a personal journey into data science
by datarich(ard)
# packages needed
library(knitr)
library(kableExtra)
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. It also authors markdown documents which can be rendered on GitHub. Note that the YAML for this notebook contains:
output: github_document
GitHub is very useful for sharing documents and results. However much of my work involves tabulating data and for some reason GitHub does not render tables very well in Jupyter notebooks. So this experiment is to see how GitHub handles tables produced in a R markdown document.
Let’s begin by trying a basic table:
mtcars
## mpg cyl disp hp drat wt qsec vs am gear carb
## Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4
## Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4
## Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1
## Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1
## Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2
## Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1
## Duster 360 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4
## Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2
## Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2
## Merc 280 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4
## Merc 280C 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4 4
## Merc 450SE 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3
## Merc 450SL 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3
## Merc 450SLC 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3 3
## Cadillac Fleetwood 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3 4
## Lincoln Continental 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3 4
## Chrysler Imperial 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3 4
## Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1
## Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2
## Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1
## Toyota Corona 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3 1
## Dodge Challenger 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3 2
## AMC Javelin 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3 2
## Camaro Z28 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3 4
## Pontiac Firebird 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2
## Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1
## Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2
## Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2
## Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4
## Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6
## Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8
## Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2
The motorcars dataframe is a long (32 rows) and wide (11 columns) table,
so it won’t fit on the markdown page and we definitely don’t want to
print all of it. However it also is printing as code-text rather than as
a nice table.
Let’s see if adding kable() helps:
dt <- mtcars[1:5, 1:6]
head(dt) %>%
kable(caption = "default")
| mpg | cyl | disp | hp | drat | wt | |
|---|---|---|---|---|---|---|
| Mazda RX4 | 21.0 | 6 | 160 | 110 | 3.90 | 2.620 |
| Mazda RX4 Wag | 21.0 | 6 | 160 | 110 | 3.90 | 2.875 |
| Datsun 710 | 22.8 | 4 | 108 | 93 | 3.85 | 2.320 |
| Hornet 4 Drive | 21.4 | 6 | 258 | 110 | 3.08 | 3.215 |
| Hornet Sportabout | 18.7 | 8 | 360 | 175 | 3.15 | 3.440 |
kable prints nicer tables, along with a centered heading.
kable also provides a format argument. There are five options: latex, markdown, html, pandoc and rst. It is automatically set but providing the argument should override that. Let’s try markdown:
head(dt) %>%
kable(format = "markdown", caption = "Markdown")
| mpg | cyl | disp | hp | drat | wt | |
|---|---|---|---|---|---|---|
| Mazda RX4 | 21.0 | 6 | 160 | 110 | 3.90 | 2.620 |
| Mazda RX4 Wag | 21.0 | 6 | 160 | 110 | 3.90 | 2.875 |
| Datsun 710 | 22.8 | 4 | 108 | 93 | 3.85 | 2.320 |
| Hornet 4 Drive | 21.4 | 6 | 258 | 110 | 3.08 | 3.215 |
| Hornet Sportabout | 18.7 | 8 | 360 | 175 | 3.15 | 3.440 |
Same as kable except the heading/caption seems to be missing.
Let’s try html:
head(dt) %>%
kable(format = "html", caption = "HTML")
| mpg | cyl | disp | hp | drat | wt | |
|---|---|---|---|---|---|---|
| Mazda RX4 | 21.0 | 6 | 160 | 110 | 3.90 | 2.620 |
| Mazda RX4 Wag | 21.0 | 6 | 160 | 110 | 3.90 | 2.875 |
| Datsun 710 | 22.8 | 4 | 108 | 93 | 3.85 | 2.320 |
| Hornet 4 Drive | 21.4 | 6 | 258 | 110 | 3.08 | 3.215 |
| Hornet Sportabout | 18.7 | 8 | 360 | 175 | 3.15 | 3.440 |
With html, we get the requested heading/caption “html” but the layout (row height) looks a bit spacier.
Testing pandoc:
head(dt) %>%
kable(format = "pandoc", caption = "Pandoc")
| mpg | cyl | disp | hp | drat | wt | |
|---|---|---|---|---|---|---|
| Mazda RX4 | 21.0 | 6 | 160 | 110 | 3.90 | 2.620 |
| Mazda RX4 Wag | 21.0 | 6 | 160 | 110 | 3.90 | 2.875 |
| Datsun 710 | 22.8 | 4 | 108 | 93 | 3.85 | 2.320 |
| Hornet 4 Drive | 21.4 | 6 | 258 | 110 | 3.08 | 3.215 |
| Hornet Sportabout | 18.7 | 8 | 360 | 175 | 3.15 | 3.440 |
Pandoc
Same as kable except the heading/caption appears at the bottom left.
