I've created tables in Rmarkdown using xtable.
I need to convert them to either .doc or .rtf in order to submit to a journal.
I can successfully convert to .html and .pdf but when I convert these formats to .doc or .rtf, the nice equation formatting disappears.
I've tried opening the files in word and converting to .rtf. Is there a way to do this without re-doing the tables entirely? I am fairly new to Markdown and Pandoc.
Here is the reproducible code.
---
title: ''
output:
html_document:
df_print: paged
pdf_document:
fig_caption: yes
keep_tex: yes
latex_engine: xelatex
header-includes:
- \usepackage{lineno}
- \linenumbers
---
```{r, results='asis', echo=FALSE}
library(xtable)
Parameter <- c("T","V","$i$")
Definition <- c("Temperature (C)","Velocity (cm/s)","Prey class within $I$ 1 mm bins")
Method <- c("Field data","Field data","$EC = SC + MC$","$NEI = GEI - EC$")
Reference <-c("","", [1,2]")
table1_df <- cbind.data.frame(Parameter, Definition,Method,Reference)
table1 <- xtable(table1_df, include.rownames=FALSE, caption="This should be a pretty table")
print(table1, comment=FALSE, include.rownames=FALSE, caption.placement="top",size="\\fontsize{9pt}{10pt}\\selectfont", sanitize.text.function=function(x){x}, type="html")
```
Related
I'm trying to generate Greek letters in the axis labels or titles of plots in an RMarkdown file that is generating a PDF. When I run the code the editor or in the console, I see the letter fine, but when the PDF is generated, they disappear. In the short example below, I can see that the subscript operation is working but the Greek letter theta isn't present.
I've tried changing the Typeset LaTeX in PDF using: option - I have pdfLaTeX and XeLaTex - but I see no difference.
---
title: "Untitled"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
plot(1:100, 1:100, xlab = expression(theta[5]))
plot(1:100, 1:100, xlab = expression('theta'[5]))
```
I was using Latin modern font and came across the same problem. The following code fixed it for me. Make sure the math library for the font you are using is called for.
---
title: "Untitled"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r, fig.showtext=TRUE}
library("showtext")
font_add("LM Roman 10", regular = "/usr/share/texmf/fonts/opentype/public/lm/lmroman10-regular.otf")
font_add("LM Roman 10", regular = "/usr/share/texmf/fonts/opentype/public/lm-math/latinmodern-math.otf")
plot(1:100, 1:100, xlab = expression(theta[5]))
```
I'm using RMarkdown to create Supplementary documents for a paper. These supplements contain many tables. Let's call these documents Supplement A and Supplement B. I want the table numbering to reflect the supplement letter, that is, Table A1 or Table 1A for the first table in Supplement A and so on for all tables.
How can I modify the table numbering to add a letter into the table numbering schema?
Here's an example that will produce a table with normal numbering:
---
title: "Supplement A"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(knitr)
library(kableExtra)
```
```{r cars}
kable(mtcars[1:5, ], booktabs=TRUE, caption="MTCars") %>%
kable_styling(latex_options="hold_position", position="left")
```
An inelegant solution using the captioner package (details provided here: https://datascienceplus.com/r-markdown-how-to-number-and-reference-tables/) can create captions and insert them manually just before the code chunk. Combining this with the Latex package caption makes it possible to remove the automatic table naming and numbering if the caption is generated within the code chunk (How to suppress automatic table name and number in an .Rmd file using xtable or knitr::kable?). I've done this in the YAML with \captionsetup[table]{labelformat=empty}, but it can be done in the document body also. Either way, the caption can then be generated within the code chunk, which was important in my case.
This solution stops bookdown referencing from working (because labelformat cannot be empty), but a workaround for table referencing was provided in the link for using the captioner package (and is included below).
---
title: "Supplement A"
header-includes:
- \usepackage{caption}
\captionsetup[table]{labelformat=empty}
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(knitr)
library(kableExtra)
library(captioner)
library(stringr)
```
```{r captions}
# Create the caption(s)
caption <- captioner("Table A", FALSE)
tab_1_cap <- caption("Tab_1", "MTCars")
# Create a function for referring to the tables in text
ref <- function(x) str_extract(x, "[^:]*")
```
The following table is `r ref(tab_1_cap)`.
```{r cars}
kable(mtcars[1:5, ], booktabs=TRUE, caption=tab_1_cap) %>%
kable_styling(latex_options="hold_position", position="left")
```
An alternative solution is avaiable via LaTeX. Add the following somewhere in the body of the document to change the default figure and table names to include the letter.
\def\figurename{Figure A}
\def\tablename{Table A}
To reference a table or figure in text use, e.g., Table A\#ref(tab:label), after defining the table label as normal.
