Workflow and Formatting

Author

STA199 TA team

Rubrics for workflow and formatting

Breakdown of overall workflow and formatting grading listed below:

  • 1 pts: 1 point given if all code chunks are appropriately labelled
    • take off 0.5 pt if anything less
    • take off 1 pt if none of the code chunks are appropriately labelled
  • 3 pts: Consistent code style.
  • 1 point given if narrative and text does not exceed the 80 character limit.
  • 1 point given for consistent use of operators (i.e. %>% or |> and <- or = but not both)
  • 1 point given for consistent and appropriate use of spacing (i.e. pipes and layers followed by newline and binary operators like + and - are surrounded by spaces)
  • 1 pt: author name updated to the student’s name at the YAML (at the top) of the document.

Common Mistakes

1. meaningless labels

── Attaching packages ─────────────────────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.0     ✔ purrr   0.3.5
✔ tibble  3.1.8     ✔ dplyr   1.0.9
✔ tidyr   1.2.1     ✔ stringr 1.4.1
✔ readr   2.1.3     ✔ forcats 0.5.2
Warning: package 'ggplot2' was built under R version 4.2.2
Warning: package 'tidyr' was built under R version 4.2.2
Warning: package 'readr' was built under R version 4.2.2
Warning: package 'purrr' was built under R version 4.2.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
iris |>
  glimpse()
Rows: 150
Columns: 5
$ Sepal.Length <dbl> 5.1, 4.9, 4.7, 4.6, 5.0, 5.4, 4.6, 5.0, 4.4, 4.9, 5.4, 4.…
$ Sepal.Width  <dbl> 3.5, 3.0, 3.2, 3.1, 3.6, 3.9, 3.4, 3.4, 2.9, 3.1, 3.7, 3.…
$ Petal.Length <dbl> 1.4, 1.4, 1.3, 1.5, 1.4, 1.7, 1.4, 1.5, 1.4, 1.5, 1.5, 1.…
$ Petal.Width  <dbl> 0.2, 0.2, 0.2, 0.2, 0.2, 0.4, 0.3, 0.2, 0.2, 0.1, 0.2, 0.…
$ Species      <fct> setosa, setosa, setosa, setosa, setosa, setosa, setosa, s…

Some good examples

iris |>
  glimpse()
Rows: 150
Columns: 5
$ Sepal.Length <dbl> 5.1, 4.9, 4.7, 4.6, 5.0, 5.4, 4.6, 5.0, 4.4, 4.9, 5.4, 4.…
$ Sepal.Width  <dbl> 3.5, 3.0, 3.2, 3.1, 3.6, 3.9, 3.4, 3.4, 2.9, 3.1, 3.7, 3.…
$ Petal.Length <dbl> 1.4, 1.4, 1.3, 1.5, 1.4, 1.7, 1.4, 1.5, 1.4, 1.5, 1.5, 1.…
$ Petal.Width  <dbl> 0.2, 0.2, 0.2, 0.2, 0.2, 0.4, 0.3, 0.2, 0.2, 0.1, 0.2, 0.…
$ Species      <fct> setosa, setosa, setosa, setosa, setosa, setosa, setosa, s…
iris |>
  glimpse()
Rows: 150
Columns: 5
$ Sepal.Length <dbl> 5.1, 4.9, 4.7, 4.6, 5.0, 5.4, 4.6, 5.0, 4.4, 4.9, 5.4, 4.…
$ Sepal.Width  <dbl> 3.5, 3.0, 3.2, 3.1, 3.6, 3.9, 3.4, 3.4, 2.9, 3.1, 3.7, 3.…
$ Petal.Length <dbl> 1.4, 1.4, 1.3, 1.5, 1.4, 1.7, 1.4, 1.5, 1.4, 1.5, 1.5, 1.…
$ Petal.Width  <dbl> 0.2, 0.2, 0.2, 0.2, 0.2, 0.4, 0.3, 0.2, 0.2, 0.1, 0.2, 0.…
$ Species      <fct> setosa, setosa, setosa, setosa, setosa, setosa, setosa, s…

If you have multiple models or plots for the homework/labs, you can number them.

