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06-workflow_scripts_and_projects.Rmd
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06-workflow_scripts_and_projects.Rmd
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# Workflow: scripts and projects
**Learning objectives:**
- Create scripts and Understand **script diagnostics** in RStudio.
- Create an **Rstudio project.**
- Understand working directories in Rstudio and the `getwd()` function.
- Differentiate between relative paths and absolute paths.
## Scripts {-}
- Use the script editor instead of the console -> complex pipelines and graphics.
- File -> New file -> R script, or `Cmd/Ctrl + Shift + N`
- a place for experimenting your R code
- Edit the script and re-run the code
- Save it as a R code file: `yourfilename.R`
::: {style="text-align:center;"}
:::
## Scripts: panes layout {-}
- You can move panes around too.
- Move focus to script `CTRL/Cmd + 1`
- Move focus to console `CTRL/Cmd + 2`
- Move focus to Terminal `ALT + Shift + M`
::: {style="text-align:center;"}
:::
## Running Code {-}
- The keyboard shortcuts
- `Ctrl/Cmd + Enter` to run the current R expression in the console. The cursor will move to the next code block.
- `Ctrl/Cmd + Shift + S` to run the entire script.
- **Tip:** Always start your script with the packages you need, but do not include `install.packages()` in a script you plan on sharing.
## RStudio Dianostics {-}
- Squiggly line highlights errors.
- Hover over cross to see problem.
::: {style="text-align:left;"}
:::
<br/>
::: {style="text-align:left;"}
:::
## Saving and Naming Files {-}
1. File names should be **machine readable**
- avoid spaces, symbols, and special characters. Don't rely on case sensitivity to distinguish files.
2. File names should be **human readable**
- use file names to describe what's in the file.
3. File names should **play well with default ordering**
- start file names with numbers so that alphabetical sorting puts them in the order they get used.
Examples of good names:
```
01-load-data.R
02-exploratory-analysis.R
03-model-approach-1.R
04-model-approach-2.R
fig-01.png
fig-02.png
report-2022-03-20.qmd
report-2022-04-02.qmd
report-draft-notes.txt
```
[Jenny Bryan's talk on 'How to name files like a Normie'](https://github.com/jennybc/how-to-name-files)
[More File Naming Conventions](https://huridocs.org/resource-library/organising-a-collection-of-human-rights-information/file-naming-conventions/#:~:text=To%20ensure%20that%20files%20are,%2C%20then%20month%2C%20then%20date.)
## Projects {-}
### What Is the Source of Truth? {-}
- Instruct RStudio not to preserve your workspace between sessions.
- `usethis::use_blank_slate()`
- or go to Tools -> Global Options -> General
::: {style="text-align:left;"}
:::
- `Cmd/Ctrl + Shift + 0/F10` to start R
- `Cmd/Ctrl + Shift + S` to rerun the R script
## Where Does Your Analysis Live? {-}
- You can always find the working directory by looking at top of console:
- `getwd()` to identify the current working directory
- `setwd()` to change the working directory (an absolute path) : **not recommended**
## RStudio Projects {-}
- Self contained projects are the way to go! [Read more about project-oriented workflow by Jenny Brian here](https://www.tidyverse.org/blog/2017/12/workflow-vs-script/)
- First create a new project
- File -> New Project, or
- Go to the top right of RStudio and click on New Project.
- And then follow these steps to create a new project.
- This will create a file called `something.Rproj` in the directory you chose which you can double click to open the project.
## Relative and Absolute Paths {-}
- A relative path is relative to the working directory, i.e. the project's home.
- Absolute paths point to the same place regardless of your working directory.
- Mac/Linux: a slash `/`
- `/Users/hadley/Documents/r4ds/data/diamonds.csv`
- Windows: backlashes `\`
- `\Users\hadley\Documents\r4ds\data\diamonds.csv`
- R can work with either type, but is recommended to always use Mac/Lynux style `/`.
- You should **never use absolute paths in your scripts, because they hinder sharing.**
## Package here {-}
- [Package here website](https://here.r-lib.org/index.html)
- The package here helps with easy file referencing and building file paths.
- After installing the package and loading the library you can:
- See the top level directory with `here::here()`
- Use `here::here('dir', 'file.txt')` to build a path relative to the top-level directory in order to build the full path to a file.
- For example, if you want to import a csv file you can use the function `here` to indicate the relative path of the file you want to read:
```{r, eval=FALSE}
readr::read_csv(
here("directory", "your_file.csv")
)
```
## Exercises {-}
1. Go to the RStudio Tips Twitter account, <https://twitter.com/rstudiotips> and find one tip that looks interesting. Practice using it!