This alone will leave a space in the table/figure caption (e.g., 'Table A 1' instead of 'Table A1'). This can be solved by adding the following to the YAML:
header-includes:
- \usepackage{caption}
- \DeclareCaptionLabelFormat{nospace}{#1#2}
- \captionsetup[figure]{labelformat=nospace}
- \captionsetup[table]{labelformat=nospace}
The \DeclareCaptionLabelFormat creates a function (here labeled nospace), which overrides the default caption label when called. #1 represents the label assigned to refer to tables or figures (e.g., 'Table A') and #2 represents the number of the table or figure. The captionsetup lines change the label format for all tables and figures to the format defined by 'nospace'.
Thus, the code produces, e.g., 'Table A1: Table name' as the caption. If instead you wanted, e.g., 'Table A-1: Table name', the code in \DeclareCaptionLabelFormat should be changed to {#1-#2}.
---
title: "Supplement A"
output: bookdown::pdf_document2
toc: false
header-includes:
- \usepackage{caption}
- \DeclareCaptionLabelFormat{nospace}{#1#2}
- \captionsetup[figure]{labelformat=nospace}
- \captionsetup[table]{labelformat=nospace}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(knitr)
library(kableExtra)
library(bookdown)
```
\def\figurename{Figure A}
\def\tablename{Table A}
See Table A\#ref(tab:cars) for something about cars.
(ref:cars) Table caption
```{r cars}
kable(mtcars[1:5, ], booktabs=TRUE, caption="(ref:cars)") %>%
kable_styling(latex_options="hold_position", position="left")
```
Answer inspired by: Figure name in caption using RMarkdown
Caption latex package documentation: https://ctan.org/pkg/caption
I cannot get two simple highcharter charts in an Rmarkdown file I want to share. It works fine and renders in my PC or Mac, but when I share the file, people only see text.
They are not part of a loop, as mentioned in few articles. They are just two charts. For the reproducible example, I literally just opened a new rmarkdown doc and selected html. I replaced the "summary table" of cars with highcharter code. I even tried htmltools::tagList(chart1, chart2) and it does not work.
I am supplying the code. If you please show me how to do it with one chart, I can do it with the second.
Thank you.
---
title: "Untitled"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```{r echo=FALSE}
library(magrittr)
library(highcharter)
highchart() %>%
hc_add_series(cars, type = "scatter", hcaes(speed, dist))
I apologize if the tick marks hide the code background, but the three chunks are wrapped with the three tickmarks at the beginning and end of each chunk.
Thank you again.
Yes the code below produces the file below the code. I now have an entire .html file that has the highchart self contained in the file.
---
output:
html_document:
self_contained: yes
mode: selfcontained
---
{r echo=FALSE}
library(magrittr)
library(highcharter)
highchart() %>%
hc_add_series(cars, type = "scatter", hcaes(speed, dist))
I would like to show, in an rmarkdown document, the printed output of a tibble as shown in the console. i.e.
First line: dimension summary;
then the column headers;
then classes of variables;
then first 10 lines of the tibble;
then number of rows not shown.
However, by default, tibbles and other data.frame objects are automatically converted to a tabbed, paginated table showing all contents.
I note that the option to turn off this default behaviour can be set for a whole markdown document by changing the df_print option to tibble in the YAML.
However, how do I set the df_print option to tibble for just a single R code chunk, so that I can show in an Rmarkdown document what the user will see on the console?
Thanks,
Jon
There's no need to touch the global setting. You can explicitly call the print function tibble:::print.tbl_df(df)
Example:
title: "Untitled"
author: "TC"
date: "7/27/2018"
output:
html_document:
df_print: "kable"
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## print tibble
```{r}
df <- tibble::as.tibble(mtcars)
tibble:::print.tbl_df(head(df))
```
## print kable (set in YAML header)
```{r}
head(df)
```
output html
Here is my example:
---
title: "There is a reproductible example"
output: pdf_document
---
```{r table-simple, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'}
require(pander)
panderOptions('table.split.table', Inf)
set.caption("My great data")
my.data <- " # replace the text below with your table data
Anticonstitutionnellement|Anticonstitutionnellement|Anticonstitutionnellement|Anticonstitutionnellement|Anticonstitutionnellement
Anticonstitutionnellement|Anticonstitutionnellement|Anticonstitutionnellement|Anticonstitutionnellement|Anticonstitutionnellement
Anticonstitutionnellement|Anticonstitutionnellement|Anticonstitutionnellement|Anticonstitutionnellement|Anticonstitutionnellement
Anticonstitutionnellement|Anticonstitutionnellement|Anticonstitutionnellement|Anticonstitutionnellement|Anticonstitutionnellement "
df <- read.delim(textConnection(my.data),header=FALSE,sep="|",strip.white=TRUE,stringsAsFactors=FALSE)
names(df) <- unname(as.list(df[1,])) # put headers on
df <- df[-1,] # remove first row
row.names(df)<-NULL
pander(df, style = 'rmarkdown')
```
In the final PDF outputs, Words overlap.
I use "kable", "table", "print"
Do you have an idea that the words do not overlap?
If the table is very huge, I want that the table rotate automatically in landscape format. Is it possible?
You could try to add the option:
classoption: landscape
in your head section
---
title: "There is a reproductible example"
output: pdf_document
classoption: landscape
---
This will produce a landscape version of the document.