One of cells in my RMarkdown document
```{r echo=FALSE}
head(data,3) %>% knitr::kable(caption = "Pierwsze 3 wiersze ze zbioru danych Lista_1.csv", digits = 2, booktabs = T)
gives weird result after knitting to pdf:
Of course there shouldn't be "\begin{table}" ,"\caption{}" and "\end{table}" parts. I use knitr::kable often and it never worked this way. Does anyone know how to fix it?
Edit: I have also noticed that all section headers (like "##Section2") below the table are centered. They shouldn't.
I've just found this question: How do I prevent kable from leaving raw latex in the final document if I include a caption in a table?
and used tip from comment (format = pandoc). It worked for me.
Related
I am pretty new in R markdown and while creating a report "I like to hide data parsing code"
I have tried "echo=FALSE", but it does not doing the job in this particular case.
Any help would be much appreciated.
**Data Parsing**
```{r echo=FALSE}
library(ggplot2)
library(readr)
SU1 <- read_csv("......./SU.csv")
I like to hide the below chunk in the report
Thanks
Thanks.In fact i was able to solve it by adding Message= FALSE.
I am currently writing my thesis in RMarkdown using the template Oxforddown (which is ultimately based on bookdown). I have been reading the documentation but I confess I am lost. I am trying to create a table that contains an overview of the experimental conditions and items I used in my empirical study, so it is not data that I can load into R and then use the kable function on. However, I do not understand how I could generate such a table. Generating RMarkdown tables outside code chunks seems to work, but then the captions and referencing are very different than the rest of the captions used so far, which I usually set up within code chunks. Example below:
{r pilot-short7, echo=FALSE, fig.scap="Pilot 2: ....", out.width="65%", message=FALSE, fig.pos='H', fig.align = 'center'}
When I am trying to include RMarkdown tables inside a code chunks, things go wrong. What would my options be?
Any help would be very much appreciated!
I prepared a markdown template for you.
Here I made a table with flextable library.
But you can use another, which you like, f.e.: kableExtra, gt etc.
As you can see, you should put \label{tab:caption} and after refer in the text by \ref{tab:caption}.
---
title: "Hello World"
header-includes:
- \usepackage{caption}
output:
pdf_document:
latex_engine: xelatex
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r, include = FALSE}
library(flextable)
library(dplyr)
table2 <- flextable(mtcars[1:5, 1:6])
```
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
\begin{table}[hbtp]
\captionof{table}{Text of the caption.}
\label{tab:caption}
`r table2`
\end{table}
Table \ref{tab:caption} is the baddest table in the World
I would like to keep all the columns of the summary output in same line, do you have a solution?
as shown in the picture, the last column goes to a new line, how to avoid it?
Thanks a lot in advance!
Without a code example, I can't help edit the code. In your Rmarkdown initial set up chunk, put the code below
```
{r setup}
knitr::opts_chunk$set(echo = TRUE)
options(width = 1000)
```
the width = 1000 will need to be adjusted to meet your needs.
here is a link that might help you get more information
In R markdown when using Beamer slides if you try to plot you need to specify the plot sizes (unlike in the reports) so that the plots fit on a page. This can often result in the plots appearing to be squashed together, as apposed to just a smaller version of the plot.
Is there some method to change the default slide size to alleviate this problem?
I have tried
header-includes:
- \usepackage[papersize={25.6cm,19.2cm}]{geometry}
in the yaml header, and I get the error
! LaTeX Error: Missing \begin{document}.
Using R Markdown I shouldn't need to use this though.
A reproducible example is shown below
---
title: "Plots look bad"
author: "Beavis"
date: "`r format(Sys.time(), '%d/%m/%Y')`"
output: beamer_presentation
header-includes:
- \usepackage{float}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
knitr::opts_chunk$set(results = 'hide')
knitr::opts_chunk$set(warning = FALSE)
knitr::opts_chunk$set(cache=TRUE)
knitr::opts_chunk$set(fig.height=3.5)
```
# Introduction
```{r}
pca <- prcomp(iris[,1:4])
biplot(pca)
```
Here, you if you run this the second slide looks like this As you can see the plot is rubbish. What is the best way to avoid this problem?
The biplot function uses par(pty = "s") to force a square plot, so it's not going to fill a rectangular slide. You can make it look better by asking the fig.height to be bigger, but then it will overflow the bottom of the slide. To prevent this, you can set both fig.height to a large number, and out.height (which will be a LaTeX measurement) to something that will fit on a slide. For example, using this chunk
```{r fig.height=10, out.height="0.8\\textheight"}
pca <- prcomp(iris[,1:4])
biplot(pca)
```
I see this output:
I'd recommend a smaller fig.height, but your preference may be different.
Both fig.height and out.height could be specified using knitr::opts_chunk$set as defaults for all slides if you want.
You could also specify out.width="\\textwidth" for a really ugly stretched plot that fills the slide, but I wouldn't recommend it.
I am using captioner (https://cran.r-project.org/web/packages/captioner/vignettes/using_captioner.html) to create table captions in Rmarkdown - the main reason is because I am using huxtable for conditional formatting and exporting to word. This is the only I have found to have numbered captions.
I was trying to reference the captions but the caption number is not in sequential order when citing the captions but only if the table_nums(..., display="cite") is before the tables. I was trying to give the range of table numbers and it changed the number of the last table. I The number isn't changed if the r table_nums('third_cars_table',display = "cite") is put after the captions. Is there a way to make sure that table numbers remain in sequential order? I'd also be happy with a better solution for numbered captions.
Reproducible example:
---
title: "Untitled"
output: bookdown::word_document2
---
```{r setup, include=FALSE}
library(captioner)
library(huxtable)
library(knitr)
library(pander)
table_nums <- captioner(prefix = "Table")
fig_nums <- captioner(prefix = "Figure")
knitr::opts_chunk$set(echo = TRUE)
```
## Description of tables
I am trying to put a description of tables
and say that these results are shown table numbers ranging
from the first table (`r table_nums('first_cars_table',display = "cite")`)
to the last table (`r table_nums('third_cars_table',display = "cite")`)
```{r, results='asis',echo=FALSE,eval.after=TRUE}
tablecap1=cat(table_nums(name="first_cars_table",caption='First car table'))
kable((cars[1:5,]))
tablecap2=cat(table_nums(name="second_cars_table",caption='second car table'))
kable(cars[6:10,])
tablecap3=cat(table_nums(name="third_cars_table",caption='third car table'))
kable(cars[10:15,])
```
The results:
A (terrible) workaround is to manually give the number ordering using display = FALSE. For example, inserting the following at the start of the document will ensure t1-t5 are sequentially numbered, no matter where the tables or first citations appear:
`r table_nums('t1', display = FALSE)`
`r table_nums('t2', display = FALSE)`
`r table_nums('t3', display = FALSE)`
`r table_nums('t4', display = FALSE)`
`r table_nums('t5', display = FALSE)`
I have not examined the captioner code but I expect that the document is read from top to bottom once and hence the numbering is stored in a first come, first served basis. Thus, I am not sure there are any other ways to get around this as it would involve some kind of pre-processing stage.