Computation

From R Markdown to Quarto
rstudio::conf 2022

Andrew Bray

Getting Exercise

To get the materials for each part of this course packed in an RStudio Project, run:

```{r}
usethis::use_course("rmd-to-quarto/computation")
```

Code Blocks

Pandoc’s Fenced Code Block

Sandwich the code between “fences” of at least three backticks¹. An optional language provides syntax highlighting.

```cobol
1 + 1
```

Useful for displaying source code, not running it
Note that the language is not in { }
Pandoc supports 140 languages!

R Markdown’s Code Chunk

```{r, echo=FALSE}
rnorm(3)
```

Poll: What syntax is being used in echo=FALSE?

HTML
Pandoc attribute syntax
YAML
CSS
R

Results

Generalizing the Code Chunk

How can this be generalized to other languages?

```{r, echo=FALSE}
rnorm(3)
```

Executable code flagged by { }

Generalizing the Code Chunk

How can this be generalized to other languages?

```{language, echo=FALSE}
code
```

Executable code flagged by { }
Support R, Python, Julia
Also support mermaid and dot diagram languages¹.

Generalizing the Code Chunk

How can this be generalized to other languages?

```{language}
#| echo: false

code
```

Executable code flagged by { }
Support R, Python, Julia
Also support mermaid and dot diagram languages¹
Cell options live inside the cell after #| (the hash pipe!)²

This is a Quarto Code Cell.

The Perks of the Hashpipe `#|`

Line breaks prevent chunk options that go on {r, and=on, and=on, and=on, and=on, and=on, and=on}

Chunk options are now pan-language with <commentchar>|.

```{python}
#| echo: false
```

```{mermaid}
%%| echo: false
```

No more yelling! (eval=FALSE)

Execution Options

Control how the code is executed with options.

Option	Description
`eval`	Evaluate the code chunk (if `false`, just echos the code into the output).
`echo`	Include the source code in output
`output`	Include the results of executing the code in the output (`true`, `false`, or `asis` to indicate that the output is raw markdown and should not have any of Quarto’s standard enclosing markdown).
`warning`	Include warnings in the output.
`error`	Include errors in the output.
`include`	Catch all for preventing any output (code or results) from being included (e.g. `include: false` suppresses all output from the code block).

Setting `knitr` options

The knitr syntax for passing options still works since Quarto uses knitr.

Source

```{r, error=TRUE}
#| echo: true

rnorm(5       # this is missing a parens
```

Output

rnorm(5       # this is missing a parens

Error: <text>:2:0: unexpected end of input
1: rnorm(5       # this is missing a parens
   ^

While it’s possible to use R chunks options, hash pipe options are more portable across computational engines.

Don’t forget to use tab-completion to see the available options!

From Cell Option to YAML

---
title: My Doc
format: html
---

```{r}
#| echo: true

pi + 1
```

From Cell Option to YAML

---
title: My Doc
format: html
execute:
  echo: true
---

```{r}
pi + 1
```

Options can be moved into YAML under the execute key to apply to all chunks. Exceptions to that option can be set cell-by-cell.

From Cell Option to YAML

---
title: My Doc
format: html
execute:
  echo: true
knitr:
  opts_chunk: 
    collapse: true
---

```{r}
pi + 1
```

Options can be moved into YAML under the execute key to apply to all chunks. Exceptions to that option can be set cell-by-cell.
You can also pass options via YAML to knitr through the knitr key¹.

From Cell Option to YAML

---
title: My Doc
format: html
execute:
  echo: true
knitr:
  opts_chunk: 
    collapse: true
    R.options:
      digits: 2
---

```{r}
pi + 1
```

Options can be moved into YAML under the execute key to apply to all chunks. Exceptions to that option can be set cell-by-cell.
You can also pass options via YAML to knitr through the knitr key¹.
You can use knitr to pass options that control your R session.

Figure Output

Figures Compared

Figure output options are similar to those from markdown figures except YAML syntax is swapped in for Pandoc’s markdown syntax. Some examples:

Figure output

fig-width: 5
fig-height: 3
fig-align: center
fig-cap: "The dog watch."
fig-alt: "Dog watching watch."

Markdown figures

width=5
height=3
align=center
fig-cap="The dog watch."
fig-alt="Dog watching watch."

Quarto defaults to inches. Pandoc defaults to pixels but can be changed.

fig-width=5, fig-width = 5, fig-width=5px, all work in Pandoc markdown. fig-width=5 px does not.
Other units besides px: cm, mm, in, inch and %.

Figure Output Example

```{r}
library(palmerpenguins)
library(ggplot2)

ggplot(penguins, aes(x = bill_length_mm,
                     y = bill_depth_mm,
                     col = island)) +
  geom_point()
```

Figure Output Example

```{r}
#| fig-width: 5
#| fig-height: 3

library(palmerpenguins)
library(ggplot2)

ggplot(penguins, aes(x = bill_length_mm,
                     y = bill_depth_mm,
                     col = island)) +
  geom_point()
```

Figure Output Example

```{r}
#| fig-width: 5
#| fig-height: 3
#| fig-cap: "Size of penguins on three islands in the Palmer Archipelago."
#| fig-alt: "Scatterplot showing the bill sizes of penguins across three islands."

library(palmerpenguins)
library(ggplot2)

ggplot(penguins, aes(x = bill_length_mm,
                     y = bill_depth_mm,
                     col = island)) +
  geom_point()
```

Scatterplot showing the bill sizes of penguins across three islands. — Size of penguins on three islands in the Palmer Archipelago.

Save time/code by moving figure sizing defaults up to the YAML.

Data Frame Output

A very modest data frame

R’s default isn’t designed for effective display.

```{r}
penguins
```

# A tibble: 344 × 8
   species island    bill_length_mm bill_depth_mm flipper_length_mm body_mass_g
   <fct>   <fct>              <dbl>         <dbl>             <int>       <int>
 1 Adelie  Torgersen           39.1          18.7               181        3750
 2 Adelie  Torgersen           39.5          17.4               186        3800
 3 Adelie  Torgersen           40.3          18                 195        3250
 4 Adelie  Torgersen           NA            NA                  NA          NA
 5 Adelie  Torgersen           36.7          19.3               193        3450
 6 Adelie  Torgersen           39.3          20.6               190        3650
 7 Adelie  Torgersen           38.9          17.8               181        3625
 8 Adelie  Torgersen           39.2          19.6               195        4675
 9 Adelie  Torgersen           34.1          18.1               193        3475
10 Adelie  Torgersen           42            20.2               190        4250
# … with 334 more rows, and 2 more variables: sex <fct>, year <int>

