last polishing

slides/01_intro.qmd

@@ -20,7 +20,7 @@ image: thumbnails/hello.jpg
 ::: {.column width="70%"}
 -   Ph.D. in Statistics from University of Zurich, Bayesian Model Selection
 -   Biostatistician at Roche for 5 years, Data Scientist at Google for 2 years, Statistical Software Engineer at Roche for the last 4 years
--   Co-founder of [RCONIS](rconis.com)
+-   Co-founder of [inferential.bio](https://inferential.bio) and [RCONIS](https://rconis.com)
 -   Multiple R packages on CRAN and Bioconductor, co-wrote book on Likelihood and Bayesian Inference, chair of `openstatsware`
 -   Feel free to connect
     [`r fontawesome::fa("linkedin")`](https://www.linkedin.com/in/danielsabanesbove/)
@@ -32,15 +32,15 @@ image: thumbnails/hello.jpg
 ## `openstatsware`
 
 ::: columns
-::: {.column width="50%"}
+::: {.column width="70%"}
 - [openstatsware.org](https://openstatsware.org)
 - Since: 19 August 2022 - almost 2 years now!
 - Where: American Statistical Association (ASA) Biopharmaceutical Section (BIOP), European Federation of Statisticians in the Pharmaceutical Industry (EFSPI)
 - Who: Currently more than 50 statisticians from more than 30 organizations
 - What: Engineer packages and spread best practices
 :::
 
-::: {.column width="50%"}
+::: {.column width="30%"}
 ![](https://raw.githubusercontent.com/RConsortium/asa-biop-swe-wg/main/sticker/openstatsware-hex.svg){height="300"}
 :::
 :::
@@ -51,17 +51,16 @@ image: thumbnails/hello.jpg
 -   Create your own R `r fontawesome::fa("cube")`
 -   Learn about & apply professional `r fontawesome::fa("cube")` development workflow
 -   Learn & apply fundamentals of quality control for R `r fontawesome::fa("cube")`
--   Get crash-course in version control to stay organized
--   Try out modern collaboration techniques on GitHub.com
--   Optimize your R code for correctness and speed
+-   Get crash-course in version control and modern collaboration techniques on GitHub.com
 -   Learn how to make an R `r fontawesome::fa("cube")` available to others
--   Get a starting point for sustainable Shiny app development
+-   Optimize your R code for correctness and speed
+-   Learn how to approach the design and modularity of Shiny apps and how to test them
 
 ## Program outline: Day 1
 
 ```{r}
 #| echo: false
-#| style: font-size:0.95em!important;
+#| style: font-size:0.8em!important;
 readr::read_csv("resources/program.csv", col_types = "cc") |>
   dplyr::filter(day == "1") |> 
   dplyr::select(- day) |> 
@@ -72,7 +71,7 @@ readr::read_csv("resources/program.csv", col_types = "cc") |>
 
 ```{r}
 #| echo: false
-#| style: font-size:0.95em!important;
+#| style: font-size:0.8em!important;
 readr::read_csv("resources/program.csv", col_types = "cc") |>
   dplyr::filter(day == "2") |> 
   dplyr::select(- day) |> 
@@ -94,38 +93,39 @@ readr::read_csv("resources/program.csv", col_types = "cc") |>
 -   Local R development environment with
     -   git `r fontawesome::fa("git-alt")`
     -   Rtools/R/Rstudio IDE `r fontawesome::fa("r-project")`
+-   Install additional R packages using the [installation script](slides/download/install.R)
 -   Curiosity `r emoji::emoji("curious")`
 -   Positive attitude `r emoji::emoji("smile")`
 
 ## Speed intros and what would you like to learn?
 
-- Name?
-- Organization?
-- Motivation for this workshop/ what would you like to learn
-- Favorite food?
-- Favorite music?
+- Name? `r emoji::emoji("face")`
+- Organization? `r emoji::emoji("office")`
+- Motivation for this workshop/ what would you like to learn `r emoji::emoji("brain")`
+- Favorite food? `r emoji::emoji("food")`
+- Favorite music? `r emoji::emoji("music")`
 
 ## What do we mean by GSWEP4R\*?
 
 ::: aside
 \* Good Software Engineering Practice for R
 :::
 
--   Applying concept of GxP to SWE with R
--   Improve **quality** of R code/packages, particularly in regulated enviroments but not limited to!
+-   Applying concept of "Good XYZ Practice" to SWE with R
+-   Improve **quality** and **longevity** of R code/packages  
 -   Not a universal standard; we share our perspectives
 -   Collection of best practices
--   Do not reinvent the wheel: learn from IT/open source space
+-   Do not reinvent the wheel: learn from the community
 
 ## Why care about GSWEP4R?
 
--   Move to / integration of R in pharma is clear trend
+-   R is one of the most successfull statistical programming languages
 -   R is a powerful yet complex *ecosystem*
     -   Core component: R packages
     -   Mature analysts: users & contributors
     -   Deep understanding crucial, even to just assess quality
--   Analyses increasingly require complex scripts/programs </br> $\leadsto$ line between programming and data analysis blurs
--   Value: de-risking use of R and efficiency gains
+-   Analyses increasingly require complex scripts/programs
+-   The concepts are applicable to other languages, too (Python, Julia, etc.)
 