2. What other common mistakes will RStudio diagnostics report? Read <https://support.posit.co/hc/en-us/articles/205753617-Code-Diagnostics> to find out.
## Meeting Videos {-}
### Cohort 5
`r knitr::include_url("https://www.youtube.com/embed/2LFWCGNiuoE")`
<details>
<summary>Meeting chat log</summary>
```
00:40:51 Becki R. (she/her): It works both ways, I think. It's just convention to use <-.
00:45:11 Wai-Yin: You can use <- or = for assignment. <- is the convention in R. -> results in ab error.
00:58:59 lucus w: https://www.rocker-project.org/
01:01:43 Bruno A. Machado: tks Lucus for the link 👍
01:13:48 Susie N.: I have to head out! Thank you Ryan for the great breakdown
01:14:07 Federica Gazzelloni: Thanks!
01:14:19 Becki R. (she/her): Thanks everyone, see you next week!
01:17:04 Bruno A. Machado: tks team
01:17:21 Eileen Murphy: Thank you Ryan
```
</details>
`r knitr::include_url("https://www.youtube.com/embed/VYYxhIBuDys")`
<details>
<summary>Meeting chat log</summary>
```
00:05:55 [email protected]: Hello!
00:07:40 Becki R. (she/her): Hello!
00:07:52 Sandra Muroy: Hi!
00:07:57 Federica Gazzelloni: Hi!
00:09:49 Eileen: Hello!
00:15:44 Becki R. (she/her): Very cool!
00:29:31 Jon Harmon (jonthegeek): https://CRAN.R-project.org/package=renv
00:31:35 lucus w: Or just here::here() package, it’s my favorite
00:32:48 Ryan Metcalf: Ah, Thank you Lucas! I think you may have solved an error I was trying to overcome!
00:32:57 Jon Harmon (jonthegeek): here::here("my_dir", "myfile.R")
00:33:06 lucus w: There you go, yup
00:34:37 Jon Harmon (jonthegeek): usethis
00:34:38 lucus w: You can use usethis
00:37:56 Jon Harmon (jonthegeek): .Last.value
00:38:58 lucus w: It’s a life saver especially working in databases
00:44:32 Federica Gazzelloni: reticulate
00:45:11 Federica Gazzelloni: https://rstudio.github.io/reticulate/articles/r_markdown.html
00:48:18 Ryan Metcalf: @Shamsuddeen, what was that command again? Cmd + Shift + P?
00:48:40 Susan Neilson: That’s right
00:49:43 Ryan Metcalf: Awesome! Ive never used that before. These bookclub meetups are so helpful! Thank you everyone!
00:50:04 Federica Gazzelloni: yep! very useful
00:50:09 Shamsuddeen Muhammad: https://speakerdeck.com/jennybc/how-to-name-files
00:50:28 Shamsuddeen Muhammad: Naming things
00:51:10 Jon Harmon (jonthegeek): 20210904
00:51:55 Shamsuddeen Muhammad: Chapter 2 Project-oriented workflow : https://rstats.wtf/project-oriented-workflow.html
00:52:13 Jon Harmon (jonthegeek): Had to google that tab: https://bookdown.org/ndphillips/YaRrr/
00:52:15 Shamsuddeen Muhammad: What They Forgot to Teach You About R
00:55:05 Jon Harmon (jonthegeek): https://github.com/MonkmanMH/EIKIFJB
00:55:38 Ryan Metcalf: Transmute I think…..
00:56:27 Jon Harmon (jonthegeek): tidyr::replace_na()
00:56:54 lucus w: Check out janitor
01:02:32 Shamsuddeen Muhammad: https://tidyr.tidyverse.org/reference/replace_na.html
01:02:42 Shamsuddeen Muhammad: df %>% dplyr::mutate(x = replace_na(x, 0))
01:03:30 Jon Harmon (jonthegeek): ""
01:04:16 Ryan Metcalf: You’ve discovered the beauty of a programmer!!!
01:04:28 Shamsuddeen Muhammad: Yes Yes !!!
01:05:22 Susan Neilson: “95% of being a programmer is knowing how to Google” - my programmer friend
01:06:27 Ryan Metcalf: I find googling the package and then reading the PDF Manual. CRAN is your friend.
01:10:38 Sandra Muroy: thanks everyone for your input!
01:10:57 Ryan Metcalf: Thank you Susie! Great presentation and conversation!
01:11:04 Susan Neilson: Thanks everyone !
