So basically I have been writing a paper in Rmarkdown. The paper includes an abstract which has numbers/results that are generated from the code chunks within the markdown itself. Up to now, the workaround has been to place the abstract at the end of the paper, so that all the code chunks are run and the results generated before they are needed in the abstract.
Now that I am actually working on the final drafts, It would be ideal to have the abstract in the beginning. Is this even possible?
Thank you!
If your values won't change from run to run, one option is to use knitr::load_cache to load values from the cache of later chunks in your abstract section. The main downside is that this will only work on the second time knitting the document. The first time, load_cache will give NULL, then the later chunk will be run and the value cached. The second time, the cache will exist and will be used in the abstract.
```{r abstract}
y = knitr::load_cache('test-a', 'y')
print(y)
```
```{r test-a, cache=TRUE}
y = 2*pi
```
The first time you run it will give you this:
But knit it again and you'll see this:
This is kind of awkward, but was the recommended solution from yihui, the creator of rmarkdown. See this github issue: https://github.com/yihui/knitr/issues/868#issuecomment-68129294
You have to be careful with cached chunks – make sure that there is nothing that would change between runs and clear the cache before doing your final (2-step) knitting.
Related
I have read previously asked similar questions here, here, and here (among many more).
Unfortunately, none of the solutions offered to those questions seem to solve my issue.
I tried the function written by #bryanshalloway here but that did not have the desired result.
For more context, I am producing scientific manuscripts using an R Markdown workflow. I perform EDA in one notebook and later come back to write the manuscript in a different notebook. I import the data, wrangle it, create tables, and do some basic visualizations in the EDA notebook and include narrative text (mostly for myself).
I then create a separate notebook to write the manuscript. To keep it reproducible, I want to include all of the steps from the EDA with respect to data import, tidying, and wrangling, however I do not need the commentary that went along with it. Additionally, I may want some (but definitely not all) of the tables and basic visualizations I created during the EDA, but I would need to build them up substantially to get them publication ready.
My current workflow is just copying and pasting the relevant code chunks and then adding to those where necessary for tables and figures (i.e., adding labels and captions to a ggplot).
Is there a way to "source" these individual code chunks from one R Markdown file/R Notebook into another? Perhaps using knit_child (but not bring the entire R Markdown file into the current parent file)?
I would like to avoid copying the desired code chunks into separate R scripts.
Thanks!
It is very possible with knitr purl and spin:
Ok lets say this is your initial Rmarkdown report:
call the file report1.Rmd
---
title: Use `purl()` to extract R code
---
The function `knitr::purl()` extracts R code chunks from
a **knitr** document and save the code to an R script.
Below is a simple chunk:
```{r, simple, echo=TRUE}
1 + 1
```
Inline R expressions like `r 2 * pi` are ignored by default.
If you do not want certain code chunks to be extracted,
you can set the chunk option `purl = FALSE`, e.g.,
```{r, ignored, purl=FALSE}
x = rnorm(1000)
```
Then you go to the console and purl the file:
> knitr::purl("report1.Rmd")
this creates an R file called report1.R in the same directory you are in,
with only the chunks that are not purl=false.
Its an simple R script looking like this:
## ---- simple, echo=TRUE----------------------------------------------------------------------------
1 + 1
Lets rename the file for safety purposes:
> file.rename("report1.R", "report_new.R")
Finally lets spin it back to report_new.Rmd :
> knitr::spin("report_new.R", format = "Rmd", knit=F)
This gives you a new Rmd file called report_new.Rmd containing only the relevant chunks and nothing else
```{r simple, echo=TRUE}
1 + 1
```
I have an uncleaned dataset. So, I have imported it to my R studio.Then when I run nrow(adult) in the rmarkdown file and press ctrl+Enter it works, but when i press the knit the following error appears:'
When you knit something it gets executed in a new environment.
The object adult is in your environment at the moment, but not in the new one knit creates.
You probably did not include the code to read or load adult in the knit.
If you clear your workspace, as per #sebastian-c comment, you will see that even ctrl+enter does not work.
You have to create the adult object inside your knit. For example, if your data in from a csv add
adult <- read.csv2('Path/to/file')
in the first chunk.
Hope this is clear enough.
Another option, in the same way as the previous, but really useful in case you have a lot of diferent data
Once you have all your data generated from your R scripts, write in your "normal code" ( any of your R scripts):
save.image (file = "my_work_space.RData")
And then, in your R-Markdown script, load the image of the data saved previously and the libraries you need.
```{r , include=FALSE}
load("my_work_space.RData")
library (tidyverse)
library (skimr)
library(incidence)
```
NOTE: Make sure to save your data after any modification and before running knitr.