`knitr::kable` in an Rmd

kable() creates tables for $\LaTeX$, HTML, and Markdown output.

```{r}
knitr::kable(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
Adelie	Torgersen	38.9	17.8	181	3625	female	2007
Adelie	Torgersen	39.2	19.6	195	4675	male	2007
Adelie	Torgersen	34.1	18.1	193	3475	NA	2007
Adelie	Torgersen	42.0	20.2	190	4250	NA	2007
Adelie	Torgersen	37.8	17.1	186	3300	NA	2007
Adelie	Torgersen	37.8	17.3	180	3700	NA	2007
Adelie	Torgersen	41.1	17.6	182	3200	female	2007
Adelie	Torgersen	38.6	21.2	191	3800	male	2007
Adelie	Torgersen	34.6	21.1	198	4400	male	2007
Adelie	Torgersen	36.6	17.8	185	3700	female	2007
Adelie	Torgersen	38.7	19.0	195	3450	female	2007
Adelie	Torgersen	42.5	20.7	197	4500	male	2007
Adelie	Torgersen	34.4	18.4	184	3325	female	2007
Adelie	Torgersen	46.0	21.5	194	4200	male	2007
Adelie	Biscoe	37.8	18.3	174	3400	female	2007
Adelie	Biscoe	37.7	18.7	180	3600	male	2007
Adelie	Biscoe	35.9	19.2	189	3800	female	2007
Adelie	Biscoe	38.2	18.1	185	3950	male	2007
Adelie	Biscoe	38.8	17.2	180	3800	male	2007
Adelie	Biscoe	35.3	18.9	187	3800	female	2007
Adelie	Biscoe	40.6	18.6	183	3550	male	2007
Adelie	Biscoe	40.5	17.9	187	3200	female	2007
Adelie	Biscoe	37.9	18.6	172	3150	female	2007
Adelie	Biscoe	40.5	18.9	180	3950	male	2007
Adelie	Dream	39.5	16.7	178	3250	female	2007
Adelie	Dream	37.2	18.1	178	3900	male	2007
Adelie	Dream	39.5	17.8	188	3300	female	2007
Adelie	Dream	40.9	18.9	184	3900	male	2007
Adelie	Dream	36.4	17.0	195	3325	female	2007
Adelie	Dream	39.2	21.1	196	4150	male	2007
Adelie	Dream	38.8	20.0	190	3950	male	2007
Adelie	Dream	42.2	18.5	180	3550	female	2007
Adelie	Dream	37.6	19.3	181	3300	female	2007
Adelie	Dream	39.8	19.1	184	4650	male	2007
Adelie	Dream	36.5	18.0	182	3150	female	2007
Adelie	Dream	40.8	18.4	195	3900	male	2007
Adelie	Dream	36.0	18.5	186	3100	female	2007
Adelie	Dream	44.1	19.7	196	4400	male	2007
Adelie	Dream	37.0	16.9	185	3000	female	2007
Adelie	Dream	39.6	18.8	190	4600	male	2007
Adelie	Dream	41.1	19.0	182	3425	male	2007
Adelie	Dream	37.5	18.9	179	2975	NA	2007
Adelie	Dream	36.0	17.9	190	3450	female	2007
Adelie	Dream	42.3	21.2	191	4150	male	2007
Adelie	Biscoe	39.6	17.7	186	3500	female	2008
Adelie	Biscoe	40.1	18.9	188	4300	male	2008
Adelie	Biscoe	35.0	17.9	190	3450	female	2008
Adelie	Biscoe	42.0	19.5	200	4050	male	2008
Adelie	Biscoe	34.5	18.1	187	2900	female	2008
Adelie	Biscoe	41.4	18.6	191	3700	male	2008
Adelie	Biscoe	39.0	17.5	186	3550	female	2008
Adelie	Biscoe	40.6	18.8	193	3800	male	2008
Adelie	Biscoe	36.5	16.6	181	2850	female	2008
Adelie	Biscoe	37.6	19.1	194	3750	male	2008
Adelie	Biscoe	35.7	16.9	185	3150	female	2008
Adelie	Biscoe	41.3	21.1	195	4400	male	2008
Adelie	Biscoe	37.6	17.0	185	3600	female	2008
Adelie	Biscoe	41.1	18.2	192	4050	male	2008
Adelie	Biscoe	36.4	17.1	184	2850	female	2008
Adelie	Biscoe	41.6	18.0	192	3950	male	2008
Adelie	Biscoe	35.5	16.2	195	3350	female	2008
Adelie	Biscoe	41.1	19.1	188	4100	male	2008
Adelie	Torgersen	35.9	16.6	190	3050	female	2008
Adelie	Torgersen	41.8	19.4	198	4450	male	2008
Adelie	Torgersen	33.5	19.0	190	3600	female	2008
Adelie	Torgersen	39.7	18.4	190	3900	male	2008
Adelie	Torgersen	39.6	17.2	196	3550	female	2008
Adelie	Torgersen	45.8	18.9	197	4150	male	2008
Adelie	Torgersen	35.5	17.5	190	3700	female	2008
Adelie	Torgersen	42.8	18.5	195	4250	male	2008
Adelie	Torgersen	40.9	16.8	191	3700	female	2008
Adelie	Torgersen	37.2	19.4	184	3900	male	2008
Adelie	Torgersen	36.2	16.1	187	3550	female	2008
Adelie	Torgersen	42.1	19.1	195	4000	male	2008
Adelie	Torgersen	34.6	17.2	189	3200	female	2008
Adelie	Torgersen	42.9	17.6	196	4700	male	2008
Adelie	Torgersen	36.7	18.8	187	3800	female	2008
Adelie	Torgersen	35.1	19.4	193	4200	male	2008
Adelie	Dream	37.3	17.8	191	3350	female	2008
Adelie	Dream	41.3	20.3	194	3550	male	2008
Adelie	Dream	36.3	19.5	190	3800	male	2008
Adelie	Dream	36.9	18.6	189	3500	female	2008
Adelie	Dream	38.3	19.2	189	3950	male	2008
Adelie	Dream	38.9	18.8	190	3600	female	2008
Adelie	Dream	35.7	18.0	202	3550	female	2008
Adelie	Dream	41.1	18.1	205	4300	male	2008
Adelie	Dream	34.0	17.1	185	3400	female	2008
Adelie	Dream	39.6	18.1	186	4450	male	2008
Adelie	Dream	36.2	17.3	187	3300	female	2008
Adelie	Dream	40.8	18.9	208	4300	male	2008
Adelie	Dream	38.1	18.6	190	3700	female	2008
Adelie	Dream	40.3	18.5	196	4350	male	2008
Adelie	Dream	33.1	16.1	178	2900	female	2008
Adelie	Dream	43.2	18.5	192	4100	male	2008
Adelie	Biscoe	35.0	17.9	192	3725	female	2009
Adelie	Biscoe	41.0	20.0	203	4725	male	2009
Adelie	Biscoe	37.7	16.0	183	3075	female	2009
Adelie	Biscoe	37.8	20.0	190	4250	male	2009
Adelie	Biscoe	37.9	18.6	193	2925	female	2009
Adelie	Biscoe	39.7	18.9	184	3550	male	2009
Adelie	Biscoe	38.6	17.2	199	3750	female	2009
Adelie	Biscoe	38.2	20.0	190	3900	male	2009
Adelie	Biscoe	38.1	17.0	181	3175	female	2009
Adelie	Biscoe	43.2	19.0	197	4775	male	2009
Adelie	Biscoe	38.1	16.5	198	3825	female	2009
Adelie	Biscoe	45.6	20.3	191	4600	male	2009
Adelie	Biscoe	39.7	17.7	193	3200	female	2009
Adelie	Biscoe	42.2	19.5	197	4275	male	2009
Adelie	Biscoe	39.6	20.7	191	3900	female	2009
Adelie	Biscoe	42.7	18.3	196	4075	male	2009
Adelie	Torgersen	38.6	17.0	188	2900	female	2009
