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)

  1. Learners can apply functions from dplyr to change specific values of a variable in a dataframe.
  2. Learners can apply functions from the lubridate package to convert dates not in ISO 8601 to the date class in R.
  3. Learners can apply functions from knitr and gt package to display and cross-reference tables in HTML output reports.
  4. Learners can understand the relevance a data dictionary to describe variable names in a data set.

Homework module 4

Part 1: Reading

  1. Read Broman and Woo (2018): “Data organization in spreadsheets”.
  2. Chose two of the recommendations and come up with real-world examples or scenarios where the recommendations could be applied in your work.
  3. 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 frame
  • case_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.

A pixel art style image of a serene beach scene. The beach is lined with tall, lush palm trees swaying gently in the breeze. The sand is golden and pristine, meeting the clear blue waters of the ocean. The sky is a gradient of soft blues, with a few fluffy white clouds drifting lazily. The sun is setting in the background, casting warm orange and pink hues across the sky and sea, creating a tranquil and picturesque setting.
10:00

Image generated with DALL-E 3 by OpenAI

Your turn: md-05-exercises - conditions

  1. Open posit.cloud in your browser (use your bookmark).
  2. Open the ds4owd workspace for the course.
  3. In the File Manager in the bottom right window, locate the md-05a-conditions-your-turn.qmd file and click on it to open it in the top left window.
  4. Follow instructions in the file
20:00

Task 1

  1. A mistake happened during data entry for sample id 16. Use mutate() and case_when() to change the ts value of 0.72 to 8.72.
sludge |> 
    mutate(ts = case_when(
        ts ==  0.72 ~ 8.72,
        .default = ts
    ))
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

  1. Another mistake happened during data entry for sample id 6. Use mutate() and case_when() to change the system value of id 6 from “pit latrine” to “septic tank”.
sludge |> 
    mutate(system = case_when(
        id ==  6 ~ "septic tank",
        .default = system
    ))
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)

  1. Add a new variable with the name ts_cat to the dataframe. that categorises sludge samples into low, medium and high solids content.Use mutate() and case_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)

sludge |> 
    mutate(ts_cat = case_when(
        ts < 15 ~ "low",
        ts >= 15 & ts <= 50 ~ "medium",
        ts > 50 ~ "high"
    ))
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)

sludge |> 
    mutate(ts_cat = case_when(
        ts < 15 ~ "low",
        ts >= 15 & ts <= 50 ~ "medium",
        ts > 50 ~ "high"
    )) |> 
  count(ts_cat)
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.

A pixel art style image of a serene beach scene. The beach is lined with tall, lush palm trees swaying gently in the breeze. The sand is golden and pristine, meeting the clear blue waters of the ocean. The sky is a gradient of soft blues, with a few fluffy white clouds drifting lazily. The sun is setting in the background, casting warm orange and pink hues across the sky and sea, creating a tranquil and picturesque setting.
10:00

Image generated with DALL-E 3 by OpenAI

Tables display

R packages for displaying tables

  • Many packages for displaying tables in R
  • gt package is one of the most popular and flexible
  • kable() function of knitr package useful for simple tables

Our turn: md-05-exercises - tables

  1. Open posit.cloud in your browser (use your bookmark).
  2. Open the ds4owd workspace for the course.
  3. Click Start next to md-05-exercises.
  4. In the File Manager in the bottom right window, locate the md-05c-tables.qmd file 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- or tbl-.
    • 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.

```{r}
#| label: tbl-penguins
#| tbl-cap: A few penguins

head(penguins) |> 
  gt()
```
Table 1: 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

rbtl-fs24.github.io/website/modules/md-05.html

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

rbtl-fs24.github.io/website/

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.