iris_sum <- iris |>
  as_tibble() |>
  lm(formula = Petal.Width ~ Sepal.Width) |>
  summary()
iris_boxplot <- iris |>
  as_tibble() |>
  ggplot(aes(y = Petal.Width, x = Species)) + geom_boxplot()

2. Inconsistent use of operator

Bad examples: use both %>% and |>, both <- and = in the homework/lab.

iris_boxplot <- iris |>
  as_tibble() %>%
  ggplot(aes(y = Petal.Width, x = Species)) + 
  geom_boxplot()
iris_tbl <- iris |>
  as_tibble()
iris_boxplot = ggplot(iris_tbl, aes(y = Petal.Width, x = Species)) + 
  geom_boxplot()

Good examples:

iris_boxplot <- iris |>
  as_tibble() |>
  ggplot(aes(y = Petal.Width, x = Species)) + 
  geom_boxplot()
iris_tbl <- iris |>
  as_tibble()
iris_boxplot <- ggplot(iris_tbl, aes(y = Petal.Width, x = Species)) + 
  geom_boxplot()

3. Narrative and text exceeding character limit

Bad examples: text overflow. Only part of the text will appear in both coding part and plot.

iris |>
  as_tibble() |>
  ggplot(aes(y = Petal.Width, x = Species)) + 
  geom_boxplot() +
  labs(title = "The title is super long and exceeds the word limits. Please do not take my points off.")

Possible solutions: have a new line inside your code or have subtitle. It is always a good idea to do proofreading on your knitted pdf file.

iris |>
  as_tibble() |>
  ggplot(aes(y = Petal.Width, x = Species)) + 
  geom_boxplot() +
  labs(title = "The title is super long and exceeds the word limits.
       Please do not take my points off.")

iris |>
  as_tibble() |>
  ggplot(aes(y = Petal.Width, x = Species)) + 
  geom_boxplot() +
  labs(title = "The title is super long and exceeds the word limits.",
       subtitle = "Please do not take my points off.")

Bad examples: text overflow when the functions have a lot of arguments needed specification

iris_boxplot <- iris |>
  as_tibble() |>
  ggplot(aes(y = Petal.Width, x = Species, fill = Species)) + 
  geom_boxplot() +
  labs(title = "Boxplot for petal width versus species", x = "species", y = "petal width", fill = "species")

A solution: represent them in separate lines

iris_boxplot <- iris |>
  as_tibble() |>
  ggplot(aes(y = Petal.Width, x = Species, fill = Species)) + 
  geom_boxplot() +
  labs(title = "Boxplot for petal width versus species", 
       x = "species", 
       y = "petal width", 
       fill = "species")

4. Inappropriate use of spacing

Bad example: +/-/=/</| are not surrounded by spaces

iris_boxplot<-iris|>
  as_tibble()|>
  ggplot(aes(y=Petal.Width, x=Species, fill=Species))+ 
  geom_boxplot()

Good example:

iris_boxplot <- iris |>
  as_tibble() |>
  ggplot(aes(y = Petal.Width, x = Species, fill = Species)) + 
  geom_boxplot()

5. New layer/pipline not begin with a newline

The code should be in a newline if it is a new function, such as pipeline, ggplot layers, model fitting.

Bad examples:

iris_boxplot <- iris |> as_tibble() |>
  ggplot(aes(y = Petal.Width, x = Species)) + 
  geom_boxplot() 
iris_boxplot <- iris |> 
  as_tibble() |>
  ggplot(aes(y = Petal.Width, x = Species)) + geom_boxplot() 
iris_boxplot <- iris |> 
  as_tibble() |>
  ggplot(aes(y = Petal.Width, x = Species)) + 
  geom_boxplot() + ggtitle("Boxplot for width versus species")
iris_sum <- iris |>
  as_tibble() |>
  lm(formula = Petal.Width ~ Sepal.Width) |> summary()

Good examples

iris_boxplot <- iris |> 
  as_tibble() |>
  ggplot(aes(y = Petal.Width, x = Species)) + 
  geom_boxplot() + 
  ggtitle("Boxplot for width versus species")