How to render two different tables with Elsevier extension in quarto? #13084
Replies: 6 comments 27 replies
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Could you remove pieces of your code one by one to end up with something small? Preferably something that does both require external dependencies such as janitor. Also, please if we don't need the 100+ packages from the tidyverse, please don't include I'm assuming the extension is the one that can be installed with Thank you for your help! |
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FWIW, I have no issues with the following code. ---
title: Imaginary title
author:
- name: FirstName LastName
email: email@address
abstract: |
{{< lipsum 1 >}}
format:
elsevier-pdf: default
execute:
echo: false
warning: false
---
# Introduction
```{r}
#| label: r-libraries
library(gt)
data(penguins)
```
```{r}
#| label: tbl-data1
#| tbl-cap: Table caption for data set one.
#| tbl-pos: "!h"
gt(head(penguins, c(5L, 5L)))
```
```{r}
#| label: tbl-data2
#| tbl-cap: This table show information for two variables.
#| tbl-pos: "!h"
gt(head(penguins, c(5L, 5L)))
``` |
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Yes, you were correct in assuming I was referring to the extension that can be installed with I took the example you provided and modified the code for the second table to create the output I was having problems with. The issue was with the html code contained in the second table of my original post. I added a comment to indicate the location in the code below. I originally wrote the code to render as a docx before I realized there was an extension available. I used the html code to italicize some text in the table headers. If the html code is removed from the second table below, the document will render correctly, but it seems to create two other problems. One, I still need to italicize some text in the table headers, but I don't know how to achieve that using the extension. Second, the second table is rendered wider than the page and I don't know if there are options to adjust the table and still be able to use the extension. ---
title: Imaginary title
author:
- name: FirstName LastName
email: email@address
abstract: |
{{< lipsum 1 >}}
format:
elsevier-pdf: default
execute:
echo: false
warning: false
---
# Introduction
```{r}
#| label: r-libraries
library(gt)
data(penguins)
```
```{r}
#| label: tbl-data1
#| tbl-cap: Table caption for data set one.
#| tbl-pos: "!h"
gt(head(penguins, c(5L, 5L)))
```
```{r}
#| label: tbl-data2
#| tbl-cap: This table shows information for two variables.
#| tbl-pos: "!h"
males <- penguins |>
dplyr::filter(island == 'Torgersen' & sex == 'male' & year == 2007) |>
head(c(4L, 4L))
females <- penguins |>
dplyr::filter(island == 'Torgersen' & sex == 'female' & year == 2007) |>
head(c(4L, 4L)) |>
dplyr::select(bill_len, bill_dep)
first_four <- penguins |>
dplyr::filter(island == 'Torgersen' & year == 2007) |>
head(c(4L, 4L)) |>
dplyr::select(bill_len, bill_dep)
peng_tbl <- cbind(males, females, first_four) |>
janitor::clean_names() |>
gt() |>
tab_spanner(label = 'Male', columns = c('bill_len', 'bill_dep')) |>
tab_spanner(label = 'Female', columns = c('bill_len_2', 'bill_dep_2')) |>
tab_spanner(label = 'M + F', columns = c('bill_len_3', 'bill_dep_3')) |>
cols_label(
# note the html in the line below that is creating the problem
bill_len_2 = html('<em>bill_len</em>'),
bill_dep_2 = 'bill_dep',
bill_len_3 = 'bill_len',
bill_dep_3 = 'bill_dep')
peng_tbl
```
|
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Why overcomplicating the example? Do as shown in ---
title: Imaginary title
author:
- name: FirstName LastName
email: email@address
abstract: |
{{< lipsum 1 >}}
format:
elsevier-pdf: default
execute:
echo: false
warning: false
---
# Introduction
```{r}
#| label: r-libraries
library(gt)
data(penguins)
```
```{r}
#| label: tbl-data1
#| tbl-cap: Table caption for data set one.
#| tbl-pos: "!h"
gt(head(penguins, c(5L, 5L)))
```
```{r}
#| label: tbl-data2
#| tbl-cap: This table show information for two variables.
