few small fixes before tomorrow's workshop (#3)

openpharma · Oct 27, 2024 · dd9a7d1 · dd9a7d1
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diff --git a/_quarto.yml b/_quarto.yml
@@ -18,11 +18,7 @@ website:
   page-footer:
     center:
       - text: "About"
-        href: https://rconis.com/about/
-      - text: "Imprint"
-        href: https://rconis.com/imprint/
-      - text: "Contact"
-        href: https://rconis.com/contact/
+        href: https://rinpharma.com/
 
 format:
   html:

diff --git a/index.qmd b/index.qmd
@@ -55,19 +55,19 @@ Learn, understand, and practice good software engineering rules. Participants wi
 | Time                | Topic                                        |
 |---------------------|:---------------------------------------------|
 | 12:00 - 12:15 GMT+8 | Introduction and outline                     |
-| 12:15 - 12:55 GMT+8 | R packages, what are they? + practical       |
-| 12:55 - 13:25 GMT+8 | Workflow for creating R packages + practical |
+| 12:15 - 12:55 GMT+8 | R packages, what are they?                   |
+| 12:55 - 13:25 GMT+8 | Workflow for creating R packages             |
 | 13:25 - 13:40 GMT+8 | Break                                        |
-| 13:40 - 14:20 GMT+8 | Package quality + exercise                   |
-| 14:20 - 14:50 GMT+8 | Publication + practical                      |
-| 15:50 - 15:00 GMT+8 | Conclusion                                   |
+| 13:40 - 14:20 GMT+8 | Package quality                              |
+| 14:20 - 14:50 GMT+8 | Publication                                  |
+| 14:50 - 15:00 GMT+8 | Conclusion                                   |
 
 ## Prerequisites & Technical Setup
 
 Prior to the course, participants should:
 
 -   Install the latest [R](https://www.r-project.org/) and [RStudio](https://posit.co/download/rstudio-desktop/) software.
--   Install [Rtools](https://cran.r-project.org/bin/windows/Rtools/rtools43/rtools.html) (only on Windows).
+-   Install [Rtools](https://cran.r-project.org/bin/windows/Rtools/rtools44/rtools.html) (only on Windows).
 -   Install additional R packages using the [installation script](slides/download/install.R).
 -   Download and extract [simulatr.zip](slides/download/simulatr.zip)
 

diff --git a/slides/01_intro.qmd b/slides/01_intro.qmd
@@ -21,10 +21,10 @@ author: Daniel Sabanés Bové and Joe Zhu
 -   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](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/)
-    [`r fontawesome::fa("github")`](https://github.com/danielinteractive)
-    [`r fontawesome::fa("globe")`](https://rconis.com)
+-   Feel free to connect at
+    [`r fontawesome::fa("linkedin")` LinkedIn](https://www.linkedin.com/in/danielsabanesbove/),
+    [`r fontawesome::fa("github")` GitHub](https://github.com/danielinteractive) or 
+    [`r fontawesome::fa("globe")` RCONIS](https://rconis.com)
 :::
 :::
 
@@ -48,7 +48,7 @@ author: Daniel Sabanés Bové and Joe Zhu
 ::: columns
 ::: {.column width="70%"}
 - [openstatsware.org](https://openstatsware.org)
-- Since: 19 August 2022 - almost 2 years now!
+- Since: 19 August 2022 - more than 2 years already!
 - 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
@@ -62,32 +62,30 @@ author: Daniel Sabanés Bové and Joe Zhu
 ## What you will learn here
 
 -   Understand the basic structure of an R package
--   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")`
+-   How to Create your own R `r fontawesome::fa("cube")`
+-   Learn about the professional `r fontawesome::fa("cube")` development workflow
+-   Learn and apply fundamentals of quality control for R `r fontawesome::fa("cube")`
 -   Learn how to make an R `r fontawesome::fa("cube")` available to others
 
 ## Program outline
 
-| Time               | Topic                                        |
-|--------------------|:---------------------------------------------|
+| Time                | Topic                                        |
+|---------------------|:---------------------------------------------|
 | 12:00 - 12:15 GMT+8 | Introduction and outline                     |
-| 12:15 - 12:55 GMT+8 | R packages, what are they? + practical       |
-| 12:55 - 13:25 GMT+8 | Workflow for creating R packages + practical |
+| 12:15 - 12:55 GMT+8 | R packages, what are they?                   |
+| 12:55 - 13:25 GMT+8 | Workflow for creating R packages             |
 | 13:25 - 13:40 GMT+8 | Break                                        |
-| 13:40 - 14:20 GMT+8 | Package quality + exercise                   |
-| 14:20 - 14:50 GMT+8 | Publication + practical                      |
-| 15:50 - 15:00 GMT+8 | Conclusion                                   |
-
+| 13:40 - 14:20 GMT+8 | Package quality                              |
+| 14:20 - 14:50 GMT+8 | Publication                                  |
+| 14:50 - 15:00 GMT+8 | Conclusion                                   |
 