Adelie	Torgersen	37.3	20.5	199	3775	male	2009
Adelie	Torgersen	35.7	17.0	189	3350	female	2009
Adelie	Torgersen	41.1	18.6	189	3325	male	2009
Adelie	Torgersen	36.2	17.2	187	3150	female	2009
Adelie	Torgersen	37.7	19.8	198	3500	male	2009
Adelie	Torgersen	40.2	17.0	176	3450	female	2009
Adelie	Torgersen	41.4	18.5	202	3875	male	2009
Adelie	Torgersen	35.2	15.9	186	3050	female	2009
Adelie	Torgersen	40.6	19.0	199	4000	male	2009
Adelie	Torgersen	38.8	17.6	191	3275	female	2009
Adelie	Torgersen	41.5	18.3	195	4300	male	2009
Adelie	Torgersen	39.0	17.1	191	3050	female	2009
Adelie	Torgersen	44.1	18.0	210	4000	male	2009
Adelie	Torgersen	38.5	17.9	190	3325	female	2009
Adelie	Torgersen	43.1	19.2	197	3500	male	2009
Adelie	Dream	36.8	18.5	193	3500	female	2009
Adelie	Dream	37.5	18.5	199	4475	male	2009
Adelie	Dream	38.1	17.6	187	3425	female	2009
Adelie	Dream	41.1	17.5	190	3900	male	2009
Adelie	Dream	35.6	17.5	191	3175	female	2009
Adelie	Dream	40.2	20.1	200	3975	male	2009
Adelie	Dream	37.0	16.5	185	3400	female	2009
Adelie	Dream	39.7	17.9	193	4250	male	2009
Adelie	Dream	40.2	17.1	193	3400	female	2009
Adelie	Dream	40.6	17.2	187	3475	male	2009
Adelie	Dream	32.1	15.5	188	3050	female	2009
Adelie	Dream	40.7	17.0	190	3725	male	2009
Adelie	Dream	37.3	16.8	192	3000	female	2009
Adelie	Dream	39.0	18.7	185	3650	male	2009
Adelie	Dream	39.2	18.6	190	4250	male	2009
Adelie	Dream	36.6	18.4	184	3475	female	2009
Adelie	Dream	36.0	17.8	195	3450	female	2009
Adelie	Dream	37.8	18.1	193	3750	male	2009
Adelie	Dream	36.0	17.1	187	3700	female	2009
Adelie	Dream	41.5	18.5	201	4000	male	2009
Gentoo	Biscoe	46.1	13.2	211	4500	female	2007
Gentoo	Biscoe	50.0	16.3	230	5700	male	2007
Gentoo	Biscoe	48.7	14.1	210	4450	female	2007
Gentoo	Biscoe	50.0	15.2	218	5700	male	2007
Gentoo	Biscoe	47.6	14.5	215	5400	male	2007
Gentoo	Biscoe	46.5	13.5	210	4550	female	2007
Gentoo	Biscoe	45.4	14.6	211	4800	female	2007
Gentoo	Biscoe	46.7	15.3	219	5200	male	2007
Gentoo	Biscoe	43.3	13.4	209	4400	female	2007
Gentoo	Biscoe	46.8	15.4	215	5150	male	2007
Gentoo	Biscoe	40.9	13.7	214	4650	female	2007
Gentoo	Biscoe	49.0	16.1	216	5550	male	2007
Gentoo	Biscoe	45.5	13.7	214	4650	female	2007
Gentoo	Biscoe	48.4	14.6	213	5850	male	2007
Gentoo	Biscoe	45.8	14.6	210	4200	female	2007
Gentoo	Biscoe	49.3	15.7	217	5850	male	2007
Gentoo	Biscoe	42.0	13.5	210	4150	female	2007
Gentoo	Biscoe	49.2	15.2	221	6300	male	2007
Gentoo	Biscoe	46.2	14.5	209	4800	female	2007
Gentoo	Biscoe	48.7	15.1	222	5350	male	2007
Gentoo	Biscoe	50.2	14.3	218	5700	male	2007
Gentoo	Biscoe	45.1	14.5	215	5000	female	2007
Gentoo	Biscoe	46.5	14.5	213	4400	female	2007
Gentoo	Biscoe	46.3	15.8	215	5050	male	2007
Gentoo	Biscoe	42.9	13.1	215	5000	female	2007
Gentoo	Biscoe	46.1	15.1	215	5100	male	2007
Gentoo	Biscoe	44.5	14.3	216	4100	NA	2007
Gentoo	Biscoe	47.8	15.0	215	5650	male	2007
Gentoo	Biscoe	48.2	14.3	210	4600	female	2007
Gentoo	Biscoe	50.0	15.3	220	5550	male	2007
Gentoo	Biscoe	47.3	15.3	222	5250	male	2007
Gentoo	Biscoe	42.8	14.2	209	4700	female	2007
Gentoo	Biscoe	45.1	14.5	207	5050	female	2007
Gentoo	Biscoe	59.6	17.0	230	6050	male	2007
Gentoo	Biscoe	49.1	14.8	220	5150	female	2008
Gentoo	Biscoe	48.4	16.3	220	5400	male	2008
Gentoo	Biscoe	42.6	13.7	213	4950	female	2008
Gentoo	Biscoe	44.4	17.3	219	5250	male	2008
Gentoo	Biscoe	44.0	13.6	208	4350	female	2008
Gentoo	Biscoe	48.7	15.7	208	5350	male	2008
Gentoo	Biscoe	42.7	13.7	208	3950	female	2008
Gentoo	Biscoe	49.6	16.0	225	5700	male	2008
Gentoo	Biscoe	45.3	13.7	210	4300	female	2008
Gentoo	Biscoe	49.6	15.0	216	4750	male	2008
Gentoo	Biscoe	50.5	15.9	222	5550	male	2008
Gentoo	Biscoe	43.6	13.9	217	4900	female	2008
Gentoo	Biscoe	45.5	13.9	210	4200	female	2008
Gentoo	Biscoe	50.5	15.9	225	5400	male	2008
Gentoo	Biscoe	44.9	13.3	213	5100	female	2008
Gentoo	Biscoe	45.2	15.8	215	5300	male	2008
Gentoo	Biscoe	46.6	14.2	210	4850	female	2008
Gentoo	Biscoe	48.5	14.1	220	5300	male	2008
Gentoo	Biscoe	45.1	14.4	210	4400	female	2008
Gentoo	Biscoe	50.1	15.0	225	5000	male	2008
Gentoo	Biscoe	46.5	14.4	217	4900	female	2008
Gentoo	Biscoe	45.0	15.4	220	5050	male	2008
Gentoo	Biscoe	43.8	13.9	208	4300	female	2008
Gentoo	Biscoe	45.5	15.0	220	5000	male	2008
Gentoo	Biscoe	43.2	14.5	208	4450	female	2008
Gentoo	Biscoe	50.4	15.3	224	5550	male	2008
Gentoo	Biscoe	45.3	13.8	208	4200	female	2008
Gentoo	Biscoe	46.2	14.9	221	5300	male	2008
Gentoo	Biscoe	45.7	13.9	214	4400	female	2008
Gentoo	Biscoe	54.3	15.7	231	5650	male	2008
Gentoo	Biscoe	45.8	14.2	219	4700	female	2008
Gentoo	Biscoe	49.8	16.8	230	5700	male	2008
Gentoo	Biscoe	46.2	14.4	214	4650	NA	2008
Gentoo	Biscoe	49.5	16.2	229	5800	male	2008
Gentoo	Biscoe	43.5	14.2	220	4700	female	2008
Gentoo	Biscoe	50.7	15.0	223	5550	male	2008
Gentoo	Biscoe	47.7	15.0	216	4750	female	2008
Gentoo	Biscoe	46.4	15.6	221	5000	male	2008
Gentoo	Biscoe	48.2	15.6	221	5100	male	2008
Gentoo	Biscoe	46.5	14.8	217	5200	female	2008
Gentoo	Biscoe	46.4	15.0	216	4700	female	2008
Gentoo	Biscoe	48.6	16.0	230	5800	male	2008
Gentoo	Biscoe	47.5	14.2	209	4600	female	2008
Gentoo	Biscoe	51.1	16.3	220	6000	male	2008
Gentoo	Biscoe	45.2	13.8	215	4750	female	2008
Gentoo	Biscoe	45.2	16.4	223	5950	male	2008
Gentoo	Biscoe	49.1	14.5	212	4625	female	2009
