is, connected with, or sponsored, endorsed, or granted official status by, the Licensor or others designated to receive attribution as provided in Section 3(a)(1)(A)(i) .
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+Moral rights, such as the right of integrity, are not licensed under this Public License, nor are publicity, privacy, and/or other similar personality rights; however, to the extent possible, the Licensor waives and/or agrees not to assert any such rights held by the Licensor to the limited extent necessary to allow You to exercise the Licensed Rights, but not otherwise.
+Patent and trademark rights are not licensed under this Public License.
+To the extent possible, the Licensor waives any right to collect royalties from You for the exercise of the Licensed Rights, whether directly or through a collecting society under any voluntary or waivable statutory or compulsory licensing scheme. In all other cases the Licensor expressly reserves any right to collect such royalties.
+Section 3 – License Conditions.
+Your exercise of the Licensed Rights is expressly made subject to the following conditions.
+
+Attribution .
+If You Share the Licensed Material (including in modified form), You must:
+
+retain the following if it is supplied by the Licensor with the Licensed Material:
+identification of the creator(s) of the Licensed Material and any others designated to receive attribution, in any reasonable manner requested by the Licensor (including by pseudonym if designated);
+a copyright notice;
+a notice that refers to this Public License;
+a notice that refers to the disclaimer of warranties;
+a URI or hyperlink to the Licensed Material to the extent reasonably practicable;
+indicate if You modified the Licensed Material and retain an indication of any previous modifications; and
+indicate the Licensed Material is licensed under this Public License, and include the text of, or the URI or hyperlink to, this Public License.
+You may satisfy the conditions in Section 3(a)(1) in any reasonable manner based on the medium, means, and context in which You Share the Licensed Material. For example, it may be reasonable to satisfy the conditions by providing a URI or hyperlink to a resource that includes the required information.
+If requested by the Licensor, You must remove any of the information required by Section 3(a)(1)(A) to the extent reasonably practicable.
+If You Share Adapted Material You produce, the Adapter's License You apply must not prevent recipients of the Adapted Material from complying with this Public License.
+Section 4 – Sui Generis Database Rights.
+Where the Licensed Rights include Sui Generis Database Rights that apply to Your use of the Licensed Material:
+
+for the avoidance of doubt, Section 2(a)(1) grants You the right to extract, reuse, reproduce, and Share all or a substantial portion of the contents of the database;
+if You include all or a substantial portion of the database contents in a database in which You have Sui Generis Database Rights, then the database in which You have Sui Generis Database Rights (but not its individual contents) is Adapted Material; and
+You must comply with the conditions in Section 3(a) if You Share all or a substantial portion of the contents of the database.
+For the avoidance of doubt, this Section 4 supplements and does not replace Your obligations under this Public License where the Licensed Rights include other Copyright and Similar Rights.
+
+Section 5 – Disclaimer of Warranties and Limitation of Liability.
+Unless otherwise separately undertaken by the Licensor, to the extent possible, the Licensor offers the Licensed Material as-is and as-available, and makes no representations or warranties of any kind concerning the Licensed Material, whether express, implied, statutory, or other. This includes, without limitation, warranties of title, merchantability, fitness for a particular purpose, non-infringement, absence of latent or other defects, accuracy, or the presence or absence of errors, whether or not known or discoverable. Where disclaimers of warranties are not allowed in full or in part, this disclaimer may not apply to You.
+To the extent possible, in no event will the Licensor be liable to You on any legal theory (including, without limitation, negligence) or otherwise for any direct, special, indirect, incidental, consequential, punitive, exemplary, or other losses, costs, expenses, or damages arising out of this Public License or use of the Licensed Material, even if the Licensor has been advised of the possibility of such losses, costs, expenses, or damages. Where a limitation of liability is not allowed in full or in part, this limitation may not apply to You.
+The disclaimer of warranties and limitation of liability provided above shall be interpreted in a manner that, to the extent possible, most closely approximates an absolute disclaimer and waiver of all liability.
+Section 6 – Term and Termination.
+This Public License applies for the term of the Copyright and Similar Rights licensed here. However, if You fail to comply with this Public License, then Your rights under this Public License terminate automatically.
+Where Your right to use the Licensed Material has terminated under Section 6(a), it reinstates:
+
+automatically as of the date the violation is cured, provided it is cured within 30 days of Your discovery of the violation; or
+upon express reinstatement by the Licensor.
+For the avoidance of doubt, this Section 6(b) does not affect any right the Licensor may have to seek remedies for Your violations of this Public License.
+
+For the avoidance of doubt, the Licensor may also offer the Licensed Material under separate terms or conditions or stop distributing the Licensed Material at any time; however, doing so will not terminate this Public License.
+Sections 1 , 5 , 6 , 7 , and 8 survive termination of this Public License.
+Section 7 – Other Terms and Conditions.
+The Licensor shall not be bound by any additional or different terms or conditions communicated by You unless expressly agreed.
+Any arrangements, understandings, or agreements regarding the Licensed Material not stated herein are separate from and independent of the terms and conditions of this Public License.
+Section 8 – Interpretation.
+For the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License.
+To the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions.
+No term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor.
+Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority.

index.qmd

@@ -43,4 +43,11 @@ appropiate. Key changes to the web-site are tracked here:
 :::
 
 
+::: {.content-visible when-profile="public"}
+## License information
+
+- The material on this website is provided under a CC BY 4.0 [license](https://github.com/Novartis/bamdd/tree/main/docs/public/LICENSE)
+- The source code is provided under a GPL-2 [license](https://github.com/Novartis/bamdd/tree/main/LICENSE)
+:::
+
 

src/02_case_studies.qmd

@@ -16,7 +16,6 @@ overview <- dplyr::tribble(
                        "[Meta-analysis to estimate treatment effects](02ab_meta_analysis_trtdiff.qmd)", "aggregate data modeling & varying exposure times of count data",
                        "[Dose finding](02b_dose_finding.qmd)", "non-linear models",
                        "[Oncology dose escalation](02c_dose_escalation.qmd)",  "constrained parameters",
-                       "[Variable selection](02d_horseshoe.qmd)", "shrinkage priors & monotonic effects of ordinal variables",
                        "[Multiple imputation](02e_multiple_imputation.qmd)", "multi-variate outcome modeling",
                        "[Longitudinal data](02g_longitudinal.qmd)", "longitudinal modeling with different covariance structures (MMRM)",
                        "[Bayesian Mixed effects Model for Repeated Measures (MMRM)](02h_mmrm.qmd)", "unstructured MMRM for a continuous endpoint",

src/02a_meta_analysis.qmd

@@ -10,7 +10,7 @@ source(here::here("src", "setup.R"))
 ##knitr::opts_chunk$set(cache=FALSE) 
 ```
 
-{{< Include _macros.qmd >}}
+{{< include _macros.qmd >}}
 
 Here we will demonstrate the use of historical control data as an
 example for a meta-analytic predictive (MAP) prior approach based on

src/install_dependencies.R

@@ -63,4 +63,3 @@ if(length(missing_dependencies) > 0) {
     install.packages(pkg)
   }
 }
-