Table in Bookdown/Huskydown with several features (Citation, Caption, URL, PNG Figure, ...) - r-markdown

Question

I would like to include a table in an R markdown document (Bookdown/Huskydown) which should meet the following requirements. Ideally, the table works with several output formats, e.g. LaTex/PDF and HTML.
Requirements:
Table width: fixed
Cell width: fixed
Vertical alignment: cell content aligned to the top
Text formatting: like bold or italics (best would be if md formatting supported, such that code is output agnostic) and allow for line breaks in longer texts
Citations: should be rendered
URLs: as clickable links both in HTML and LaTex/PDF
Figures: include
figures stored locally, either in
a markdown way ![](Rlogo.png) or
a knitr way knitr::include_graphics("Rlogo.png")
figures taken straight from the web
Caption for the table
Captions text formatting: caption should also allow for text formatting
Footnote: include footnotes in the table
Table numeration: tables are should be numerated
Referencing the table: in the document is needed
Notes regarding different approaches
Fixed cell width: in markdown the number of "-"s in table header determine cell width
Linebreaks:
LaTex:\\linebreak
All others: <br/>
Referencing
LaTex: add \label{foo} => \ref{foo} ( \#ref(foo))
Markdown: add Table: (\#tab:md-table) Caption==> \#ref(tab:md-table))
Comments on different approaches
Markdown: easy coding of tables in markdown
Kable & kableExtra: Versatile R markdown coding of the table, but vertical text alignment obscure and figures are not included in PDF
Pander: achieves the most, but no vertical alignment and footnotes
Huxtable: most promising, but figures are not included in PDF