Gentoo	Biscoe	52.5	15.6	221	5450	male	2009
Gentoo	Biscoe	47.4	14.6	212	4725	female	2009
Gentoo	Biscoe	50.0	15.9	224	5350	male	2009
Gentoo	Biscoe	44.9	13.8	212	4750	female	2009
Gentoo	Biscoe	50.8	17.3	228	5600	male	2009
Gentoo	Biscoe	43.4	14.4	218	4600	female	2009
Gentoo	Biscoe	51.3	14.2	218	5300	male	2009
Gentoo	Biscoe	47.5	14.0	212	4875	female	2009
Gentoo	Biscoe	52.1	17.0	230	5550	male	2009
Gentoo	Biscoe	47.5	15.0	218	4950	female	2009
Gentoo	Biscoe	52.2	17.1	228	5400	male	2009
Gentoo	Biscoe	45.5	14.5	212	4750	female	2009
Gentoo	Biscoe	49.5	16.1	224	5650	male	2009
Gentoo	Biscoe	44.5	14.7	214	4850	female	2009
Gentoo	Biscoe	50.8	15.7	226	5200	male	2009
Gentoo	Biscoe	49.4	15.8	216	4925	male	2009
Gentoo	Biscoe	46.9	14.6	222	4875	female	2009
Gentoo	Biscoe	48.4	14.4	203	4625	female	2009
Gentoo	Biscoe	51.1	16.5	225	5250	male	2009
Gentoo	Biscoe	48.5	15.0	219	4850	female	2009
Gentoo	Biscoe	55.9	17.0	228	5600	male	2009
Gentoo	Biscoe	47.2	15.5	215	4975	female	2009
Gentoo	Biscoe	49.1	15.0	228	5500	male	2009
Gentoo	Biscoe	47.3	13.8	216	4725	NA	2009
Gentoo	Biscoe	46.8	16.1	215	5500	male	2009
Gentoo	Biscoe	41.7	14.7	210	4700	female	2009
Gentoo	Biscoe	53.4	15.8	219	5500	male	2009
Gentoo	Biscoe	43.3	14.0	208	4575	female	2009
Gentoo	Biscoe	48.1	15.1	209	5500	male	2009
Gentoo	Biscoe	50.5	15.2	216	5000	female	2009
Gentoo	Biscoe	49.8	15.9	229	5950	male	2009
Gentoo	Biscoe	43.5	15.2	213	4650	female	2009
Gentoo	Biscoe	51.5	16.3	230	5500	male	2009
Gentoo	Biscoe	46.2	14.1	217	4375	female	2009
Gentoo	Biscoe	55.1	16.0	230	5850	male	2009
Gentoo	Biscoe	44.5	15.7	217	4875	NA	2009
Gentoo	Biscoe	48.8	16.2	222	6000	male	2009
Gentoo	Biscoe	47.2	13.7	214	4925	female	2009
Gentoo	Biscoe	NA	NA	NA	NA	NA	2009
Gentoo	Biscoe	46.8	14.3	215	4850	female	2009
Gentoo	Biscoe	50.4	15.7	222	5750	male	2009
Gentoo	Biscoe	45.2	14.8	212	5200	female	2009
Gentoo	Biscoe	49.9	16.1	213	5400	male	2009
Chinstrap	Dream	46.5	17.9	192	3500	female	2007
Chinstrap	Dream	50.0	19.5	196	3900	male	2007
Chinstrap	Dream	51.3	19.2	193	3650	male	2007
Chinstrap	Dream	45.4	18.7	188	3525	female	2007
Chinstrap	Dream	52.7	19.8	197	3725	male	2007
Chinstrap	Dream	45.2	17.8	198	3950	female	2007
Chinstrap	Dream	46.1	18.2	178	3250	female	2007
Chinstrap	Dream	51.3	18.2	197	3750	male	2007
Chinstrap	Dream	46.0	18.9	195	4150	female	2007
Chinstrap	Dream	51.3	19.9	198	3700	male	2007
Chinstrap	Dream	46.6	17.8	193	3800	female	2007
Chinstrap	Dream	51.7	20.3	194	3775	male	2007
Chinstrap	Dream	47.0	17.3	185	3700	female	2007
Chinstrap	Dream	52.0	18.1	201	4050	male	2007
Chinstrap	Dream	45.9	17.1	190	3575	female	2007
Chinstrap	Dream	50.5	19.6	201	4050	male	2007
Chinstrap	Dream	50.3	20.0	197	3300	male	2007
Chinstrap	Dream	58.0	17.8	181	3700	female	2007
Chinstrap	Dream	46.4	18.6	190	3450	female	2007
Chinstrap	Dream	49.2	18.2	195	4400	male	2007
Chinstrap	Dream	42.4	17.3	181	3600	female	2007
Chinstrap	Dream	48.5	17.5	191	3400	male	2007
Chinstrap	Dream	43.2	16.6	187	2900	female	2007
Chinstrap	Dream	50.6	19.4	193	3800	male	2007
Chinstrap	Dream	46.7	17.9	195	3300	female	2007
Chinstrap	Dream	52.0	19.0	197	4150	male	2007
Chinstrap	Dream	50.5	18.4	200	3400	female	2008
Chinstrap	Dream	49.5	19.0	200	3800	male	2008
Chinstrap	Dream	46.4	17.8	191	3700	female	2008
Chinstrap	Dream	52.8	20.0	205	4550	male	2008
Chinstrap	Dream	40.9	16.6	187	3200	female	2008
Chinstrap	Dream	54.2	20.8	201	4300	male	2008
Chinstrap	Dream	42.5	16.7	187	3350	female	2008
Chinstrap	Dream	51.0	18.8	203	4100	male	2008
Chinstrap	Dream	49.7	18.6	195	3600	male	2008
Chinstrap	Dream	47.5	16.8	199	3900	female	2008
Chinstrap	Dream	47.6	18.3	195	3850	female	2008
Chinstrap	Dream	52.0	20.7	210	4800	male	2008
Chinstrap	Dream	46.9	16.6	192	2700	female	2008
Chinstrap	Dream	53.5	19.9	205	4500	male	2008
Chinstrap	Dream	49.0	19.5	210	3950	male	2008
Chinstrap	Dream	46.2	17.5	187	3650	female	2008
Chinstrap	Dream	50.9	19.1	196	3550	male	2008
Chinstrap	Dream	45.5	17.0	196	3500	female	2008
Chinstrap	Dream	50.9	17.9	196	3675	female	2009
Chinstrap	Dream	50.8	18.5	201	4450	male	2009
Chinstrap	Dream	50.1	17.9	190	3400	female	2009
Chinstrap	Dream	49.0	19.6	212	4300	male	2009
Chinstrap	Dream	51.5	18.7	187	3250	male	2009
Chinstrap	Dream	49.8	17.3	198	3675	female	2009
Chinstrap	Dream	48.1	16.4	199	3325	female	2009
Chinstrap	Dream	51.4	19.0	201	3950	male	2009
Chinstrap	Dream	45.7	17.3	193	3600	female	2009
Chinstrap	Dream	50.7	19.7	203	4050	male	2009
Chinstrap	Dream	42.5	17.3	187	3350	female	2009
Chinstrap	Dream	52.2	18.8	197	3450	male	2009
Chinstrap	Dream	45.2	16.6	191	3250	female	2009
Chinstrap	Dream	49.3	19.9	203	4050	male	2009
Chinstrap	Dream	50.2	18.8	202	3800	male	2009
Chinstrap	Dream	45.6	19.4	194	3525	female	2009
Chinstrap	Dream	51.9	19.5	206	3950	male	2009
Chinstrap	Dream	46.8	16.5	189	3650	female	2009
Chinstrap	Dream	45.7	17.0	195	3650	female	2009
Chinstrap	Dream	55.8	19.8	207	4000	male	2009
Chinstrap	Dream	43.5	18.1	202	3400	female	2009
Chinstrap	Dream	49.6	18.2	193	3775	male	2009
Chinstrap	Dream	50.8	19.0	210	4100	male	2009
Chinstrap	Dream	50.2	18.7	198	3775	female	2009

`knitr::kable` in Quarto

df-print: kable available as a document-level option.

---
format:
  html:
    df-print: kable
---

