Chapter 2 - Workflow basics
Vebash Naidoo
23/08/2020
Last updated: 2020-09-02
Checks: 7 0
Knit directory: r4ds_book/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20200814) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version 7305596. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .Rproj.user/
Untracked files:
Untracked: analysis/images/
Untracked: code_snipp.txt
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were made to the R Markdown (analysis/ch2_workflow.Rmd) and HTML (docs/ch2_workflow.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | d627f04 | sciencificity | 2020-08-26 | Build site. |
| Rmd | 50ff8a5 | sciencificity | 2020-08-26 | Corrected page flow |
| html | b3395ae | sciencificity | 2020-08-23 | Build site. |
| Rmd | e684831 | sciencificity | 2020-08-23 | Added latest learnings |
| html | 6373aef | sciencificity | 2020-08-23 | Build site. |
| Rmd | b96b2ff | sciencificity | 2020-08-23 | Latest additions |
| html | 28dbedf | sciencificity | 2020-08-23 | Build site. |
| html | 5c5ee45 | sciencificity | 2020-08-23 | Build site. |
| Rmd | 865e66f | sciencificity | 2020-08-23 | Ch1 more complete, plus started Ch2 |
Workflow …
object_name <- value can be read as “object name gets value”
Find the <- tedious to enter? RStudio has a shortcut Alt + - to enter it for you.
Alternately there’s the great {styler} package that you may use to convert your code to the preferred style.
- Go to Tools -> Install Packages and install
styler - Else go to the Github page to install.
In your code select the section you want to format (not necessary if you want to do for the entire file).
- Go to Addins
- STYLER
- Choose
Style selectionor the option appropriate for your task.
Sometime you have an assignment, but you also want to print your variable to view its contents. Do this by surrounding the assignment with ().
( y <- seq(1, 10, length.out = 5) )
[1] 1.00 3.25 5.50 7.75 10.00
Exercises
Why does this code not work?
my_variable <- 10 my_varıable[1] 10Look carefully! (This may seem like an exercise in pointlessness, but training your brain to notice even the tiniest difference will pay off when programming.)
It doesn’t work because the
iin themy_variablehas been replaced by another characterı.Tweak each of the following R commands so that they run correctly:
library(tidyverse) ggplot(dota = mpg) + geom_point(mapping = aes(x = displ, y = hwy)) fliter(mpg, cyl = 8) filter(diamond, carat > 3)library(tidyverse)
ggplot(data = mpg) +
geom_point(mapping = aes(x = displ, y = hwy))
filter(mpg, cyl == 8)# A tibble: 70 x 11 manufacturer model displ year cyl trans drv cty hwy fl class <chr> <chr> <dbl> <int> <int> <chr> <chr> <int> <int> <chr> <chr> 1 audi a6 quatt~ 4.2 2008 8 auto(~ 4 16 23 p mids~ 2 chevrolet c1500 su~ 5.3 2008 8 auto(~ r 14 20 r suv 3 chevrolet c1500 su~ 5.3 2008 8 auto(~ r 11 15 e suv 4 chevrolet c1500 su~ 5.3 2008 8 auto(~ r 14 20 r suv 5 chevrolet c1500 su~ 5.7 1999 8 auto(~ r 13 17 r suv 6 chevrolet c1500 su~ 6 2008 8 auto(~ r 12 17 r suv 7 chevrolet corvette 5.7 1999 8 manua~ r 16 26 p 2sea~ 8 chevrolet corvette 5.7 1999 8 auto(~ r 15 23 p 2sea~ 9 chevrolet corvette 6.2 2008 8 manua~ r 16 26 p 2sea~ 10 chevrolet corvette 6.2 2008 8 auto(~ r 15 25 p 2sea~ # ... with 60 more rowsfilter(diamonds, carat > 3)# A tibble: 32 x 10 carat cut color clarity depth table price x y z <dbl> <ord> <ord> <ord> <dbl> <dbl> <int> <dbl> <dbl> <dbl> 1 3.01 Premium I I1 62.7 58 8040 9.1 8.97 5.67 2 3.11 Fair J I1 65.9 57 9823 9.15 9.02 5.98 3 3.01 Premium F I1 62.2 56 9925 9.24 9.13 5.73 4 3.05 Premium E I1 60.9 58 10453 9.26 9.25 5.66 5 3.02 Fair I I1 65.2 56 10577 9.11 9.02 5.91 6 3.01 Fair H I1 56.1 62 10761 9.54 9.38 5.31 7 3.65 Fair H I1 67.1 53 11668 9.53 9.48 6.38 8 3.24 Premium H I1 62.1 58 12300 9.44 9.4 5.85 9 3.22 Ideal I I1 62.6 55 12545 9.49 9.42 5.92 10 3.5 Ideal H I1 62.8 57 12587 9.65 9.59 6.03 # ... with 22 more rowsPress Alt + Shift + K. What happens? How can you get to the same place using the menus?
It opens the shortcuts popup page. You may close the page by pressing
ESC.To get there through the menus go to Tools -> Keyboard Shortcuts Help
sessionInfo()R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_South Africa.1252 LC_CTYPE=English_South Africa.1252
[3] LC_MONETARY=English_South Africa.1252 LC_NUMERIC=C
[5] LC_TIME=English_South Africa.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] flair_0.0.2 forcats_0.5.0 stringr_1.4.0 dplyr_1.0.0
[5] purrr_0.3.4 readr_1.3.1 tidyr_1.1.0 tibble_3.0.3
[9] ggplot2_3.3.0 tidyverse_1.3.0 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] tidyselect_1.1.0 xfun_0.13 haven_2.2.0 lattice_0.20-38
[5] colorspace_1.4-1 vctrs_0.3.2 generics_0.0.2 htmltools_0.5.0
[9] yaml_2.2.1 utf8_1.1.4 rlang_0.4.7 later_1.0.0
[13] pillar_1.4.6 withr_2.2.0 glue_1.4.1 DBI_1.1.0
[17] dbplyr_1.4.3 modelr_0.1.6 readxl_1.3.1 lifecycle_0.2.0
[21] munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0 rvest_0.3.5
[25] evaluate_0.14 labeling_0.3 knitr_1.28 httpuv_1.5.2
[29] fansi_0.4.1 broom_0.5.6 Rcpp_1.0.4.6 promises_1.1.0
[33] backports_1.1.6 scales_1.1.0 jsonlite_1.7.0 farver_2.0.3
[37] fs_1.4.1 hms_0.5.3 digest_0.6.25 stringi_1.4.6
[41] grid_3.6.3 rprojroot_1.3-2 cli_2.0.2 tools_3.6.3
[45] magrittr_1.5 crayon_1.3.4 whisker_0.4 pkgconfig_2.0.3
[49] ellipsis_0.3.1 xml2_1.3.2 reprex_0.3.0 lubridate_1.7.8
[53] rstudioapi_0.11 assertthat_0.2.1 rmarkdown_2.1 httr_1.4.2
[57] R6_2.4.1 nlme_3.1-144 git2r_0.26.1 compiler_3.6.3