I use RMarkdown and would like to source multiple .R files before knitting the document. I split my .R files into "read.R" and "calc.R", but rmarkdown returns an error with this method. However if I combine read.R and calc.R into a single file ("combined.R") it runs with no problem.
Here's what I'd like to do.
Read this data in one .R file.
# Read.R
game <- c(1,2,3,4,5)
royals <- c(5,7,3,5,7)
mets <- c(4,1,9,3,2)
data <- data.frame(game,royals,mets)
Then calc in another .R file.
# Calc.R
data$winner <- ifelse(data$royals>data$mets,"royals","mets")
Then run rmarkdown. This doesn't work (sourcing separate files)...
---
title: "rmd_test"
author: "me"
date: "Monday, November 02, 2015"
output: word_document
---
```{r}
source("read.R")
source("calc.R")
print(data)
```
But sourcing a single combined file does...
# Combined.R
# Read data
game <- c(1,2,3,4,5)
royals <- c(5,7,3,5,7)
mets <- c(4,1,9,3,2)
data <- data.frame(game,royals,mets)
# Calc
data$winner <- ifelse(data$royals>data$mets,"royals","mets")
Here's the same rmarkdown file sourcing a single combined.R file.
---
title: "rmd_test"
author: "me"
date: "Monday, November 02, 2015"
output: word_document
---
```{r}
source("combined.R")
print(data)
```
I would like to split the files because my "read.R" files are fairly generic and stable, but the "calc.R" changes and is variable. So it is more convenient to split the two.
If you want to share code between different scripts or even projects. You should consider to put this in a separate package. While this is truly more effort at the beginning, this might pay off later, when your projects are growing or you want to share your code with others.
If you are a "R-package" newbie (like me), there is a very good book by Hadley Wickham available online: http://r-pkgs.had.co.nz/
Related
I would love a convenient and easy way to print my word count automatically in quarto and stumbled across this nice add-in from Ben Marwick:
https://github.com/benmarwick/wordcountaddin
It is sound for rmarkdown and I presumed it should be no issue with quarto too. However, when I use the add-in, though it can count out the number of words within my RStudio session, it doesn't print it in my final pdf format and just returns [1] NA.
{r, #wordcountdev, message = FALSE, warning = FALSE, echo = FALSE}
wordstats <- wordcountaddin:::text_stats('CMI Write Up.qmd')
words <- substr(wordstats[3], start=19, stop=30)
print(words)
I don't understand what is going on here, it is seemingly simple, would anyone know of a better way to achieve what I'm trying?
You could take a look at the wordcounts pandoc filter, e.g. as a starting point it prints the number of words in the body to the console while rendering:
---
format: html
filters: [wordcounts.lua]
---
Hello there, how many words are in the body?
Or: You can use the development version (devtools::install_github("benmarwick/wordcountaddin", type = "source", dependencies = TRUE)) of the above mentioned package:
---
format: html
---
```{r}
#| echo: false
#| label: wordstats
#| warning: false
#| message: false
wordcount <- wordcountaddin::text_stats('wordcount.qmd')
words <- substr(wordcount[3], start=19, stop=30)
```
Hello there, how many words are in the body?
There are `r words` words in the whole document.
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$set(echo = TRUE)
```
```{r, include = FALSE}
library(flextable)
library(dplyr)
table2 <- flextable(mtcars[1:5, 1:6])
```
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
\begin{table}[hbtp]
\captionof{table}{Text of the caption.}
\label{tab:caption}
`r table2`
\end{table}
Table \ref{tab:caption} is the baddest table in the World
I cannot get two simple highcharter charts in an Rmarkdown file I want to share. It works fine and renders in my PC or Mac, but when I share the file, people only see text.
They are not part of a loop, as mentioned in few articles. They are just two charts. For the reproducible example, I literally just opened a new rmarkdown doc and selected html. I replaced the "summary table" of cars with highcharter code. I even tried htmltools::tagList(chart1, chart2) and it does not work.
I am supplying the code. If you please show me how to do it with one chart, I can do it with the second.
Thank you.
---
title: "Untitled"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$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))
Due to different journal requirements, I need to frequently change certain text styles within Rmarkdown from one kind to another. For instance, here is an example Rmarkdown document.
---
title: "Changing format of Rmarkdown"
author: "Paul Hargarten"
date: "5/9/2019"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an $\mathcal{R}$ Markdown document. Markdown is a simple formatting syntax for authoring **HTML**, **PDF**, and **MS Word* documents. For more details on using $\mathcal{R}$ Markdown see <http://rmarkdown.rstudio.com>. $\matcal{R}$ is based on $\mathcal{S}$.
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. Calculate a `summary` as follows:
```{r cars}
summary(cars)
```
## Including Plots
You can also embed plots, for example: `r plot(pressure)`.
Without searching for the exact phrase, suppose that I would like to find and replace the following items:
1. Change items in bold ** ... ** to italics _ ... _.
2. Change items that look like $\mathcal{ ... }$ to bold ** ... **.
3. Change special font `...`, except those that start with r, to \code{ ... }.
4. Add dollar signs to `r ... ` => $`r ... `$.
Is this possible to use regex to make these formatting style changes in
Rmarkdown? Thanks!
This is something that LaTeX is good at, but it will be harder with Markdown.
If you were entirely in LaTeX, you could define your own macros based on the uses for that markup. For example,
\newcommand{\booktitle}[1]{\textbf #1}
used for book titles as \booktitle{The Book}. If you wanted to switch book titles to italic, you'd just change that definition.
Doing this in R Markdown is possible, but you wouldn't be able to mark book titles using **. You could do it (you can embed LaTeX in R Markdown), but it's ugly. For example,
---
title: Using LaTeX
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
\newcommand{\booktitle}[1]{\textbf{#1}}
This is \booktitle{The Book}.
Once you're doing this, you might as well switch to Sweave-like *.Rnw format, or all the way to LaTeX.
I want to write about the binomial distribution in a rmd document but I cannot work out how to represent the large bracket which surround two values written above one another. (Reads x choose y)
Any thoughts?
Tried various configurations of "choose" and "binom" but no joy.
Using RStudio, this is what my .Rmd file looks like:
---
title: "Untitled"
author: "sahir"
date: "March 12, 2015"
output: html_document
---
$$P(X \leq k) = \sum_{y \leq k} \binom{n}{y} p^y (1-p)^{n-y}$$