```{r}
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
Adelie	Torgersen	38.9	17.8	181	3625	female	2007
Adelie	Torgersen	39.2	19.6	195	4675	male	2007
Adelie	Torgersen	34.1	18.1	193	3475	NA	2007
Adelie	Torgersen	42.0	20.2	190	4250	NA	2007
Adelie	Torgersen	37.8	17.1	186	3300	NA	2007
Adelie	Torgersen	37.8	17.3	180	3700	NA	2007
Adelie	Torgersen	41.1	17.6	182	3200	female	2007
Adelie	Torgersen	38.6	21.2	191	3800	male	2007
Adelie	Torgersen	34.6	21.1	198	4400	male	2007
Adelie	Torgersen	36.6	17.8	185	3700	female	2007
Adelie	Torgersen	38.7	19.0	195	3450	female	2007
Adelie	Torgersen	42.5	20.7	197	4500	male	2007
Adelie	Torgersen	34.4	18.4	184	3325	female	2007
Adelie	Torgersen	46.0	21.5	194	4200	male	2007
Adelie	Biscoe	37.8	18.3	174	3400	female	2007
Adelie	Biscoe	37.7	18.7	180	3600	male	2007
Adelie	Biscoe	35.9	19.2	189	3800	female	2007
Adelie	Biscoe	38.2	18.1	185	3950	male	2007
Adelie	Biscoe	38.8	17.2	180	3800	male	2007
Adelie	Biscoe	35.3	18.9	187	3800	female	2007
Adelie	Biscoe	40.6	18.6	183	3550	male	2007
Adelie	Biscoe	40.5	17.9	187	3200	female	2007
Adelie	Biscoe	37.9	18.6	172	3150	female	2007
Adelie	Biscoe	40.5	18.9	180	3950	male	2007
Adelie	Dream	39.5	16.7	178	3250	female	2007
Adelie	Dream	37.2	18.1	178	3900	male	2007
Adelie	Dream	39.5	17.8	188	3300	female	2007
Adelie	Dream	40.9	18.9	184	3900	male	2007
Adelie	Dream	36.4	17.0	195	3325	female	2007
Adelie	Dream	39.2	21.1	196	4150	male	2007
Adelie	Dream	38.8	20.0	190	3950	male	2007
Adelie	Dream	42.2	18.5	180	3550	female	2007
Adelie	Dream	37.6	19.3	181	3300	female	2007
Adelie	Dream	39.8	19.1	184	4650	male	2007
Adelie	Dream	36.5	18.0	182	3150	female	2007
Adelie	Dream	40.8	18.4	195	3900	male	2007
Adelie	Dream	36.0	18.5	186	3100	female	2007
Adelie	Dream	44.1	19.7	196	4400	male	2007
Adelie	Dream	37.0	16.9	185	3000	female	2007
Adelie	Dream	39.6	18.8	190	4600	male	2007
Adelie	Dream	41.1	19.0	182	3425	male	2007
Adelie	Dream	37.5	18.9	179	2975	NA	2007
Adelie	Dream	36.0	17.9	190	3450	female	2007
Adelie	Dream	42.3	21.2	191	4150	male	2007
Adelie	Biscoe	39.6	17.7	186	3500	female	2008
Adelie	Biscoe	40.1	18.9	188	4300	male	2008
Adelie	Biscoe	35.0	17.9	190	3450	female	2008
Adelie	Biscoe	42.0	19.5	200	4050	male	2008
Adelie	Biscoe	34.5	18.1	187	2900	female	2008
Adelie	Biscoe	41.4	18.6	191	3700	male	2008
Adelie	Biscoe	39.0	17.5	186	3550	female	2008
Adelie	Biscoe	40.6	18.8	193	3800	male	2008
Adelie	Biscoe	36.5	16.6	181	2850	female	2008
Adelie	Biscoe	37.6	19.1	194	3750	male	2008
Adelie	Biscoe	35.7	16.9	185	3150	female	2008
Adelie	Biscoe	41.3	21.1	195	4400	male	2008
Adelie	Biscoe	37.6	17.0	185	3600	female	2008
Adelie	Biscoe	41.1	18.2	192	4050	male	2008
Adelie	Biscoe	36.4	17.1	184	2850	female	2008
Adelie	Biscoe	41.6	18.0	192	3950	male	2008
Adelie	Biscoe	35.5	16.2	195	3350	female	2008
Adelie	Biscoe	41.1	19.1	188	4100	male	2008
Adelie	Torgersen	35.9	16.6	190	3050	female	2008
Adelie	Torgersen	41.8	19.4	198	4450	male	2008
Adelie	Torgersen	33.5	19.0	190	3600	female	2008
Adelie	Torgersen	39.7	18.4	190	3900	male	2008
Adelie	Torgersen	39.6	17.2	196	3550	female	2008
Adelie	Torgersen	45.8	18.9	197	4150	male	2008
Adelie	Torgersen	35.5	17.5	190	3700	female	2008
Adelie	Torgersen	42.8	18.5	195	4250	male	2008
Adelie	Torgersen	40.9	16.8	191	3700	female	2008
Adelie	Torgersen	37.2	19.4	184	3900	male	2008
Adelie	Torgersen	36.2	16.1	187	3550	female	2008
Adelie	Torgersen	42.1	19.1	195	4000	male	2008
Adelie	Torgersen	34.6	17.2	189	3200	female	2008
Adelie	Torgersen	42.9	17.6	196	4700	male	2008
Adelie	Torgersen	36.7	18.8	187	3800	female	2008
Adelie	Torgersen	35.1	19.4	193	4200	male	2008
Adelie	Dream	37.3	17.8	191	3350	female	2008
Adelie	Dream	41.3	20.3	194	3550	male	2008
Adelie	Dream	36.3	19.5	190	3800	male	2008
Adelie	Dream	36.9	18.6	189	3500	female	2008
Adelie	Dream	38.3	19.2	189	3950	male	2008
Adelie	Dream	38.9	18.8	190	3600	female	2008
Adelie	Dream	35.7	18.0	202	3550	female	2008
Adelie	Dream	41.1	18.1	205	4300	male	2008
Adelie	Dream	34.0	17.1	185	3400	female	2008
Adelie	Dream	39.6	18.1	186	4450	male	2008
Adelie	Dream	36.2	17.3	187	3300	female	2008
Adelie	Dream	40.8	18.9	208	4300	male	2008
Adelie	Dream	38.1	18.6	190	3700	female	2008
Adelie	Dream	40.3	18.5	196	4350	male	2008
Adelie	Dream	33.1	16.1	178	2900	female	2008
Adelie	Dream	43.2	18.5	192	4100	male	2008
Adelie	Biscoe	35.0	17.9	192	3725	female	2009
Adelie	Biscoe	41.0	20.0	203	4725	male	2009
Adelie	Biscoe	37.7	16.0	183	3075	female	2009
Adelie	Biscoe	37.8	20.0	190	4250	male	2009
Adelie	Biscoe	37.9	18.6	193	2925	female	2009
Adelie	Biscoe	39.7	18.9	184	3550	male	2009
Adelie	Biscoe	38.6	17.2	199	3750	female	2009
Adelie	Biscoe	38.2	20.0	190	3900	male	2009
Adelie	Biscoe	38.1	17.0	181	3175	female	2009
Adelie	Biscoe	43.2	19.0	197	4775	male	2009
Adelie	Biscoe	38.1	16.5	198	3825	female	2009
Adelie	Biscoe	45.6	20.3	191	4600	male	2009
Adelie	Biscoe	39.7	17.7	193	3200	female	2009
Adelie	Biscoe	42.2	19.5	197	4275	male	2009
Adelie	Biscoe	39.6	20.7	191	3900	female	2009
Adelie	Biscoe	42.7	18.3	196	4075	male	2009
Adelie	Torgersen	38.6	17.0	188	2900	female	2009
Adelie	Torgersen	37.3	20.5	199	3775	male	2009