Answer 1

This is less an answer than providing MWEs for the table shown above
```{r}
# create some random text
library(stringi)
some_text <- stri_rand_lipsum(1)
some_text <- substr(some_text, 1, 75)
# create dataframe with some stuff
figpath <- "figure/"
df <- data.frame(
Citation = c("#R-base", "#R-bookdown"),
Textfield = c("**Formatted** string<br/> -- _Everyone_ needs H^2^O", some_text),
URL = c("[R-url](https://www.r-project.org/)", "[bookdown](https://bookdown.org/)"),
fig_local_md = c(
paste0("![](", figpath, "Rlogo.png){ width=10% height=5% }"),
paste0("![](", figpath, "bookdownlogo.png){ height='36px' width='36px' }")
)#,
# not working:
# fig_local_knitr = c("knitr::include_graphics('figure/Rlogo.png')", "knitr::include_graphics('figure/bookdownlogo.png')")
)
# only include if output format is HTML, else pander throws error
if (knitr::is_html_output()) {
df$fig_web <- c("![](https://www.picgifs.com/glitter-gifs/a/arrows/picgifs-arrows-110130.gif)")
output_format <- "html"
}
if (knitr::is_latex_output()) {
output_format <- "latex"
}
```
markdown
Table: markdown table: markdown styling works in HTML (*italics*, **bold**), LaTex styling in PDF (\\textbf{bold})
| Image | Description |
| :--------------------------------------------------------- | :----------------------------------------------------------- |
| ![](figure/Rlogo.png){ width=10% height=5% } | **Image description** [#R-base] <br/>Lorem ipsum dolor sit amet, ... [R-url](https://www.r-project.org/) |
| ![](figure/bookdownlogo.png){ height='36px' width='36px' } | **Image description** [#R-bookdown] <br/>Lorem ipsum dolor sit amet, ... [bookdown](https://bookdown.org/) |
kable table
```{r kable-table, echo=FALSE, out.width='90%', fig.align = "center", results='asis'}
library(knitr)
kable(df,
caption = "kable table: markdown styling works in HTML (*italics*, **bold**), LaTex styling in PDF (\\textbf{bold})",
caption.short = "md styling works in HTML (*italics*, **bold**), LaTex styling in PDF (\\textbf{bold})"
)
```
kableExtra table
```{r kableExtra-table, echo=FALSE, out.width='90%', fig.align = "center", results='asis'}
library(kableExtra)
# http://haozhu233.github.io/kableExtra/awesome_table_in_pdf.pdf
kable(
df,
caption = "kableExtra table: markdown styling works in HTML (*italics*, **bold**), LaTex styling in PDF (\\textbf{bold})",
output_format, booktabs = T, # output_format = latex, html (specify above)
# align = "l",
valign = "top"
) %>%
kable_styling(full_width = F,
latex_options = c(#"striped",
"hold_position", # stop table floating
"repeat_header") # for long tables
) %>%
column_spec(1, bold = T, border_right = T, width = "30em") %>%
column_spec(2, width = "50em") %>%
column_spec(3, width = "5em") %>%
column_spec(4, width = "10em") %>%
column_spec(5, width = "10em") %>%
footnote(general = "Here is a general comments of the table. ",
number = c("Footnote 1; ", "Footnote 2; "),
alphabet = c("Footnote A; ", "Footnote B; "),
symbol = c("Footnote Symbol 1; ", "Footnote Symbol 2"),
general_title = "General: ", number_title = "Type I: ",
alphabet_title = "Type II: ", symbol_title = "Type III: ",
footnote_as_chunk = T, title_format = c("italic", "underline")
)
```
pander table
```{r pander-table, echo=FALSE, out.width='90%', fig.align = "center", results='asis'}
library(pander)
# https://cran.r-project.org/web/packages/pander/vignettes/pandoc_table.html
pander(
df,
caption = "pander table: markdown styling works in HTML and PDF (*italics*, **bold**), LaTex styling in PDF (\\textbf{bold})",
# style = "multiline", # simple
split.table = Inf, # default = 80 characters; Inf = turn off table splitting
split.cells = c(15, 50, 5, 5, 5), # default = 30
# split.cells = c("25%", "50%", "5%", "10%", "10%"), # no difference
justify = "left"
)
```
huxtable table
```{r huxtable-table, echo=FALSE, out.width='90%', fig.align = "center", results='asis'}
library(dplyr)
library(huxtable)
# https://hughjonesd.github.io/huxtable/
hux <- as_hux(df) %>%
# huxtable::add_rownames(colname = '') %>%
huxtable::add_colnames() %>%
set_top_border(1, everywhere, 1) %>%
set_bottom_border(1, everywhere, 1) %>%
set_bottom_border(final(), everywhere, 1) %>%
set_bold(1, everywhere, TRUE) %>% # bold headlines
set_italic(-1, 1, TRUE) %>% # italics in first column (except the first row)
set_valign("top") %>%
set_width(1) %>%
set_col_width(c(0.10,0.45,0.05,0.10,0.10)) %>%
set_wrap(TRUE) %>%
set_position('left') %>% # fix table alignment (default is center)
add_footnote("Sample Footnote") %>%
set_font_size(4)
table_caption <- 'huxtable table: markdown styling works in HTML (*italics*, **bold**), LaTex styling in PDF (\\textbf{bold})'
# Print table conditional on output type
if (knitr::is_html_output()) {
caption(hux) <- paste0('(#tab:huxtable-table-explicit) ', table_caption)
print_html(hux) # output table html friendly (requires in chunk options "results='asis'")
}
if (knitr::is_latex_output()) {
caption(hux) <- paste0('(\\#tab:huxtable-table-explicit) ', table_caption)
hux # if using chunk option "results='asis'" simply output the table with "hux", i.e. do not use print_latex(hux)
}
```
Referencing the tables
works differently for different table types
Adding a short caption for the LoT
Finally adding a short caption for the table of figures is not really working as desired
(ref:huxtable-table-caption) huxtable-table caption
(ref:huxtable-table-scaption) huxtable-table short caption
```{r huxtable-table, echo=FALSE, out.width='90%', fig.align = "center", fig.cap='(ref:huxtable-table-caption)', fig.scap='(ref:huxtable-table-scaption)', results='asis'}
...
```