#| tbl-pos: "!h"
gt(head(penguins, c(5L, 5L))) |>
cols_label(species = md("*Species*"))
``` |
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To clarify and avoid any confusion, Quarto does parse HTML table to render a table in other format not supporting HTML. So it could be valid to output raw HTML from a cell and expect a table in PDF output. However, it would not be the same styled table as it would be processed through HTML -> Pandoc Table AST -> LaTeX conversion in Pandoc. So in the examples shared above, if the cells are outputing HTML and there is a failure due to some LaTeX produced, this could be seen as an issue we need to handle in our HTML table processing. However, gt can produce LaTeX directly, so it is probably indeed better to use LaTeX output, and use the markdown support from gt to let Quarto handle some markdown syntax processing. I'll investigate to confirm the problem. |
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To be clear, from my example: gt(head(penguins, c(5L, 5L))) |>
cols_label(species = html("<em>Species</em>"))produces a literal gt(head(penguins, c(5L, 5L))) |>
cols_label(species = html("<em>Species</em>")) |>
as_raw_html()produces the italicise label (because of Quarto). |
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It was clear from your examples. Nothing to be added. I added precision regarding original examples, as they have |
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Thank you. As I stated, I was originally rendering to a docx, and I didn't realize the nuances between HTML and LaTeX when trying to create the pdf that required a modification. You have provided a very simple solution to the first problem I mentioned. As for the complication of the example, I don't see how to make it simpler with my code experience because I need a table that is multiple columns wide or at least wider than the table you created in your example to illustrate how it does not fit the page. I'm sure there is a more elegant way to create the wide table, but nonetheless, I needed a wider table. Landscape orientation could solve the problem, but this was not necessary when I originally rendered to a docx. I also tried ---
title: Imaginary title
author:
- name: FirstName LastName
email: email@address
abstract: |
{{< lipsum 1 >}}
format:
elsevier-pdf: default
execute:
echo: false
warning: false
---
# Introduction
```{r}
#| label: r-libraries
library(gt)
data(penguins)
```
```{r}
#| label: tbl-data2
#| tbl-cap: This table shows information for two variables.
#| tbl-pos: "!h"
males <- penguins |>
dplyr::filter(island == 'Torgersen' & sex == 'male' & year == 2007) |>
head(c(4L, 4L))
females <- penguins |>
dplyr::filter(island == 'Torgersen' & sex == 'female' & year == 2007) |>
head(c(4L, 4L)) |>
dplyr::select(bill_len, bill_dep)
first_four <- penguins |>
dplyr::filter(island == 'Torgersen' & year == 2007) |>
head(c(4L, 4L)) |>
dplyr::select(bill_len, bill_dep)
peng_tbl <- cbind(males, females, first_four) |>
janitor::clean_names() |>
gt() |>
tab_spanner(label = 'Male', columns = c('bill_len', 'bill_dep')) |>
tab_spanner(label = 'Female', columns = c('bill_len_2', 'bill_dep_2')) |>
tab_spanner(label = 'M + F', columns = c('bill_len_3', 'bill_dep_3')) |>
cols_label(
bill_len_2 = md('*bill*_len'),
bill_dep_2 = 'bill_dep',
bill_len_3 = 'bill_len',
bill_dep_3 = 'bill_dep')
peng_tbl
``` |
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When trying to figure out what is not working, it's no longer about your end goal. In the end you get something small that exhibits the issue. |
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The following works: markdown + html + spanner. So what version of Quarto CLI and ---
title: Imaginary title
author:
- name: FirstName LastName
email: email@address
abstract: |
{{< lipsum 1 >}}
format:
elsevier-pdf: default
execute:
echo: false
warning: false
---
# Introduction
```{r}
#| label: r-libraries
library(gt)
data(penguins)
```
```{r}
#| label: tbl-data2
#| tbl-cap: This table show information for two variables.