Adelie	Torgersen	35.7	17.0	189	3350	female	2009
Adelie	Torgersen	41.1	18.6	189	3325	male	2009
Adelie	Torgersen	36.2	17.2	187	3150	female	2009
Adelie	Torgersen	37.7	19.8	198	3500	male	2009
Adelie	Torgersen	40.2	17.0	176	3450	female	2009
Adelie	Torgersen	41.4	18.5	202	3875	male	2009
Adelie	Torgersen	35.2	15.9	186	3050	female	2009
Adelie	Torgersen	40.6	19.0	199	4000	male	2009
Adelie	Torgersen	38.8	17.6	191	3275	female	2009
Adelie	Torgersen	41.5	18.3	195	4300	male	2009
Adelie	Torgersen	39.0	17.1	191	3050	female	2009
Adelie	Torgersen	44.1	18.0	210	4000	male	2009
Adelie	Torgersen	38.5	17.9	190	3325	female	2009
Adelie	Torgersen	43.1	19.2	197	3500	male	2009
Adelie	Dream	36.8	18.5	193	3500	female	2009
Adelie	Dream	37.5	18.5	199	4475	male	2009
Adelie	Dream	38.1	17.6	187	3425	female	2009
Adelie	Dream	41.1	17.5	190	3900	male	2009
Adelie	Dream	35.6	17.5	191	3175	female	2009
Adelie	Dream	40.2	20.1	200	3975	male	2009
Adelie	Dream	37.0	16.5	185	3400	female	2009
Adelie	Dream	39.7	17.9	193	4250	male	2009
Adelie	Dream	40.2	17.1	193	3400	female	2009
Adelie	Dream	40.6	17.2	187	3475	male	2009
Adelie	Dream	32.1	15.5	188	3050	female	2009
Adelie	Dream	40.7	17.0	190	3725	male	2009
Adelie	Dream	37.3	16.8	192	3000	female	2009
Adelie	Dream	39.0	18.7	185	3650	male	2009
Adelie	Dream	39.2	18.6	190	4250	male	2009
Adelie	Dream	36.6	18.4	184	3475	female	2009
Adelie	Dream	36.0	17.8	195	3450	female	2009
Adelie	Dream	37.8	18.1	193	3750	male	2009
Adelie	Dream	36.0	17.1	187	3700	female	2009
Adelie	Dream	41.5	18.5	201	4000	male	2009
Gentoo	Biscoe	46.1	13.2	211	4500	female	2007
Gentoo	Biscoe	50.0	16.3	230	5700	male	2007
Gentoo	Biscoe	48.7	14.1	210	4450	female	2007
Gentoo	Biscoe	50.0	15.2	218	5700	male	2007
Gentoo	Biscoe	47.6	14.5	215	5400	male	2007
Gentoo	Biscoe	46.5	13.5	210	4550	female	2007
Gentoo	Biscoe	45.4	14.6	211	4800	female	2007
Gentoo	Biscoe	46.7	15.3	219	5200	male	2007
Gentoo	Biscoe	43.3	13.4	209	4400	female	2007
Gentoo	Biscoe	46.8	15.4	215	5150	male	2007
Gentoo	Biscoe	40.9	13.7	214	4650	female	2007
Gentoo	Biscoe	49.0	16.1	216	5550	male	2007
Gentoo	Biscoe	45.5	13.7	214	4650	female	2007
Gentoo	Biscoe	48.4	14.6	213	5850	male	2007
Gentoo	Biscoe	45.8	14.6	210	4200	female	2007
Gentoo	Biscoe	49.3	15.7	217	5850	male	2007
Gentoo	Biscoe	42.0	13.5	210	4150	female	2007
Gentoo	Biscoe	49.2	15.2	221	6300	male	2007
Gentoo	Biscoe	46.2	14.5	209	4800	female	2007
Gentoo	Biscoe	48.7	15.1	222	5350	male	2007
Gentoo	Biscoe	50.2	14.3	218	5700	male	2007
Gentoo	Biscoe	45.1	14.5	215	5000	female	2007
Gentoo	Biscoe	46.5	14.5	213	4400	female	2007
Gentoo	Biscoe	46.3	15.8	215	5050	male	2007
Gentoo	Biscoe	42.9	13.1	215	5000	female	2007
Gentoo	Biscoe	46.1	15.1	215	5100	male	2007
Gentoo	Biscoe	44.5	14.3	216	4100	NA	2007
Gentoo	Biscoe	47.8	15.0	215	5650	male	2007
Gentoo	Biscoe	48.2	14.3	210	4600	female	2007
Gentoo	Biscoe	50.0	15.3	220	5550	male	2007
Gentoo	Biscoe	47.3	15.3	222	5250	male	2007
Gentoo	Biscoe	42.8	14.2	209	4700	female	2007
Gentoo	Biscoe	45.1	14.5	207	5050	female	2007
Gentoo	Biscoe	59.6	17.0	230	6050	male	2007
Gentoo	Biscoe	49.1	14.8	220	5150	female	2008
Gentoo	Biscoe	48.4	16.3	220	5400	male	2008
Gentoo	Biscoe	42.6	13.7	213	4950	female	2008
Gentoo	Biscoe	44.4	17.3	219	5250	male	2008
Gentoo	Biscoe	44.0	13.6	208	4350	female	2008
Gentoo	Biscoe	48.7	15.7	208	5350	male	2008
Gentoo	Biscoe	42.7	13.7	208	3950	female	2008
Gentoo	Biscoe	49.6	16.0	225	5700	male	2008
Gentoo	Biscoe	45.3	13.7	210	4300	female	2008
Gentoo	Biscoe	49.6	15.0	216	4750	male	2008
Gentoo	Biscoe	50.5	15.9	222	5550	male	2008
Gentoo	Biscoe	43.6	13.9	217	4900	female	2008
Gentoo	Biscoe	45.5	13.9	210	4200	female	2008
Gentoo	Biscoe	50.5	15.9	225	5400	male	2008
Gentoo	Biscoe	44.9	13.3	213	5100	female	2008
Gentoo	Biscoe	45.2	15.8	215	5300	male	2008
Gentoo	Biscoe	46.6	14.2	210	4850	female	2008
Gentoo	Biscoe	48.5	14.1	220	5300	male	2008
Gentoo	Biscoe	45.1	14.4	210	4400	female	2008
Gentoo	Biscoe	50.1	15.0	225	5000	male	2008
Gentoo	Biscoe	46.5	14.4	217	4900	female	2008
Gentoo	Biscoe	45.0	15.4	220	5050	male	2008
Gentoo	Biscoe	43.8	13.9	208	4300	female	2008
Gentoo	Biscoe	45.5	15.0	220	5000	male	2008
Gentoo	Biscoe	43.2	14.5	208	4450	female	2008
Gentoo	Biscoe	50.4	15.3	224	5550	male	2008
Gentoo	Biscoe	45.3	13.8	208	4200	female	2008
Gentoo	Biscoe	46.2	14.9	221	5300	male	2008
Gentoo	Biscoe	45.7	13.9	214	4400	female	2008
Gentoo	Biscoe	54.3	15.7	231	5650	male	2008
Gentoo	Biscoe	45.8	14.2	219	4700	female	2008
Gentoo	Biscoe	49.8	16.8	230	5700	male	2008
Gentoo	Biscoe	46.2	14.4	214	4650	NA	2008
Gentoo	Biscoe	49.5	16.2	229	5800	male	2008
Gentoo	Biscoe	43.5	14.2	220	4700	female	2008
Gentoo	Biscoe	50.7	15.0	223	5550	male	2008
Gentoo	Biscoe	47.7	15.0	216	4750	female	2008
Gentoo	Biscoe	46.4	15.6	221	5000	male	2008
Gentoo	Biscoe	48.2	15.6	221	5100	male	2008
Gentoo	Biscoe	46.5	14.8	217	5200	female	2008
Gentoo	Biscoe	46.4	15.0	216	4700	female	2008
Gentoo	Biscoe	48.6	16.0	230	5800	male	2008
Gentoo	Biscoe	47.5	14.2	209	4600	female	2008
Gentoo	Biscoe	51.1	16.3	220	6000	male	2008
Gentoo	Biscoe	45.2	13.8	215	4750	female	2008
Gentoo	Biscoe	45.2	16.4	223	5950	male	2008
