Example
Milan Malfait, Ghent University
October 27, 2022
1 R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.
When you click the Knit button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
summary(cars)## speed dist
## Min. : 4.0 Min. : 2.00
## 1st Qu.:12.0 1st Qu.: 26.00
## Median :15.0 Median : 36.00
## Mean :15.4 Mean : 42.98
## 3rd Qu.:19.0 3rd Qu.: 56.00
## Max. :25.0 Max. :120.002 Including Plots
You can also embed plots, for example:
Note that the echo = FALSE parameter was added to the
code chunk to prevent printing of the R code that generated the
plot.
3 Caching
The GHA workflow maintains cached knitr results between
subsequent runs to reduce runtime. Caching can be enabled by specifying
cache=TRUE in the code chunk header.
Note that this should be used with caution, as caches may become invalid when code is changed, potentially leading to unsuspected results.
## Run with caching enabled
Sys.time()## [1] "2022-10-27 13:49:35 UTC"Session info
Session info
## [1] "2022-10-27 13:49:36 UTC"## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.1 (2022-06-23)
## os Ubuntu 20.04.5 LTS
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate C.UTF-8
## ctype C.UTF-8
## tz UTC
## date 2022-10-27
## pandoc 2.19.2 @ /usr/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## ! package * version date (UTC) lib source
## P bslib 0.4.0 2022-07-16 [?] CRAN (R 4.2.1)
## P cachem 1.0.6 2021-08-19 [?] CRAN (R 4.2.1)
## P cli 3.4.1 2022-09-23 [?] CRAN (R 4.2.1)
## codetools 0.2-18 2020-11-04 [2] CRAN (R 4.2.1)
## P colorspace 2.0-3 2022-02-21 [?] CRAN (R 4.2.1)
## P digest 0.6.30 2022-10-18 [?] CRAN (R 4.2.1)
## P evaluate 0.17 2022-10-07 [?] CRAN (R 4.2.1)
## P fansi 1.0.3 2022-03-24 [?] CRAN (R 4.2.1)
## P farver 2.1.1 2022-07-06 [?] CRAN (R 4.2.1)
## P fastmap 1.1.0 2021-01-25 [?] CRAN (R 4.2.1)
## P ggplot2 * 3.3.6 2022-05-03 [?] CRAN (R 4.2.1)
## P glue 1.6.2 2022-02-24 [?] CRAN (R 4.2.1)
## P gtable 0.3.1 2022-09-01 [?] CRAN (R 4.2.1)
## P highr 0.9 2021-04-16 [?] CRAN (R 4.2.1)
## P htmltools 0.5.3 2022-07-18 [?] CRAN (R 4.2.1)
## P jquerylib 0.1.4 2021-04-26 [?] CRAN (R 4.2.1)
## P jsonlite 1.8.3 2022-10-21 [?] CRAN (R 4.2.1)
## P knitr 1.40 2022-08-24 [?] CRAN (R 4.2.1)
## P labeling 0.4.2 2020-10-20 [?] CRAN (R 4.2.1)
## P lifecycle 1.0.3 2022-10-07 [?] CRAN (R 4.2.1)
## P magrittr 2.0.3 2022-03-30 [?] CRAN (R 4.2.1)
## P munsell 0.5.0 2018-06-12 [?] CRAN (R 4.2.1)
## P pillar 1.8.1 2022-08-19 [?] CRAN (R 4.2.1)
## P pkgconfig 2.0.3 2019-09-22 [?] CRAN (R 4.2.1)
## P R6 2.5.1 2021-08-19 [?] CRAN (R 4.2.1)
## P renv 0.15.4 2022-03-03 [?] CRAN (R 4.2.1)
## P rlang 1.0.6 2022-09-24 [?] CRAN (R 4.2.1)
## P rmarkdown 2.17 2022-10-07 [?] CRAN (R 4.2.1)
## P sass 0.4.2 2022-07-16 [?] CRAN (R 4.2.1)
## P scales 1.2.1 2022-08-20 [?] CRAN (R 4.2.1)
## P sessioninfo 1.2.2 2021-12-06 [?] CRAN (R 4.2.1)
## P stringi 1.7.8 2022-07-11 [?] CRAN (R 4.2.1)
## P stringr 1.4.1 2022-08-20 [?] CRAN (R 4.2.1)
## P tibble 3.1.8 2022-07-22 [?] CRAN (R 4.2.1)
## P utf8 1.2.2 2021-07-24 [?] CRAN (R 4.2.1)
## P vctrs 0.5.0 2022-10-22 [?] CRAN (R 4.2.1)
## P withr 2.5.0 2022-03-03 [?] CRAN (R 4.2.1)
## P xfun 0.34 2022-10-18 [?] CRAN (R 4.2.1)
## P yaml 2.3.6 2022-10-18 [?] CRAN (R 4.2.1)
##
## [1] /home/runner/work/Rmd-website/Rmd-website/renv/library/R-4.2/x86_64-pc-linux-gnu
## [2] /opt/R/4.2.1/lib/R/library
##
## P ── Loaded and on-disk path mismatch.
##
## ──────────────────────────────────────────────────────────────────────────────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