Different behavior between pdf_document and bookdown::pdf_document2 when using compareGroups
I am having an issue when knit-ing documents using bookdown::pdf_document2 that don't appear when using the standard pdf_document.
Specifically, I am using the compareGroups library and the export2md function to output comparison tables such as the one shown below:
This is successful when I use output:pdf_document. However, The table is not properly created when I use output: bookdown:pdf_document2.
There are clearly differences in the tex files and I am manually able to copy the table from the tex outputed by pdf_document to pdf_document2. Does anyone have any thoughts on how to get bookdown to correctly create the table? I have create a repo with my bug found here for more details: https://github.com/vitallish/bookdown-bug
Overview
bookdown::pdf_document2() is different from rmarkdwon::pdf_document(), the former set $opts_knit$kable.force.latex to TRUE while the latter leaves that to default value (FALSE).
check .md file
I think that the process from .md to .tex should be the same, and the difference in .tex files might due to the difference in .md files. So I run the following code to keep the intermediate .md files.
rmarkdown::render('pdf_document.Rmd', clean = FALSE)
file.remove('pdf_document.utf8.md');
rmarkdown::render('pdf_document2.Rmd', clean = FALSE)
file.remove('pdf_document2.utf8.md');
pdf_document.knit.md
Table: Summary descriptives table by groups of `Sex'
Var Male N=1101 Female N=1193 p.overall
----------------------------------------------- --------------- ----------------- -----------
Recruitment year: 0.506
1995 206 (18.7%) 225 (18.9%)
2000 390 (35.4%) 396 (33.2%)
2005 505 (45.9%) 572 (47.9%)
Age 54.8 (11.1) 54.7 (11.0) 0.840
Smoking status: <0.001
Never smoker 301 (28.1%) 900 (77.5%)
Current or former < 1y 410 (38.3%) 183 (15.7%)
Former >= 1y 360 (33.6%) 79 (6.80%)
Systolic blood pressure 134 (18.9) 129 (21.2) <0.001
Diastolic blood pressure 81.7 (10.2) 77.8 (10.5) <0.001
pdf2_document.knit.md
\begin{table}
\caption{(\#tab:md-output)Summary descriptives table by groups of `Sex'}
\centering
\begin{tabular}[t]{l|c|c|c}
\hline
Var & Male N=1101 & Female N=1193 & p.overall\\
\hline
Recruitment year: & & & 0.506\\
\hline
\ \ \ \ 1995 & 206 (18.7\%) & 225 (18.9\%) & \\
\hline
\ \ \ \ 2000 & 390 (35.4\%) & 396 (33.2\%) & \\
\hline
\ \ \ \ 2005 & 505 (45.9\%) & 572 (47.9\%) & \\
\hline
Age & 54.8 (11.1) & 54.7 (11.0) & 0.840\\
\hline
Smoking status: & & & <0.001\\
\hline
\ \ \ \ Never smoker & 301 (28.1\%) & 900 (77.5\%) & \\
\hline
\ \ \ \ Current or former < 1y & 410 (38.3\%) & 183 (15.7\%) & \\
\hline
\ \ \ \ Former >= 1y & 360 (33.6\%) & 79 (6.80\%) & \\
\hline
Systolic blood pressure & 134 (18.9) & 129 (21.2) & <0.001\\
\hline
Diastolic blood pressure & 81.7 (10.2) & 77.8 (10.5) & <0.001\\
\hline
\end{tabular}
\end{table}
That explains why you see different appearance in the pdf output.
explore
To further explore the reason,
> pdf1 <- rmarkdown::pdf_document()
> pdf2 <- bookdown::pdf_document2()
> all.equal(pdf, pdf2)
[1] "Length mismatch: comparison on first 11 components"
[2] "Component “knitr”: Component “opts_knit”: target is NULL, current is list"
[3] "Component “pandoc”: Component “args”: Lengths (8, 12) differ (string compare on first 8)"
[4] "Component “pandoc”: Component “args”: 8 string mismatches"
[5] "Component “pandoc”: Component “ext”: target is NULL, current is character"
[6] "Component “pre_processor”: target, current do not match when deparsed"
[7] "Component “post_processor”: target is NULL, current is function"
Since knitr convert Rmarkdown to pandoc markdown, I guess $knitr cause the difference in .md files.