Gentoo	Biscoe	49.1	14.5	212	4625	female	2009
Gentoo	Biscoe	52.5	15.6	221	5450	male	2009
Gentoo	Biscoe	47.4	14.6	212	4725	female	2009
Gentoo	Biscoe	50.0	15.9	224	5350	male	2009
Gentoo	Biscoe	44.9	13.8	212	4750	female	2009
Gentoo	Biscoe	50.8	17.3	228	5600	male	2009
Gentoo	Biscoe	43.4	14.4	218	4600	female	2009
Gentoo	Biscoe	51.3	14.2	218	5300	male	2009
Gentoo	Biscoe	47.5	14.0	212	4875	female	2009
Gentoo	Biscoe	52.1	17.0	230	5550	male	2009
Gentoo	Biscoe	47.5	15.0	218	4950	female	2009
Gentoo	Biscoe	52.2	17.1	228	5400	male	2009
Gentoo	Biscoe	45.5	14.5	212	4750	female	2009
Gentoo	Biscoe	49.5	16.1	224	5650	male	2009
Gentoo	Biscoe	44.5	14.7	214	4850	female	2009
Gentoo	Biscoe	50.8	15.7	226	5200	male	2009
Gentoo	Biscoe	49.4	15.8	216	4925	male	2009
Gentoo	Biscoe	46.9	14.6	222	4875	female	2009
Gentoo	Biscoe	48.4	14.4	203	4625	female	2009
Gentoo	Biscoe	51.1	16.5	225	5250	male	2009
Gentoo	Biscoe	48.5	15.0	219	4850	female	2009
Gentoo	Biscoe	55.9	17.0	228	5600	male	2009
Gentoo	Biscoe	47.2	15.5	215	4975	female	2009
Gentoo	Biscoe	49.1	15.0	228	5500	male	2009
Gentoo	Biscoe	47.3	13.8	216	4725	NA	2009
Gentoo	Biscoe	46.8	16.1	215	5500	male	2009
Gentoo	Biscoe	41.7	14.7	210	4700	female	2009
Gentoo	Biscoe	53.4	15.8	219	5500	male	2009
Gentoo	Biscoe	43.3	14.0	208	4575	female	2009
Gentoo	Biscoe	48.1	15.1	209	5500	male	2009
Gentoo	Biscoe	50.5	15.2	216	5000	female	2009
Gentoo	Biscoe	49.8	15.9	229	5950	male	2009
Gentoo	Biscoe	43.5	15.2	213	4650	female	2009
Gentoo	Biscoe	51.5	16.3	230	5500	male	2009
Gentoo	Biscoe	46.2	14.1	217	4375	female	2009
Gentoo	Biscoe	55.1	16.0	230	5850	male	2009
Gentoo	Biscoe	44.5	15.7	217	4875	NA	2009
Gentoo	Biscoe	48.8	16.2	222	6000	male	2009
Gentoo	Biscoe	47.2	13.7	214	4925	female	2009
Gentoo	Biscoe	NA	NA	NA	NA	NA	2009
Gentoo	Biscoe	46.8	14.3	215	4850	female	2009
Gentoo	Biscoe	50.4	15.7	222	5750	male	2009
Gentoo	Biscoe	45.2	14.8	212	5200	female	2009
Gentoo	Biscoe	49.9	16.1	213	5400	male	2009
Chinstrap	Dream	46.5	17.9	192	3500	female	2007
Chinstrap	Dream	50.0	19.5	196	3900	male	2007
Chinstrap	Dream	51.3	19.2	193	3650	male	2007
Chinstrap	Dream	45.4	18.7	188	3525	female	2007
Chinstrap	Dream	52.7	19.8	197	3725	male	2007
Chinstrap	Dream	45.2	17.8	198	3950	female	2007
Chinstrap	Dream	46.1	18.2	178	3250	female	2007
Chinstrap	Dream	51.3	18.2	197	3750	male	2007
Chinstrap	Dream	46.0	18.9	195	4150	female	2007
Chinstrap	Dream	51.3	19.9	198	3700	male	2007
Chinstrap	Dream	46.6	17.8	193	3800	female	2007
Chinstrap	Dream	51.7	20.3	194	3775	male	2007
Chinstrap	Dream	47.0	17.3	185	3700	female	2007
Chinstrap	Dream	52.0	18.1	201	4050	male	2007
Chinstrap	Dream	45.9	17.1	190	3575	female	2007
Chinstrap	Dream	50.5	19.6	201	4050	male	2007
Chinstrap	Dream	50.3	20.0	197	3300	male	2007
Chinstrap	Dream	58.0	17.8	181	3700	female	2007
Chinstrap	Dream	46.4	18.6	190	3450	female	2007
Chinstrap	Dream	49.2	18.2	195	4400	male	2007
Chinstrap	Dream	42.4	17.3	181	3600	female	2007
Chinstrap	Dream	48.5	17.5	191	3400	male	2007
Chinstrap	Dream	43.2	16.6	187	2900	female	2007
Chinstrap	Dream	50.6	19.4	193	3800	male	2007
Chinstrap	Dream	46.7	17.9	195	3300	female	2007
Chinstrap	Dream	52.0	19.0	197	4150	male	2007
Chinstrap	Dream	50.5	18.4	200	3400	female	2008
Chinstrap	Dream	49.5	19.0	200	3800	male	2008
Chinstrap	Dream	46.4	17.8	191	3700	female	2008
Chinstrap	Dream	52.8	20.0	205	4550	male	2008
Chinstrap	Dream	40.9	16.6	187	3200	female	2008
Chinstrap	Dream	54.2	20.8	201	4300	male	2008
Chinstrap	Dream	42.5	16.7	187	3350	female	2008
Chinstrap	Dream	51.0	18.8	203	4100	male	2008
Chinstrap	Dream	49.7	18.6	195	3600	male	2008
Chinstrap	Dream	47.5	16.8	199	3900	female	2008
Chinstrap	Dream	47.6	18.3	195	3850	female	2008
Chinstrap	Dream	52.0	20.7	210	4800	male	2008
Chinstrap	Dream	46.9	16.6	192	2700	female	2008
Chinstrap	Dream	53.5	19.9	205	4500	male	2008
Chinstrap	Dream	49.0	19.5	210	3950	male	2008
Chinstrap	Dream	46.2	17.5	187	3650	female	2008
Chinstrap	Dream	50.9	19.1	196	3550	male	2008
Chinstrap	Dream	45.5	17.0	196	3500	female	2008
Chinstrap	Dream	50.9	17.9	196	3675	female	2009
Chinstrap	Dream	50.8	18.5	201	4450	male	2009
Chinstrap	Dream	50.1	17.9	190	3400	female	2009
Chinstrap	Dream	49.0	19.6	212	4300	male	2009
Chinstrap	Dream	51.5	18.7	187	3250	male	2009
Chinstrap	Dream	49.8	17.3	198	3675	female	2009
Chinstrap	Dream	48.1	16.4	199	3325	female	2009
Chinstrap	Dream	51.4	19.0	201	3950	male	2009
Chinstrap	Dream	45.7	17.3	193	3600	female	2009
Chinstrap	Dream	50.7	19.7	203	4050	male	2009
Chinstrap	Dream	42.5	17.3	187	3350	female	2009
Chinstrap	Dream	52.2	18.8	197	3450	male	2009
Chinstrap	Dream	45.2	16.6	191	3250	female	2009
Chinstrap	Dream	49.3	19.9	203	4050	male	2009
Chinstrap	Dream	50.2	18.8	202	3800	male	2009
Chinstrap	Dream	45.6	19.4	194	3525	female	2009
Chinstrap	Dream	51.9	19.5	206	3950	male	2009
Chinstrap	Dream	46.8	16.5	189	3650	female	2009
Chinstrap	Dream	45.7	17.0	195	3650	female	2009
Chinstrap	Dream	55.8	19.8	207	4000	male	2009
Chinstrap	Dream	43.5	18.1	202	3400	female	2009
Chinstrap	Dream	49.6	18.2	193	3775	male	2009
Chinstrap	Dream	50.8	19.0	210	4100	male	2009
Chinstrap	Dream	50.2	18.7	198	3775	female	2009