Testing latex:
head(dt) %>%
kable(format = "latex", caption = "latex")
Nada.
Testing RST:
head(dt) %>%
kable(format = "rst", caption = "RST")
================= ==== === ==== === ==== ===== mpg cyl disp hp drat wt ================= ==== === ==== === ==== ===== Mazda RX4 21.0 6 160 110 3.90 2.620 Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 Datsun 710 22.8 4 108 93 3.85 2.320 Hornet 4 Drive 21.4 6 258 110 3.08 3.215 Hornet Sportabout 18.7 8 360 175 3.15 3.440 ================= ==== === ==== === ==== =====
Nope..!
So, the default options for markdown and pandoc are rendered nicely, although markdown is missing the caption and pandoc prints the caption at the bottom of the table (is this where it should be?). HTML renders nicely with a heading/caption, but it is less compact and a bit spacier than markdown or pandoc. Latex doesn’t render at all and rst is garbled.
Let’s try the kableExtra features.
head(dt) %>%
kable(caption = "kableExtra") %>%
kable_styling()
| mpg | cyl | disp | hp | drat | wt | |
|---|---|---|---|---|---|---|
| Mazda RX4 | 21.0 | 6 | 160 | 110 | 3.90 | 2.620 |
| Mazda RX4 Wag | 21.0 | 6 | 160 | 110 | 3.90 | 2.875 |
| Datsun 710 | 22.8 | 4 | 108 | 93 | 3.85 | 2.320 |
| Hornet 4 Drive | 21.4 | 6 | 258 | 110 | 3.08 | 3.215 |
| Hornet Sportabout | 18.7 | 8 | 360 | 175 | 3.15 | 3.440 |
That doesn’t change much that we have already seen, although it looks like the spacy layout of html. Let’s try some fancier options, such as grouped columns, which would be a very handy feature if it works.
Grouped columns:
kable(dt, caption = "Grouped columns") %>%
kable_styling("striped") %>%
add_header_above(c(" " = 1, "Group 1" = 2, "Group 2" = 2, "Group 3" = 2))
| mpg | cyl | disp | hp | drat | wt | |
|---|---|---|---|---|---|---|
| Mazda RX4 | 21.0 | 6 | 160 | 110 | 3.90 | 2.620 |
| Mazda RX4 Wag | 21.0 | 6 | 160 | 110 | 3.90 | 2.875 |
| Datsun 710 | 22.8 | 4 | 108 | 93 | 3.85 | 2.320 |
| Hornet 4 Drive | 21.4 | 6 | 258 | 110 | 3.08 | 3.215 |
| Hornet Sportabout | 18.7 | 8 | 360 | 175 | 3.15 | 3.440 |
Grouping by row is also possible:
kable(mtcars[1:10, 1:6], caption = "Grouped Rows") %>%
kable_styling("striped", full_width = F) %>%
pack_rows("Group 1", 4, 7) %>%
pack_rows("Group 2", 8, 10)
| mpg | cyl | disp | hp | drat | wt | |
|---|---|---|---|---|---|---|
| Mazda RX4 | 21.0 | 6 | 160.0 | 110 | 3.90 | 2.620 |
| Mazda RX4 Wag | 21.0 | 6 | 160.0 | 110 | 3.90 | 2.875 |
| Datsun 710 | 22.8 | 4 | 108.0 | 93 | 3.85 | 2.320 |
| Group 1 | ||||||
| Hornet 4 Drive | 21.4 | 6 | 258.0 | 110 | 3.08 | 3.215 |
| Hornet Sportabout | 18.7 | 8 | 360.0 | 175 | 3.15 | 3.440 |
| Valiant | 18.1 | 6 | 225.0 | 105 | 2.76 | 3.460 |
| Duster 360 | 14.3 | 8 | 360.0 | 245 | 3.21 | 3.570 |
| Group 2 | ||||||
| Merc 240D | 24.4 | 4 | 146.7 | 62 | 3.69 | 3.190 |
| Merc 230 | 22.8 | 4 | 140.8 | 95 | 3.92 | 3.150 |
| Merc 280 | 19.2 | 6 | 167.6 | 123 | 3.92 | 3.440 |