#| tbl-pos: "!h"
gt(head(penguins, c(5L, 5L))) |>
tab_spanner(label = 'species_spanner', columns = c("species")) |>
cols_label(
island = html("<em>Island</em>"), # requires gt::as_raw_html() for Quarto to be able to process this into LaTeX/OpenXML, etc.
bill_len = md("**Bill Length (mm)**")
)
```
```{r}
#| label: tbl-data2
#| tbl-cap: This table show information for two variables.
#| tbl-pos: "!h"
gt(head(penguins, c(5L, 5L))) |>
tab_spanner(label = 'species_spanner', columns = c("species")) |>
cols_label(
island = html("<em>Island</em>"), # requires gt::as_raw_html() for Quarto to be able to process this into LaTeX/OpenXML, etc.
) |>
as_raw_html() # force Quarto to process the table as HTML because the table includes HTML
``` |
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The previous example you provided will not work for me if I render the document. If I run each chunk individually, I can see the table output if I omit the Quarto 1.6.42
attached base packages: other attached packages: loaded via a namespace (and not attached): |
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All my examples were executed and rendered fully using Quarto CLI. (I'm double checking them on a clean neutral environment) Unfortunately, if you use an outdated version of Quarto CLI, there is not much we can do. The current stable version is 1.7.32. (I did not add screenshots because they bring almost nothing while they decrease accessibility) |
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Ok, It has actually nothing to do with the Elsevier extension, the use of Markdown or HTML inside the table. ---
format: pdf
---
```{r}
#| label: tbl-label-matters
library(gt)
data(penguins)
gt(head(penguins, c(5L, 5L))) |>
tab_spanner(label = "species_spanner", columns = c("species")) |>
as_raw_html()
```(can't dive more into it now) |
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I thought you wanted me to run this and generate the log on my complex example from before. Code below generated the logs above. ---
title: Imaginary title
author:
- name: FirstName LastName
email: email@address
abstract: |
{{< lipsum 1 >}}
format:
elsevier-pdf: default
execute:
echo: false
warning: false
---
# Introduction
```{r}
#| label: r-libraries
library(gt)
data(penguins)
```
```{r}
#| label: tbl-data2
#| tbl-cap: This table shows information for two variables.
#| tbl-pos: "!h"
males <- penguins |>
dplyr::filter(island == 'Torgersen' & sex == 'male' & year == 2007) |>
head(c(4L, 4L))
females <- penguins |>
dplyr::filter(island == 'Torgersen' & sex == 'female' & year == 2007) |>
head(c(4L, 4L)) |>
dplyr::select(bill_len, bill_dep)
first_four <- penguins |>
dplyr::filter(island == 'Torgersen' & year == 2007) |>
head(c(4L, 4L)) |>
dplyr::select(bill_len, bill_dep)
peng_tbl <- cbind(males, females, first_four) |>
janitor::clean_names() |>
gt() |>
tab_spanner(label = 'Male', columns = c('bill_len', 'bill_dep')) |>
tab_spanner(label = 'Female', columns = c('bill_len_2', 'bill_dep_2')) |>
tab_spanner(label = 'M + F', columns = c('bill_len_3', 'bill_dep_3')) |>
cols_label(
bill_len_2 = html('<em>bill</em>_len'),
bill_dep_2 = 'bill_dep',
bill_len_3 = 'bill_len',
bill_dep_3 = 'bill_dep') |>
as_raw_html()
peng_tbl
```
|
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Bare with me, context matters. If you drop a log without giving the context it was produced just after saying "it works", expecting a reader to not link the two is unlikely. Try to remove pieces of your example, for instance start with edit: I built 1.6 and my example works there. It seems to be a parsing issue of the HTML table that shift. |
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For the version I have (1.6.42), it does not appear that
or
does not work. ---
format: pdf
---
# Introduction
```{r}
#| label: r-libraries
library(gt)
data(penguins)
```
```{r}
#| label: tbl-data2
#| tbl-cap: This table shows information for two variables.
