Merge branch 'main' of github.com:r-devel/rcwg

Author: hturner

office_hours/2024-11-01_EMEA-APAC.md renamed to office_hours/2024-01-11_EMEA-APAC.md

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+# Welcome to the R Contributor Office Hour (EMEA/APAC)! 
+2024-01-11
+
+## Useful links 
+
+ * R Development Guide: https://contributor.r-project.org/rdevguide/ 
+ * R's Bugzilla: https://bugs.r-project.org 
+ * R Project Weblate server: https://translate.rx.studio/projects/r-project 
+ * R sources - SVN repo: https://svn.r-project.org/R/trunk/ 
+ * GitHub mirror: https://github.com/r-devel/r-svn/ 
+ * GitHub Codespace (R Dev Container) https://github.com/r-devel/r-dev-env 
+ * R-devel mailing list archives: https://stat.ethz.ch/pipermail/r-devel/, searchable GitHub repo: https://github.com/MichaelChirico/r-mailing-list-archive/tree/master/r-devel 
+ * Minutes from previous office hours: https://github.com/r-devel/rcontribution/tree/main/office_hours 
+ * Annotated list of bugs: https://docs.google.com/spreadsheets/d/1bhfPIJQXeKpydigMH79FKIkdHO9NxlBSB_bTRoCFnPY/edit#gid=0
+
+## Keeping in contact 
+
+ * Twitter: https://twitter.com/R_Contributors
+ * Mastodon: https://hachyderm.io/@R_Contributors
+ * Slack: https://contributor.r-project.org/slack 
+
+## Warm up 
+
+Please tell us a bit about yourself, following the template below: 
+
+Name: Heather Turner   
+Country I am currently in: UK  
+Something we could do or discuss together today: Bug 1161 
+    
+Name: Tomasz Gieorgijewski   
+Country I am currently in: Poland   
+Something we could do or discuss together today: 
+    
+Name: Ella Kaye   
+Country I am currently in: UK  
+Something we could do or discuss together today: I'm happy to give an update on the penguins/gait patch.
+
+Name: Joakim  
+Country I am currently in: Turkey
+Something we could do or discuss together today: 
+
+Name: Vaibhav  
+Country I am currently in: India
+Something we could do or discuss together today: 
+
+Name: Munawar  
+Country I am currently in: UK  
+Something we could do or discuss together today: GSoC/GSoD
+
+Name: Brian Terry  
+Country I am currently in: UK  
+
+## Discussion
+
+### Update from Ella on adding penguins data
+
+- Is proposing to add palmerpenguins dataset to R. Patch adding the dataset is with an R Core member for review.
+
+    - Has also prepared report to show this data may be used to reproduce some of the analysis from the orginal paper, as a way to validate the data
+
+    - Take a look at Ella's patch: https://github.com/r-devel/r-svn/pull/154. The GitHub mirror (github.com/r-devel/r-svn) of the of the official SVN repository (https://svn.r-project.org/R/trunk/) enables other people to review the patch and it is also possible to create a patch file from this which can be applied to the original Subversion repository by R Core (see https://contributor.r-project.org/rdevguide/FixBug.html#using-a-git-mirror).
+
+    - Can use `tools::checkRd` to check the syntax of an Rd file.
+
+- Has been working on updating examples to use penguins data rather than iris
+
+    - Some examples use `iris3` which is an artificial reformatting of iris data as 3-way data set. So proposing to also add gait data as an alternative to this
+
+- Challenges. 
+    - Building R on the mac: working on documentation here: https://github.com/r-devel/rcwg/blob/main/working_documents/comments_on_install_r_macOS.md
+    - R Core member who is reviewing this work wanted separate patches for the penguins and gait data. Unfortunately cannot make two forks of SVN mirror (github.com/r-svn), so worked locally for the gait data.
+
+- Question: what is the difference between the GitHub Mirror and the Subversion repo?
+   - The mirror can be a useful tool for contributors, especially when you want to share the code with other people for review. Patches created from the mirror include some git-specific text, but are compatible with SVN.