Paged Output

df-print: paged available as a document-level option.

---
format:
  html:
    df-print: paged
---

```{r}
penguins
```

Exercise 5

Create a mock analysis of the penguins data frame in the palmerspenguins R package and practice with code cell evaluation, display, and formatting.

You’re welcome to share your work on the workshop discussion thread.

Advanced Code Features

Shiny

Specify server: shiny in the YAML
Set the UI in a normal R chunk
Set the server in a chunk with #| context: server

See https://quarto.org/docs/interactive/shiny/ for an example

Pass from Yaml to R

This allows you to create parameterized reports

---
title: "My Document"
params:
  n_penguins: 50
---

```{r}
library(palmerpenguins)
library(ggplot2)
ggplot(aes(x = bill_length_mm,
           y = bill_depth_mm)) +
      geom_point()
```

The params YAML field can take many parameters as keys.
It’s available as a list in R using params$key.
Since the parameters are passed through YAML, you can easily script the generation of parameterized report using quarto CLI.

Pass from Yaml to R

You can create YAML dynamically using inline R!

Exercise 5 Redux

Revising your penguins analysis and think of parameters that you could pass to affect the R output. Knit with a few combinations of parameters and revel in the power!

Speaking Python

---
title: "matplotlib demo"
format: html
---

```{r}
rnorm(5)
```

For a line plot, see @fig-polar.

```{python}
#| label: fig-polar
#| fig-cap: "A line plot on a polar axis"

import numpy as np
import matplotlib.pyplot as plt

r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
  subplot_kw = {'projection': 'polar'} 
)
ax.plot(theta, r)
plt.show()
```

Since R is the first language detected, Quarto will have knitr run the R code and process the Python cells via the reticulate R package.

---
title: "matplotlib demo"
format: html
---

For a line plot, see @fig-polar.

```{python}
#| label: fig-polar
#| fig-cap: "A line plot on a polar axis"

import numpy as np
import matplotlib.pyplot as plt

r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(
  subplot_kw = {'projection': 'polar'} 
)
ax.plot(theta, r)
plt.show()
```

```{r}
rnorm(5)
```

Since Python is the first language detected, Quarto will have jupyter run the Python code and process the R cells via the rpy2` Python package.

The Upshot

A single qmd file is processed by a single engine running R, Python, or Julia.
A qmd running R can run Python via the reticulate R package.
A qmd running Python can run R via the rpy2 Python package.

Computation

Getting Exercise

Code Blocks

Pandoc’s Fenced Code Block

R Markdown’s Code Chunk

Results

Generalizing the Code Chunk

Generalizing the Code Chunk

Generalizing the Code Chunk

The Perks of the Hashpipe #|

Execution Options

Setting knitr options

Source

Output

From Cell Option to YAML

From Cell Option to YAML

From Cell Option to YAML

From Cell Option to YAML

Figure Output

Figures Compared

Figure output

Markdown figures

Figure Output Example

Figure Output Example

Figure Output Example

Data Frame Output

A very modest data frame

knitr::kable in an Rmd

knitr::kable in Quarto

Paged Output

Exercise 5

Advanced Code Features

Shiny

Pass from Yaml to R

Pass from Yaml to R

Exercise 5 Redux

Speaking Python

The Upshot

The Perks of the Hashpipe `#|`

Setting `knitr` options

`knitr::kable` in an Rmd

`knitr::kable` in Quarto