> all.equal(pdf$knitr, pdf2$knitr)
[1] "Component “opts_knit”: target is NULL, current is list"
> pdf2$knitr$opts_knit
$bookdown.internal.label
[1] TRUE
$kable.force.latex
[1] TRUE
kable is a function to output table, so $knitr$opts_knit$kable.force.latex might to the root reason.
verify
To test my assumption,
pdf3 <- pdf2
pdf3$knitr$opts_knit$kable.force.latex = FALSE
rmarkdown::render('pdf_document3.Rmd', clean = FALSE, output_format = pdf3)
file.remove('pdf_document3.utf8.md')
pdf_document3.knit.md
Var Male N=1101 Female N=1193 p.overall
----------------------------------------------- --------------- ----------------- -----------
Recruitment year: 0.506
1995 206 (18.7%) 225 (18.9%)
2000 390 (35.4%) 396 (33.2%)
2005 505 (45.9%) 572 (47.9%)
Age 54.8 (11.1) 54.7 (11.0) 0.840
Smoking status: <0.001
Never smoker 301 (28.1%) 900 (77.5%)
Current or former < 1y 410 (38.3%) 183 (15.7%)
Former >= 1y 360 (33.6%) 79 (6.80%)
Systolic blood pressure 134 (18.9) 129 (21.2) <0.001
Diastolic blood pressure 81.7 (10.2) 77.8 (10.5) <0.001
Wa oh!
Advanced
Actually compareGroups::export2md use knitr::kable as the working horse,
> compareGroups::export2md
function (x, which.table = "descr", nmax = TRUE, header.labels = c(),
caption = NULL, ...)
{
if (!inherits(x, "createTable"))
stop("x must be of class 'createTable'")
...
if (ww %in% c(1)) {
...
table1 <- table1[-1, , drop = FALSE]
return(knitr::kable(table1, align = align, row.names = FALSE,
caption = caption[1]))
}
if (ww %in% c(2)) {
table2 <- prepare(x, nmax = nmax, c())[[2]]
...
return(knitr::kable(table2, align = align, row.names = FALSE,
caption = caption[2]))
}
}
which use kable.force.latex as an internal option to adjust its output. If your browse the GitHub repository of knitr, you can find the following code in the R/utils.R file
kable = function(
x, format, digits = getOption('digits'), row.names = NA, col.names = NA,
align, caption = NULL, format.args = list(), escape = TRUE, ...
) {
# determine the table format
if (missing(format) || is.null(format)) format = getOption('knitr.table.format')
if (is.null(format)) format = if (is.null(pandoc_to())) switch(
out_format() %n% 'markdown',
latex = 'latex', listings = 'latex', sweave = 'latex',
html = 'html', markdown = 'markdown', rst = 'rst',
stop('table format not implemented yet!')
) else if (isTRUE(opts_knit$get('kable.force.latex')) && is_latex_output()) {
# force LaTeX table because Pandoc's longtable may not work well with floats
# http://tex.stackexchange.com/q/276699/9128
'latex'
} else 'pandoc'
if (is.function(format)) format = format()
...
structure(res, format = format, class = 'knitr_kable')
}
Conclusion
$knitr$opts_knit$kable.force.latex = TRUE cause bookdown::pdf_document2() to insert latex code in the .md file, while rmarkdown::pdf_document() preserves the markdown code, which leaves pandoc the chance to give a pretty table.
I don't think this is a bug. Yihui Xie (the author of bookdown) might have some special reason to do this. And bookdown::pdf_document2() never need to be the same as rmarkdown::pdf_document().
- Order() in R - argument is missing, with no default
- How to plot geom_bar without showing multiple lines
- R: speeding up "group by" operations
- How to manipulate NetCDF-4 groups in R?
- How to convert categorial raster to mapped RGB values in R?
- How to add a hover-over tooltip to rhandonstable header cell?
- How to detect the right encoding for read.csv?
- Rcpp Rf_warningcall compiler warnings
- Modify the name of factor variables in lm function(summary function)
- Extreme value analysis and quantile estimation using log Pearson type 3 (Pearson III) distribution - R vs Python
- How to hide NAs when using xlsx::saveWorkbook?
- How do I retrieve a simple numeric value from a named numeric vector in R?
- Adding an image in navbar and adjusting alignment in Rmarkdown
- Matching pair-wise columns from left to right across rows in one dataframe to another dataframe and adding new columns with matching values
- Income to outcome flow chart in Sankey plotly R
- color mapping in geom_conn_bundle not showing correctly
- Print R package startup message AFTER automatic package conflict messages instead of before
- Summing a set of R dataframe rows (column-wise), while retaining the first n columns
- Added variable / partial regression plots for groups in an interaction?
- how to make a topoplot in R with coordinates variable distribution
- List of all functions in base R?
- Plotting multiple plots for different initial conditions in one graph
- Printing repetitively on the same line in R
- Generating UI/Server based on initial selection
- Subset dataframe based on pickerInput
- How to let user pick the data in R-shiny?
- Couldn't show my simple bar charts separately on Shiny R dashboardBody
- How to programmatically filter contents of a second shiny app displayed via iframe
- How to select specific interesting groups for the boxplot in R Shiny app?
- Crosstable and Plot grouping with reactive values