 ## House-keeping
 
 -   Course website at [https://openpharma.github.io/workshop-r-swe-rinpharma-2024](https://openpharma.github.io/workshop-r-swe-rinpharma-2024)
     -   all slides
     -   sources available at [https://github.com/openpharma/workshop-r-swe-rinpharma-2024](https://github.com/openpharma/workshop-r-swe-rinpharma-2024)
+    -   short link: [https://tinyurl.com/3st8rvkn](https://tinyurl.com/3st8rvkn)
     -   all materials CC-BY-SA 4.0
--   We offer a [gitter chat channel](https://matrix.to/#/#workshop-r-swe_community:gitter.im)
-    -   use to ask your peers questions
 
 ## What you will need
 
@@ -100,9 +98,9 @@ author: Daniel Sabanés Bové and Joe Zhu
 
 ## Speed intros and what would you like to learn?
 
-- Name? `r emoji::emoji("face")`
-- Organization? `r emoji::emoji("office")`
-- Motivation for this workshop/ what would you like to learn `r emoji::emoji("brain")`
+- Please enter the following in the chat - in one sentence:
+  - Your name `r emoji::emoji("face")`
+  - Motivation for this workshop/ what would you like to learn `r emoji::emoji("brain")`
 
 ## What do we mean by GSWEP4R\*?
 

diff --git a/slides/02_r_packages.qmd b/slides/02_r_packages.qmd
@@ -24,6 +24,14 @@ author: Daniel Sabanés Bové
 - How to do this in a methodical and sustainable way
 - Give tips and tricks based on practical experience
 
+## How Familiar Are You with R Packages?
+
+Please enter in the chat:
+
+- 0 if you have never written an R package
+- 1 if you have written an R package but never submitted to CRAN
+- 2 if you have written an R package and submitted to CRAN
+
 # Contents of a Package
 
 ## How is a Package Structured?

diff --git a/slides/04_quality.qmd b/slides/04_quality.qmd
@@ -355,6 +355,12 @@ CCR#8: TDD
 
 ![](thumbnails/testing.jpg){fig-align="center"}
 
+## Share Your Experience
+
+Have you ever written unit tests for your code?
+
+- Enter `yes` or `no` in the chat
+
 ## Verification vs Validation
 
 ::: columns

diff --git a/slides/05_publication.qmd b/slides/05_publication.qmd
@@ -189,9 +189,11 @@ Example message informing about the rejection of the last
 ::: {.column width="70%"}
 - 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()` is comfortable
-  - Note: New API with R-hub v2 since a few weeks ([details](https://r-hub.github.io/rhub/articles/rhubv2.html))
+- Now works with GitHub Actions:
+  1. Put your package in a GitHub repository
+  1. Use `rhub::rhub_setup()` for setting up the GitHub action
+  1. Push this change to GitHub
+  1. Use `rhub::rhub_check()` to check your package
 :::
 :::
 
@@ -245,19 +247,6 @@ Example message informing about the rejection of the last
 - [R-hub builder](https://builder.r-hub.io/)
 - [Bioconductor packages](https://contributions.bioconductor.org/index.html)
 
-# Exercise
-
-Use the same repository created from template [https://github.com/kkmann/simulatr](https://github.com/kkmann/simulatr)
-
-- Run CRAN like checks in RStudio: use `--as-cran` in check options
-- Look at the CI/CD checks reported on your GitHub repository
-  - Where are the `R CMD check` results?
-- Enable github page through `use_pkgdown_github_pages`
-- Deploy the website with `pkgdown`
-  - Need to change remote to `git`
-- Deploy the website through `use_github_action("pkgdown")`
-  - (Optional) Check the automatic github page deploy action
-
 # License Information
 
 - Creators (initial authors):

diff --git a/slides/06_conclusion.qmd b/slides/06_conclusion.qmd
@@ -5,6 +5,12 @@ image: thumbnails/conclusion.jpg
 author: Daniel Sabanés Bové
 ---
 
+## Your Learnings
+
+Please enter in the chat:
+
+- What new skill did you learn in today's workshop?
+
 # Take away messages
 
 ## R package structure
@@ -64,7 +70,7 @@ library(emoji)
 
 ::: {.column width="70%"}
 -   It was great to teach you today on how to build R packages
--   Let's keep in touch e.g. via the [gitter chat channel](https://gitter.im/workshop-r-swe/community) for this course that you can connect to
+-   Let's keep in touch e.g. via LinkedIn or GitHub
 -   We welcome feedback on topics/format/content - reach out!
 :::
 :::

diff --git a/slides/_license_footer.qmd b/slides/_license_footer.qmd
@@ -1,3 +1,3 @@
 - This work is licensed under the [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-sa/4.0/).
-- The source files are hosted at [github.com/RCONIS/user2024-tutorial-gswep](https://github.com/RCONIS/user2024-tutorial-gswep), which is forked from and a subset of the original version at [github.com/RCONIS/workshop-r-swe-zrh](https://github.com/RCONIS/workshop-r-swe-zrh).
+- The source files are hosted at [github.com/openpharma/workshop-r-swe-rinpharma-2024](https://github.com/openpharma/workshop-r-swe-rinpharma-2024), which is forked from the original version at [github.com/RCONIS/user2024-tutorial-gswep](https://github.com/RCONIS/user2024-tutorial-gswep).
 - Important: To use this work you must provide the name of the creators (initial authors), a link to the material, a link to the license, and indicate if changes were made
diff --git a/slides/resources/daniel.jpg b/slides/resources/daniel.jpg