 ## Start small - from script to package
 
@@ -196,10 +196,10 @@ knitr::include_graphics("resources/pkg_graph.png")
 
 ##  {background-iframe="https://pharmaverse.org/" background-interactive="true"}
 
-## GxP + R `r fontawesome::fa("cube")` = `r fontawesome::fa("heart")`
+## Pharma perspective: GxP + R `r fontawesome::fa("cube")` = `r fontawesome::fa("heart")`
 
 -   Core infrastructure packages only through industry
--   Quality, burden sharing: open-source [pharmaverse](https://pharmaverse.org/) and others
+-   Quality, burden sharing: open-source [pharmaverse](https://pharmaverse.org/) and [openstatsware](https://openstatsware.org)
 -   Open methodological packages can de-risk innovative methods
 -   R packages make (statistical/methodological) code
     -   testable (with documented evidence thereof, [CFR Part 11](https://en.wikipedia.org/wiki/Title_21_CFR_Part_11))

slides/02_r_packages.qmd

@@ -333,7 +333,6 @@ export(my_sum)
 
 - [R Packages (2e)](https://r-pkgs.org/)
 - [Writing R Extensions](https://cran.r-project.org/doc/manuals/R-exts.html)
-- [Rewriting R code in C++](https://adv-r.hadley.nz/rcpp.html)
 - [Super technical details about R Markdown](https://www.youtube.com/watch?v=fiy32LjgGUE)
 
 # License Information

slides/05_collaboration.qmd

@@ -1,6 +1,5 @@
 ---
 title: "5 Version Control & Collaboration"
-date: "2023-10-17"
 description: "Collaboration via GitHub + practical<br/>[Photo CC0 by THIS IS ZUN on pexels.com]{.copyright}"
 image: thumbnails/collaboration.jpg
 ---

slides/06_publication.qmd

@@ -1,6 +1,5 @@
 ---
 title: "6 Publication"
-date: "2023-10-17"
 description: "Publication of R packages + practical<br/>[Photo CC0 by Andrea Piacquadio on pexels.com]{.copyright}"
 image: thumbnails/publish.jpg
 ---
@@ -24,7 +23,7 @@ image: thumbnails/publish.jpg
 
 ```yaml
 ---
-url: https://openpharma.github.io/mmrm
+url: https://openpharma.github.io/mmrm/latest-tag
 
 template:
   bootstrap: 5
@@ -52,7 +51,7 @@ reference:
       - component
 ```
 
-##  {background-iframe="https://openpharma.github.io/mmrm/main/reference/index.html" background-interactive="true"}
+##  {background-iframe="https://openpharma.github.io/mmrm/latest-tag/reference/index.html" background-interactive="true"}
 
 ## Publication as GitHub Page
 
@@ -64,7 +63,7 @@ reference:
 - To get started, use `usethis::use_pkgdown_github_pages()`
   - Or, manually deploy site with `pkgdown::deploy_to_branch()`
 
-##  {background-iframe="https://openpharma.github.io/mmrm/main/" background-interactive="true"}
+##  {background-iframe="https://openpharma.github.io/mmrm/latest-tag/" background-interactive="true"}
 
 # Licensing, Open sourcing, Versioning
 
@@ -190,7 +189,8 @@ Example message informing about the rejection of the last
 - Free `R CMD check` runs on [different operating systems](https://docs.r-hub.io/#which-platform) before submitting to CRAN
 - Supported by the R consortium
 - Typically used via the [website](https://builder.r-hub.io/)
-- There is also an R API: `rhub::check_for_cran()` is comfortable
+- There is also an R API: `rhub::check()` is comfortable
+  - Note: New API with R-hub v2 since a few weeks ([details](https://r-hub.github.io/rhub/articles/rhubv2.html))
 :::
 :::
 

slides/07_shiny.qmd

@@ -1,6 +1,5 @@
 ---
 title: "7 Shiny Development"
-date: "2023-10-17"
 description: "Best Practices for Shiny App Development<br/>[Photo by Pixabay on pexels.com]{.copyright}"
 image: thumbnails/shiny.jpg
 ---
@@ -37,6 +36,8 @@ image: thumbnails/shiny.jpg
 
 ![](resources/wireframe.png){fig-align="center"}
 
+## Shiny specific tool: `ShinyUiEditor` {background-iframe="https://rstudio.github.io/shinyuieditor/"} 
+
 # Architecture
 
 ## Architecture: Minimize code in Shiny
@@ -271,7 +272,7 @@ This "stringy" reactivity graph is easier to understand and debug
 
 # Exercise: Wireframing
 
-- Visit https://rstudio.github.io/shinyuieditor to get an overview
+- Visit [ShinyUiEditor](https://rstudio.github.io/shinyuieditor) to get an overview
 - Try to build a simple app and see how the code looks like
 - Do you have an idea what could be simplified with modules?
 