#| tbl-pos: "!h"
males <- penguins |>
dplyr::filter(island == 'Torgersen' & sex == 'male' & year == 2007) |>
head(c(4L, 4L))
females <- penguins |>
dplyr::filter(island == 'Torgersen' & sex == 'female' & year == 2007) |>
head(c(4L, 4L)) |>
dplyr::select(bill_len, bill_dep)
first_four <- penguins |>
dplyr::filter(island == 'Torgersen' & year == 2007) |>
head(c(4L, 4L)) |>
dplyr::select(bill_len, bill_dep)
peng_tbl <- cbind(males, females, first_four) |>
janitor::clean_names() |>
gt() |>
tab_spanner(label = 'Male', columns = c('bill_len', 'bill_dep')) |>
tab_spanner(label = 'Female', columns = c('bill_len_2', 'bill_dep_2')) |>
tab_spanner(label = 'M + F', columns = c('bill_len_3', 'bill_dep_3')) |>
cols_label(
bill_len_2 = md('*bill_len*'))
peng_tbl
```
|
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As your example is still far too big despite your claim about For 1.7/1.8:
For 1.6:
The following will be using the latest version of Quarto CLI. ---
format: pdf
---
:::: {#tbl-label-matters}
```{r}
library(gt)
gt(head(penguins, c(5L, 5L))) |>
tab_spanner(label = "species_spanner", columns = "species") |>
as_raw_html()
```
This will crash 1.6 in addition to all previous requirements already listed
:::Looking at the intermediate markdown file which contain the HTML code for the table, trimming the table, I end up with the following that triggers the issue: ---
format: pdf
---
::: {#tbl-label-matters tbl-cap='this will crash 1.6 in addition to all previous requirements already listed'}
```{=html}
<table>
<thead>
<tr>
<th>species_spanner</th>
<th rowspan="2">island</th>
</tr>
<tr>
<th rowspan="1">species</th>
</tr>
</thead>
</table>
```
:::You can even go deeper with: ---
format: pdf
---
::: {#tbl-label tbl-cap='Caption'}
```{=html}
<table>
<thead>
<tr><th rowspan="2">island</th></tr>
<tr></tr>
</thead>
</table>
```
:::From this, to avoid LaTeX crash, do any:
|
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Thank you for trimming down to nice reprex ! |
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TL;DR from #13084 (reply in thread) ---
format: pdf
---
::: {#tbl-label tbl-cap='Caption'}
```{=html}
<table>
<thead>
<tr><th rowspan="2">island</th></tr>
<tr></tr>
</thead>
</table>
```
:::From this, to avoid LaTeX crash, do any:
|
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cc @cderv here is the "summary" if you want to take over. |
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Yes, Thank you for trimming down to nice reprex ! This is a bug to me: HTML table will be parsed by Quarto, and this will create some LaTeX in output, that seems to be invalid when used in crossref. If this is expected to not work, we should probably detect, and stop early. We do have support for rowspan, seeing the feature format matrix: https://github.com/quarto-dev/quarto-cli/blob/2f247767e6aa2eb62a4871c4e7ccff3ac1ac3641/dev-docs/feature-format-matrix/qmd-files/raw-html/cell/rowspan/document.qmd So the issue is really when trying to reference the table. |
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So the issue is that but not if the table is not crossreferenced So probably related to quarto-cli/src/resources/formats/pdf/pandoc/tables.tex Lines 6 to 8 in 2f24776 |
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Description
The code below uses the Elsevier journal extension (which must be installed) to create two tables. The first table created in a chunk labelled @tbl-data1 works as expected. The code for the second table labelled @tbl-data2 fails. The code for the second table is currently commented out using
{{r}}. The document below will render unless the code for the second table is changed to{r}.When I try to render both tables in the document, I get the following error:
ERROR:
compilation failed- error
Undefined control sequence.
l.207 \multirow
{2}{=}{\begin{minipage}[b]{\linewidth}\raggedright
The tables are made differently. Table 1 has one column under each header column. Table 2 has two columns under each header column, which seems to be causing the problem during rendering. Does anyone know a solution that will allow both tables to render?
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