- Learners can apply functions from dplyr to change specific values of a variable in a dataframe.
- Learners can apply functions from the lubridate package to convert dates not in ISO 8601 to the date class in R.
- Learners can apply functions from knitr and gt package to display and cross-reference tables in HTML output reports.
- Learners can understand the relevance a data dictionary to describe variable names in a data set.
Conditions & Dates & Tables
Research Beyond the Lab: Open Science and Research Methods for a Global Engineer
Lars Schöbitz
2024-03-21
Learning Objectives (for this week)
Homework module 4
Part 1: Reading
- Read Broman and Woo (2018): “Data organization in spreadsheets”.
- Chose two of the recommendations and come up with real-world examples or scenarios where the recommendations could be applied in your work.
- Be prepared to share these examples and explain how the recommendations would improve your workflows. This will be in a class setting as part of small discussion group (max 3 people).
Your turn: Discuss the reading
In discussion groups of 3, share your examples and discuss how the recommendations would improve your workflows.
10:00
Rules for variable names
- avoid spaces
- avoid special characters
- use consistent naming conventions (e.g. snake_case)
use
- ts
- users
- system
avoid
- Total Solids (g/L)
- Number of users
- System (pit latrine / septic tank)
Data dictionary / codebook
- variable descriptions belong into a data dictionary / codebook (not into variable names)
- data dictionaries / codebooks are separate files
| variable_name | description |
|---|---|
| ts | Total solids in g/L. |
| users | Number of users per system. |
| system | Sanitation system in use at sample location (septic tank / pit latrine). |
Conditional statements
dplyr functions mutate() & case_when()
mutate()adds new variables to a data framecase_when()is another form of an if-else statement- combination of functions are used to create variables with new values or fix existing ones
My turn: Conditional statements
Sit back and enjoy!
20:00
Take a break
Please get up and move! Let your emails rest in peace.
10:00
Image generated with DALL-E 3 by OpenAI
Your turn: md-05-exercises - conditions
- Open posit.cloud in your browser (use your bookmark).
- Open the ds4owd workspace for the course.
- In the File Manager in the bottom right window, locate the
md-05a-conditions-your-turn.qmdfile and click on it to open it in the top left window. - Follow instructions in the file
20:00
Task 1
- A mistake happened during data entry for sample id 16. Use
mutate()andcase_when()to change the ts value of 0.72 to 8.72.
| id | date | system | location | users | ts |
|---|---|---|---|---|---|
| 1 | 2023-11-01 | pit latrine | household | 5 | 136.24 |
| 2 | 2023-11-01 | pit latrine | household | 7 | 102.45 |
| 3 | 2023-11-01 | pit latrine | household | NA | 57.02 |
| 4 | 2023-11-01 | pit latrine | household | 6 | 27.03 |
| 5 | 2023-11-01 | pit latrine | household | 12 | 97.27 |
| 6 | 2023-11-02 | pit latrine | household | 7 | 78.21 |
| 7 | 2023-11-02 | septic tank | household | 14 | 15.24 |
| 8 | 2023-11-02 | septic tank | household | 4 | 29.39 |
| 9 | 2023-11-02 | septic tank | household | 10 | 64.22 |
| 10 | 2023-11-02 | septic tank | household | 12 | 8.01 |
| 11 | 2023-11-03 | pit latrine | public toilet | 50 | 11.24 |
| 12 | 2023-11-03 | pit latrine | public toilet | 32 | 84.05 |
| 13 | 2023-11-03 | pit latrine | public toilet | 41 | 55.92 |
| 14 | 2023-11-03 | pit latrine | public toilet | 160 | 15.32 |
| 15 | 2023-11-03 | pit latrine | public toilet | 20 | 22.65 |
| 16 | 2023-11-04 | septic tank | public toilet | 26 | 8.72 |
| 17 | 2023-11-04 | septic tank | public toilet | 91 | 43.92 |
| 18 | 2023-11-04 | septic tank | public toilet | 68 | 10.37 |
| 19 | 2023-11-04 | septic tank | public toilet | 112 | 23.21 |
| 20 | 2023-11-04 | septic tank | public toilet | 59 | 15.64 |
Task 2
- Another mistake happened during data entry for sample id 6. Use
mutate()andcase_when()to change the system value of id 6 from “pit latrine” to “septic tank”.
| id | date | system | location | users | ts |
|---|---|---|---|---|---|
| 1 | 2023-11-01 | pit latrine | household | 5 | 136.24 |
| 2 | 2023-11-01 | pit latrine | household | 7 | 102.45 |
| 3 | 2023-11-01 | pit latrine | household | NA | 57.02 |
| 4 | 2023-11-01 | pit latrine | household | 6 | 27.03 |
| 5 | 2023-11-01 | pit latrine | household | 12 | 97.27 |
| 6 | 2023-11-02 | septic tank | household | 7 | 78.21 |
| 7 | 2023-11-02 | septic tank | household | 14 | 15.24 |
| 8 | 2023-11-02 | septic tank | household | 4 | 29.39 |
| 9 | 2023-11-02 | septic tank | household | 10 | 64.22 |
| 10 | 2023-11-02 | septic tank | household | 12 | 8.01 |
| 11 | 2023-11-03 | pit latrine | public toilet | 50 | 11.24 |
| 12 | 2023-11-03 | pit latrine | public toilet | 32 | 84.05 |
| 13 | 2023-11-03 | pit latrine | public toilet | 41 | 55.92 |
| 14 | 2023-11-03 | pit latrine | public toilet | 160 | 15.32 |
| 15 | 2023-11-03 | pit latrine | public toilet | 20 | 22.65 |
| 16 | 2023-11-04 | septic tank | public toilet | 26 | 0.72 |
| 17 | 2023-11-04 | septic tank | public toilet | 91 | 43.92 |
| 18 | 2023-11-04 | septic tank | public toilet | 68 | 10.37 |
| 19 | 2023-11-04 | septic tank | public toilet | 112 | 23.21 |
| 20 | 2023-11-04 | septic tank | public toilet | 59 | 15.64 |
Task 3 (stretch goal)
- Add a new variable with the name
ts_catto the dataframe. that categorises sludge samples into low, medium and high solids content.Usemutate()andcase_when()to create the new variable.