Because usually I've a lot of code that prepares the data variables effectively used in the knitr documents my workaround use two steps:
In the global environment, I save all the objects on a file using
save()
In the knitr code I load the objects from the file using load()
Is no so elegant but is the only one that I've found.
I've also tried to access to the global environment variables using the statement get() but without success
If you have added eval = FALSE the earlier R code won't execute in which you have created your object.
So when you again use that object in a different chunk it will fail with object not found message.
When knitting to PDF
```{r setup}
knitr::opts_chunk$set(cache =TRUE)
```
Worked fine.
But not when knitting to Word.
I am rendering in word. Here's what finally got my data loaded from the default document directory. I put this in the first line of my first chunk.
load("~/filename.RData")
I have a report made of several Rmd files (several layers of child documents).
I always end up doing a copy paste and forget to change the chunk names, it's annoying because the report takes minutes to knit before the error pops up.
I use the chunk names to debug, and in the end they're often the ones that make my code crash, there has to be a better way.
How can I check programmatically that everything's clear before attempting to knit ?
Apparently there exists this option that allows you to keep duplicate chunk labels and still knit:
options(knitr.duplicate.label = 'allow')
I have an uncleaned dataset. So, I have imported it to my R studio.Then when I run nrow(adult) in the rmarkdown file and press ctrl+Enter it works, but when i press the knit the following error appears:'
When you knit something it gets executed in a new environment.
The object adult is in your environment at the moment, but not in the new one knit creates.
You probably did not include the code to read or load adult in the knit.
If you clear your workspace, as per #sebastian-c comment, you will see that even ctrl+enter does not work.
You have to create the adult object inside your knit. For example, if your data in from a csv add
adult <- read.csv2('Path/to/file')
in the first chunk.
Hope this is clear enough.
Another option, in the same way as the previous, but really useful in case you have a lot of diferent data
Once you have all your data generated from your R scripts, write in your "normal code" ( any of your R scripts):
save.image (file = "my_work_space.RData")
And then, in your R-Markdown script, load the image of the data saved previously and the libraries you need.
```{r , include=FALSE}
load("my_work_space.RData")
library (tidyverse)
library (skimr)
library(incidence)
```
NOTE: Make sure to save your data after any modification and before running knitr.
Because usually I've a lot of code that prepares the data variables effectively used in the knitr documents my workaround use two steps:
In the global environment, I save all the objects on a file using
save()
In the knitr code I load the objects from the file using load()
Is no so elegant but is the only one that I've found.
I've also tried to access to the global environment variables using the statement get() but without success
If you have added eval = FALSE the earlier R code won't execute in which you have created your object.
So when you again use that object in a different chunk it will fail with object not found message.
When knitting to PDF
```{r setup}
knitr::opts_chunk$set(cache =TRUE)
```
Worked fine.
But not when knitting to Word.
I am rendering in word. Here's what finally got my data loaded from the default document directory. I put this in the first line of my first chunk.
load("~/filename.RData")
I am working on a LaTeX report template that automatically generates a beamer document, pulling in figures from specified directories and placing them one per slide.
Here is an example of the code that I am using for this, as a code chunk in my .Rnw document:
<<results='asis',echo=FALSE>>=
suppressPackageStartupMessages(library("Hmisc"))
# get the plots from the common directory
Barplots_dir<-"/home/figure/barplots"
Barplots_files<-dir(Barplots_dir)
# create a beamer slide for each plot
# use R to output LaTeX markup into the document
for(i in 1:length(Barplots_files)){
GroupingName<-gsub("_alignment_barplot.pdf", "", Barplots_files[i]) # strip this from the filename
file <- paste0(Barplots_dir,"/",Barplots_files[i]) # path to the figure
cat("\\subsubsection{", latexTranslate(GroupingName), "}\n", sep="") # don't forget you need double '\\' because one gets eaten by R !!
cat("\\begin{frame}{", latexTranslate(GroupingName), " Alignment Stats}\n", sep="")
cat("\\includegraphics[width=0.9\\linewidth,height=0.9\\textheight,keepaspectratio]{", file, "}\n", sep="")
cat("\\end{frame}\n\n")
}
#
However I recently came across this article by Yihui Xie which includes a remark about cat("\\includegraphics{}") being a bad idea. Is there a reason for this, and is there a better option?
To be clear, these figures are generated by other programs as part of a larger pipeline; generating them within the document is not an option, but I need the document to be able to dynamically find and insert them into the report. I know that there are some capabilities to do this directly from within LaTeX itself but cat'ing out the LaTeX markup I need seemed like an easier and more flexible task.
cat("\\includegraphics{}") is likely to be a bad idea if you are from the old Sweave world (where one might need to open a graphics device, draw a plot, close the device, and cat("\\includegraphics{}")). No kittens will be killed as long as you understand what you are doing. Your use case seems to be very reasonable to me, and I don't have a better approach.