01:11:08 Federica Gazzelloni: thanks
01:11:12 Becki R. (she/her): Thank you!
01:11:22 Susan Neilson: https://bookdown.org/ndphillips/YaRrr/rdata-files.html
```
</details>
### Cohort 6
`r knitr::include_url("https://www.youtube.com/embed/3SLN7bQQkDY")`
<details>
<summary>Meeting chat log</summary>
```
00:09:22 Matthew Efoli: good evening
00:09:29 Matthew Efoli: good day
00:09:35 Vrinda Kalia: Hello!
00:09:55 Daniel Adereti: Hello!
00:10:04 Shannon: Hello!
00:10:06 Daniel Adereti: ready when you are, Matthew
00:11:40 Adeyemi Olusola: Good evening everyone
00:28:31 Daniel Adereti: will it be possible to sort in ascending order as well?
00:30:39 Adeyemi Olusola: sort() should do trick
00:31:13 Adeyemi Olusola: I have issues with my audio
00:31:39 Adeyemi Olusola: lets try sort = ()
00:32:07 Vrinda Kalia: I am not sure about using sort within the count function. I am only aware of using the desc argument in the sort() function
00:33:06 Daniel Adereti: it seems the sort() has its own arguments
00:33:41 Aalekhya Reddam: Sorry everyone, I have to head out but will watch the recording. See you all next week!
00:34:33 Shannon: not_cancelled %>%
00:34:45 Shannon: oops sorry, didn't finish that...
00:36:00 Adeyemi Olusola: not_cancelled%>%
00:36:05 Adeyemi Olusola: desc()
00:37:46 Daniel Adereti: maybe we continue and figure it out next time?
00:37:53 Daniel Adereti: sorry for chopping your flow!
00:38:27 Esmeralda Cruz: maybe arrange function?
00:38:58 Esmeralda Cruz: ok
00:44:31 Daniel Adereti: thanks for that shortcut
00:50:23 Daniel Adereti: Please explain "filter(rank(desc(arr_delay)) <= 10"
00:55:38 Daniel Adereti: Thanks! noticed the same too, the descending argument does not seem to have any effect
00:56:31 Daniel Adereti: sure!
00:56:35 Daniel Adereti: thanks
00:58:00 Shannon: oh, because we didn't have a rank column in the first example?
00:59:24 Daniel Adereti: like a rank column as part of the dataset?
01:02:11 Daniel Adereti: Thanks!
01:04:01 Shannon: yes
01:10:42 Vrinda Kalia: I need to leave for a meeting. Thank you so much for leading a great discussion, Matthew!
01:11:00 Shannon: Thanks, Matthew! I liked the way you presented with both the bookdown file as well as RStudio.
01:11:09 Daniel Adereti: Thanks Matthew!
01:11:14 Maria Eleni Soilemezidi: Thank you for the presentation! That was very helpful! :)
01:11:15 Matthew Efoli: Thanks
01:11:37 Maria Eleni Soilemezidi: See you next week!
01:11:50 Esmeralda Cruz: Thank you :) for your time Matthew
01:12:05 Esmeralda Cruz: yes, both are correct
```
</details>
`r knitr::include_url("https://www.youtube.com/embed/dNtF8-lZ_pA")`
<details>
<summary>Meeting chat log</summary>
```
00:01:19 Adeyemi Olusola: Good day everyone
00:01:32 Daniel: Hello!
00:17:42 Esmeralda Cruz: nop
00:33:45 Daniel: https://jrnold.github.io/r4ds-exercise-solutions/tibbles.html
00:44:48 Esmeralda Cruz: interesting
00:46:11 Esmeralda Cruz: ok, make sense
00:49:45 Esmeralda Cruz: ok
```
</details>
### Cohort 7
`r knitr::include_url("https://www.youtube.com/embed/xrZdzkOC_Ts")`
<details>
<summary>Meeting chat log</summary>
```
00:36:35 Oluwafemi Oyedele: It is CMD + Enter on Mac
00:37:22 Oluwafemi Oyedele: CMD + Enter will run the code on Mac
00:53:06 Oluwafemi Oyedele: https://rstats.wtf/project-oriented-workflow.html#dilemma-and-a-solution
00:53:11 Oluwafemi Oyedele: http://127.0.0.1:12193/library/here/doc/here.html
00:53:58 Oluwafemi Oyedele: https://www.tidyverse.org/blog/2017/12/workflow-vs-script/
```
</details>
### Cohort 8
`r knitr::include_url("https://www.youtube.com/embed/Tf1wyQojaQk")`