Merge pull request #7 from openstatsware/edits-publication

Edits to publication slides

Author: danielinteractive

DESCRIPTION

@@ -8,4 +8,5 @@ Depends:
   emoji,
   knitr,
   testthat,
-  checkmate
+  checkmate,
+  rhub

slides/05_publication.qmd

@@ -25,36 +25,17 @@ image: thumbnails/publish.jpg
 
 ## Example `_pkgdown.yml` File
 
-```yaml
----
-url: https://openpharma.github.io/mmrm/latest-tag
-
-template:
-  bootstrap: 5
-  params:
-    ganalytics: UA-125641273-1
-
-navbar:
-  right:
-    - icon: fa-github
-      href: https://github.com/openpharma/mmrm
-
-reference:
-  - title: Package
-    contents:
-      - mmrm-package
-  - title: Functions
-    contents:
-      - mmrm
-      - fit_mmrm
-      - mmrm_control
-      - fit_single_optimizer
-      - refit_multiple_optimizers
-      - df_1d
-      - df_md
-      - component
+```{r}
+#| output: asis
+#| echo: false
+file <- readLines(con = "https://raw.githubusercontent.com/openpharma/mmrm/refs/heads/main/_pkgdown.yml")
+cat("```yaml \n---\n")
+writeLines(file[-1])
+cat("\n---\n```")
 ```
 
+Source: the [`mmrm`](https://github.com/openpharma/mmrm/blob/main/_pkgdown.yml) package documentation
+
 ##  {background-iframe="https://openpharma.github.io/mmrm/latest-tag/reference/index.html" background-interactive="true"}
 
 ## Publication as GitHub Page
@@ -69,14 +50,15 @@ reference:
 
 ##  {background-iframe="https://openpharma.github.io/mmrm/latest-tag/" background-interactive="true"}
 
-# Licensing, Open sourcing, Versioning
+# Licensing, Open Sourcing, Versioning
 
 ## Licensing
 
 - High level categorization of licenses:
   - "Permissive": Relaxed. Can be freely copied, modified, published (under the
     same license).
   - "Copyleft": Stricter. Same rights need to be preserved in derivative works.
+  - Helpful tool: <https://choosealicense.com/>
 - R itself is licensed under GPL, but packages can choose, e.g.:
     - `usethis::use_mit_license()` for permissive MIT
     - `usethis::use_gpl_license()` for copyleft GPL
@@ -91,12 +73,19 @@ reference:
   - e.g. cannot copy/paste code from a GPL package and publish in an MIT package
 - `LICENSE` file optionally can contain further restrictions of the license
 
+## Licensing (cont'd)
+
+- You don't have to include a license with your code
+- But: if no license is included, your work is under your exclusive copyright by default
+  - This means that nobody else can copy, distribute, modify it
+  - Once the work has other contributors (each being a copyright holder for their contributions), that _nobody_ starts including you
+  - The consequence is that you cannot copy, distribute, modify other people's contributions to your project
+- Even if unlicensed code is published in a public repository, as a user, you generally don't have the permission from the creators of the software to use, modify, or share the software
+
 ## Open Sourcing
 
-- The easiest way to "open source" your R package is to make the GitHub
-  repository public
-- This allows for easy open source contributions from other developers via pull
-  requests
+- The easiest way to "open source" your R package is to make the GitHub/code repository public
+- This allows for easy open source contributions from other developers via pull requests
 - Please check with your organization first:
   - Are they ok to publish the software?
   - What is the appropriate copyright holder?
@@ -137,7 +126,7 @@ reference:
 - Citations in author-year style, followed by `<doi:...>`
 - Reducing run time of tests, checks, examples, vignettes is important
 - Need to provide cross-platform portable code:
-  CRAN runs checks on Windows, Mac, several Linux OS
+  CRAN runs checks on Windows, Mac, and several Linux distributions
 
 ## CRAN (cont'd)
 
@@ -153,7 +142,7 @@ package took 5 weeks and 6 submission attempts; painful experiences:
 -   Your local Windows test system may be much faster than the CRAN system
     (e.g., 5 times)
 -   Don't use "R Package for" in your package title
--   The description of the package must be provided with a doi reference
+-   The description of the package must be provided with a DOI reference
 
 ## CRAN (cont'd) {.scrollable}
 
@@ -181,7 +170,6 @@ Example message informing about the rejection of the last
 > r-devel-linux-x86_64-debian-gcc Check: Result: Note_to_CRAN_maintainers
 > Maintainer: 'Friedrich Pahlke'
 
-
 ## R-Hub to the Rescue
 
 ::: columns
@@ -190,14 +178,31 @@ 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
+- Free `R CMD check` runs on [different operating systems](https://r-hub.github.io/rhub/reference/rhub_platforms.html) 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))
+- New v2 API relies on GitHub actions for checks
+- [Blog post](https://blog.r-hub.io/2024/04/11/rhub2/) with more details about the transition to the new API
+announcing the transition to the new API: <https://blog.r-hub.io/2024/04/11/rhub2/
+Typically used via the [website](https://builder.r-hub.io/)
 :::
 :::
 
+## R-Hub Platforms
+
+```{r}
+#| echo: true
+library(rhub)
+rhub::rhub_platforms()
+```
+
+## GitHub Actions
+
+- It is also possible to use GitHub Actions to run `R CMD check`
+- Free for public repositories, paid service for private repositories
+- Checks will be run every time someone pushes a commit to a repository hosted on GitHub
+- Easy setup from your R console: `usethis::use_github_action_check_standard()`
+- Script and documentation are developed and maintained by the `r-lib` organization [here](https://github.com/r-lib/actions/tree/v2/check-r-package)
+
 # GitHub
 
 ## Tags
@@ -243,23 +248,23 @@ Example message informing about the rejection of the last
 
 - [Licensing chapter](https://r-pkgs.org/license.html)
 - [All possible licenses for CRAN packages](https://svn.r-project.org/R/trunk/share/licenses/license.db)
+- [Compare and pick licenses](https://choosealicense.com/)
 - [GitHub releases](https://docs.github.com/en/repositories/releasing-projects-on-github/about-releases)
 - [CRAN Repository Policy](https://cran.r-project.org/web/packages/policies.html)
-- [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
+- 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`
+- 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
+  - (Optional) Check the automatic GitHub page deploy action
 
 # License Information
 
@@ -268,5 +273,7 @@ Use the same repository created from template [https://github.com/kkmann/simulat
   Friedrich Pahlke [`r fontawesome::fa("github")`](https://github.com/fpahlke/) [`r fontawesome::fa("linkedin")`](https://www.linkedin.com/in/pahlke/)
 - In the current version, changes were done by (later authors):
   Liming Li [`r fontawesome::fa("github")`](https://github.com/clarkliming),
-  Philippe Boileau [`r fontawesome::fa("globe")`](https://pboileau.ca/)
+  Philippe Boileau [`r fontawesome::fa("globe")`](https://pboileau.ca/),
+  Alessandro Gasparini [`r fontawesome::fa("linkedin")`](https://www.linkedin.com/in/ellessenne) [`r fontawesome::fa("github")`](https://www.github.com/ellessenne) [`r fontawesome::fa("globe")`](https://www.ellessenne.xyz/)
+
 {{< include _license_footer.qmd >}}

slides/download/install.R

@@ -14,5 +14,6 @@ install.packages(c(
   "styler",
   "lintr",
   "pkgdown",
-  "remotes"
+  "remotes",
+  "rhub"
 ))