+   - The actual sources are version controlled under SVN, so an svn-compatible patch must be created to propose a patch to R Core (this proposal is usually done via Bugzilla, see below).
+   - Only R Core members can make commits to the SVN repo.
+   - The GitHub mirror mostly shows mirrored commits by R core members, plus occasional commits by Jeroen Ooms, who maintains the GitHub mirror. There is some GitHub-specific code in the `.github` folder that implements the mirroring of the SVN repo.
+  
+### Brief intro to bug tracking in R
+
+- Adding something new to R (as in Ella's patch) is something that contributors rarely work on - usually only R Core members do this. The more usual path for contributors is to work on bugs in R.
+- We looked at https://bugs.r-project.org and an example bug from the unofficial annotated bug list https://docs.google.com/spreadsheets/d/1bhfPIJQXeKpydigMH79FKIkdHO9NxlBSB_bTRoCFnPY/edit#gid=0. We saw that a patch (.diff) file can be added as a comment and people reading the bug report can view a visual diff in the browser.
+- Mentioned short video on contributor home page (https://contributor.r-project.org/) that gives some pointers on finding a bug to work on.
+    
+### Discussion of Bug 1161
+
+- Heather was set up with an RStudio project that had a local copy of her fork of the GitHub mirror, i.e. a local copy of https://github.com/hturner/r-svn. This meant we could look at her local copy of the R sources, in particular the source file for `persp()`, which is in `src/library/graphics/R`.
+- First we looked at the help file for `persp`, which says: "If x is a list, its components x$x and x$y are used for x and y, respectively.".
+- Then we tried to make a reproducible example, based on the first example in the help file. Original example: 
+    
+    ```{r}
+    x <- seq(-10, 10, length.out = 30)
+    y <- x
+    f <- function(x, y) { r <- sqrt(x^2+y^2); 10 * sin(r)/r }
+    z <- outer(x, y, f)
+    op <- par(bg = "white")
+    persp(x, y, z, theta = 30, phi = 30, expand = 0.5, col = "lightblue")
+    ```
+    with a list for x:
+    ```{r}
+    persp(x = list(x = seq(-10, 10, length.out = 30), y = y), z = z,
+          theta = 30, phi = 30, expand = 0.5, col = "lightblue")
+    ```
+ - We then looked at the source code `persp()` to try to understand what's happening:
+     ```{r}
+     if (is.null(xlab))
+        xlab <- if (!missing(x) && is.name(substitute(x))) deparse1(substitute(x)) else "X"
+     ```
+     How can we ever get to the `else` condition? Turns out we can drop `x` and the plot looks the same apart from having the x label "X"
+     ```{r}
+     persp(y = y, z = z, theta = 30, phi = 30, expand = 0.5, col = "lightblue")
+     ```
+     presumably x defaults to sequence 1, 2, ...
+ - At first we (Heather!) thought that the original poster (OP) objected to having an expression for an axis label rather than a name and we tried editing `persp.default` to only deparse x when it was a name. However we realized that an expression is also used as the label for the case when `x` is not a list. Also this behaviour is more general, e.g. `plot()` will also use an expression as the axis label by default.
+ - After some discussion, and reviewing the bug report again, we realized that the issue was that it didn't make sense to label an axis (1 dimension) by a list of x and y (2 dimensions). It would make more sense to unpack the list, then continue as if x and y had been specified as separate arguments.
+ - Heather also noted that it is possible to specify a list of x, y and z values, e.g. 
+ ```{r}
+ persp(x = list(x = seq(-10, 10, length.out = 30), y = y, z = z),
+      theta = 30, phi = 30, expand = 0.5, col = "lightblue")
+ ```
+ This behaviour is undocumented.
+ - Munawar volunteered to work on a fix following the idea to unpack the elements of the list somehow.
+ - Heather mentioned the #work-out-loud channel on Slack, which can be used to discuss contributions people are working on, for feedback/help along the way.
+