- samples with less than 15 g/L are categorised as low
- samples with 15 g/L to 50 g/L are categorised as medium
- samples with more than 50 g/L are categorised as high
Task 3 (stretch goal)
| id | date | system | location | users | ts | ts_cat |
|---|---|---|---|---|---|---|
| 1 | 2023-11-01 | pit latrine | household | 5 | 136.24 | high |
| 2 | 2023-11-01 | pit latrine | household | 7 | 102.45 | high |
| 3 | 2023-11-01 | pit latrine | household | NA | 57.02 | high |
| 4 | 2023-11-01 | pit latrine | household | 6 | 27.03 | medium |
| 5 | 2023-11-01 | pit latrine | household | 12 | 97.27 | high |
| 6 | 2023-11-02 | pit latrine | household | 7 | 78.21 | high |
| 7 | 2023-11-02 | septic tank | household | 14 | 15.24 | medium |
| 8 | 2023-11-02 | septic tank | household | 4 | 29.39 | medium |
| 9 | 2023-11-02 | septic tank | household | 10 | 64.22 | high |
| 10 | 2023-11-02 | septic tank | household | 12 | 8.01 | low |
| 11 | 2023-11-03 | pit latrine | public toilet | 50 | 11.24 | low |
| 12 | 2023-11-03 | pit latrine | public toilet | 32 | 84.05 | high |
| 13 | 2023-11-03 | pit latrine | public toilet | 41 | 55.92 | high |
| 14 | 2023-11-03 | pit latrine | public toilet | 160 | 15.32 | medium |
| 15 | 2023-11-03 | pit latrine | public toilet | 20 | 22.65 | medium |
| 16 | 2023-11-04 | septic tank | public toilet | 26 | 0.72 | low |
| 17 | 2023-11-04 | septic tank | public toilet | 91 | 43.92 | medium |
| 18 | 2023-11-04 | septic tank | public toilet | 68 | 10.37 | low |
| 19 | 2023-11-04 | septic tank | public toilet | 112 | 23.21 | medium |
| 20 | 2023-11-04 | septic tank | public toilet | 59 | 15.64 | medium |
Task 3 (stretch goal)
| ts_cat | n |
|---|---|
| high | 8 |
| low | 4 |
| medium | 8 |
Dates and times
Dates and times in R
- Dates and times are stored as numbers in R
- Dates are stored as the number of days since 1970-01-01
- Times are stored as the number of seconds since 1970-01-01 00:00:00
- Dates and times are stored as numeric values, but can be formatted to look like dates and times
My turn: Dates
Sit back and enjoy!
15:00
Take a break
Please get up and move! Let your emails rest in peace.
10:00
Image generated with DALL-E 3 by OpenAI
Tables display
R packages for displaying tables
- Many packages for displaying tables in R
gtpackage is one of the most popular and flexiblekable()function ofknitrpackage useful for simple tables
Our turn: md-05-exercises - tables
- Open posit.cloud in your browser (use your bookmark).
- Open the ds4owd workspace for the course.
- Click Start next to md-05-exercises.
- In the File Manager in the bottom right window, locate the
md-05c-tables.qmdfile and click on it to open it in the top left window.
30:00
Cross references
Cross references
Help readers to navigate your document with numbered references and hyperlinks to entities like figures and tables.
Cross referencing steps:
- Add a caption to your figure or table.
- Give an ID to your figure or table, starting with
fig-ortbl-. - Refer to it with
@fig-...or@tbl-....
Table cross references
The presence of the caption (A few penguins) and label (#tbl-penguins) make this table referenceable:
See @tbl-penguins for data on a few penguins.
becomes:
See Table 1 for data on a few penguins.
| species | island | bill_length_mm | bill_depth_mm | flipper_length_mm | body_mass_g | sex | year |
|---|---|---|---|---|---|---|---|
| Adelie | Torgersen | 39.1 | 18.7 | 181 | 3750 | male | 2007 |
| Adelie | Torgersen | 39.5 | 17.4 | 186 | 3800 | female | 2007 |
| Adelie | Torgersen | 40.3 | 18.0 | 195 | 3250 | female | 2007 |
| Adelie | Torgersen | NA | NA | NA | NA | NA | 2007 |
| Adelie | Torgersen | 36.7 | 19.3 | 193 | 3450 | female | 2007 |
| Adelie | Torgersen | 39.3 | 20.6 | 190 | 3650 | male | 2007 |
Homework assignments module 5
Module 5 documentation
Homework due date
- Homework assignment due: Wednesday, March 27th
- Correction & feedback phase up to: Tuesday, April 2nd
Wrap-up
Thanks! 🌻
Slides created via revealjs and Quarto: https://quarto.org/docs/presentations/revealjs/ Access slides as PDF on GitHub
All material is licensed under Creative Commons Attribution Share Alike 4.0 International.
References
Broman, Karl W., and Kara H. Woo. 2018. “Data Organization in Spreadsheets.” The American Statistician 72 (1): 2–10. https://doi.org/10.1080/00031305.2017.1375989.
Conditions & Dates & Tables Research Beyond the Lab: Open Science and Research Methods for a Global Engineer Lars Schöbitz 2024-03-21