@@ -444,9 +445,9 @@ You'll need few extra steps:
 
 Let's look at the following examples.
 
-- Read and execute [`testServer.R`](slides/examples/shiny/testServer.R). Play around with setting different UI inputs and adding additional server tests.
-- Read and execute [`AppDriver.R`](slides/examples/shiny/AppDriver.R). Add a small additional feature to the app and test it.
-- Have a look at [`testModule.R`](slides/examples/shiny/testModule.R). What is different here? Record some additional tests and integrate them into the code.
+- Read and execute [`testServer.R`](examples/shiny/testServer.R). Play around with setting different UI inputs and adding additional server tests.
+- Read and execute [`AppDriver.R`](examples/shiny/AppDriver.R). Add a small additional feature to the app and test it.
+- Have a look at [`testModule.R`](examples/shiny/testModule.R). What is different here? Record some additional tests and integrate them into the code.
 
 # References
 

slides/08_optimization.qmd

@@ -1,6 +1,5 @@
 ---
 title: "8 Code Optimization"
-date: "2024-03-20"
 description: "Best Practices for Optimizing Code<br/>[Photo by Chris Peeters on pexels.com]{.copyright}"
 image: thumbnails/speed.jpg
 bibliography: references.bib
@@ -185,6 +184,7 @@ But it is not too difficult with [`Rcpp`](https://dirk.eddelbuettel.com/code/rcp
 
 - Starting point: `Rcpp::Rcpp.package.skeleton()` 
 - Use [`RcppArmadillo`](https://dirk.eddelbuettel.com/code/rcpp.armadillo.html) for linear algebra
+- Hadley Wickham's chapter [Rewriting R code in C++](https://adv-r.hadley.nz/rcpp.html)
 
 Note: Adding C++ code to your package will in many cases increase the maintenance effort significantly.
 
@@ -195,8 +195,8 @@ Note: Adding C++ code to your package will in many cases increase the maintenanc
 
 # Exercise
 
-- Read [`bootstrap.R`](slides/examples/optimization/bootstrap.R) and understand what is going on.
-- Run [`profbootstrap.R`](slides/examples/optimization/profbootstrap.R) to see where most of the time is spent - where?
+- Read [`bootstrap.R`](examples/optimization/bootstrap.R) and understand what is going on.
+- Run [`profbootstrap.R`](examples/optimization/profbootstrap.R) to see where most of the time is spent - where?
 - In a second version of the function, `impl_2`, only update vectors inside the loop and then create a `tibble` once at the end.
 - In a third version `impl_3` only subset the column instead of the whole `data.frame`. How much faster does it get?
 - In a fourth version `impl_4` use the [`boot`](https://cran.r-project.org/package=boot) package.
@@ -206,6 +206,6 @@ Note: Adding C++ code to your package will in many cases increase the maintenanc
 
 - Creators (initial authors): 
   Lukas A. Widmer and Michael Mayer, see their course [Go fastR – how to make R code fast(er) and run it on high performance compute (HPC) clusters](https://luwidmer.github.io/fastR-website/materials.html)
-- In the current version, changes were done by (later authors):
-  Daniel Sabanes Bove [`r fontawesome::fa("github")`](https://github.com/danielinteractive/) [`r fontawesome::fa("linkedin")`](https://www.linkedin.com/in/danielsabanesbove/),
+- In the current version, changes were done by (later author):
+  Daniel Sabanes Bove [`r fontawesome::fa("github")`](https://github.com/danielinteractive/) [`r fontawesome::fa("linkedin")`](https://www.linkedin.com/in/danielsabanesbove/)
 {{< include _license_footer.qmd >}}

slides/09_conclusion.qmd

@@ -1,6 +1,5 @@
 ---
 title: "9 Conclusion"
-date: "2023-10-17"
 description: "Discussion of learning experience, summary of workflow, conclusion and next steps.</br>[Photo by Ann H on pexels.com]{.copyright}"
 image: thumbnails/conclusion.jpg
 ---
@@ -33,9 +32,9 @@ image: thumbnails/conclusion.jpg
     Idea $\rightarrow$ Design docs $\rightarrow$ Programming $\rightarrow$ Quality check $\rightarrow$ Publication
     -   Don't waste time on maintenance
     -   Be faster with release on CRAN
-    -   Fulfill regulatory requirements
+    -   Fulfill quality requirements of yourself and stakeholders
 -   Refactor your one-off scripts that you want to use in a package
--   Use assertions for all arguments $\rightarrow$ Usability/UX
+-   Use assertions for all arguments $\rightarrow$ better user experience
 -   Implement common generics like `print` and `plot`
 
 ## Ensuring Quality
@@ -106,6 +105,8 @@ image: thumbnails/conclusion.jpg
 -   Later publish it open source on GitHub and submit it to CRAN
 -   Learn about more tips and tricks how to extend R
 
+![Photo by Pixabay on pexels.com](resources/stairs.jpg)
+
 # License information
 
 - Creators (initial authors):