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')
Related
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")
RStudio renders mynotebook.nb.html file every time R Markdown document mynotebook.Rmd is saved. This process does not involve running code in chunks, so it is much faster than knitting a notebook into mynotebook.html. However, for large .Rmd documents, saving nb.html files can take a long time, and, unfortunately, it is required to wait for it to finish before one can start using the notebook again and run code in chunks.
Is there a way to configure RStudio to not to create nb.html files on save of an R Markdown document?
I've found out you can delete relevant output entry from the top section of your file. In my case it looks like:
---
title: "Document"
output:
html_notebook: default
---
Which causes creation of .nb.html on every save. If you remove the output tag, file is no longer created automatically. You can still knit to any output file from the Knit menu on the top (or press Ctrl+Shift+K for default. This will run all the chunks again, which may take a while.
You may want to consult this guide book for more information on how YAML tags work. I'm just beginning with them!
Another reason (and solution) might be, that you clicked incidentally on the "Knit on Save" button located just under the Save-to-Disk-Symbol in RStudio. This was in my case the problem. Usually you should be able to save a rmd-file without triggering the knitting process.
So - given this scenario - just uncheck the "Knit on Save" button.
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'm trying to create a document with R-markdown but the document doesn't seem to recognise the variables in my current workspace.
Both the markdown document and the workspace are in the same working directory.
How can I set it to use them and update the document?
When you compile an R-markdown document the code is run inside a "clean" R Session. That means it will not have access to objects in the workspace. The R-markdown document chunks will only have access to objects created in another chunk of the document, or the same chunk.
One way around this would be to write out the workspace to a binary file
save.image("myWorkSpace.RData")
before knitting, and then in the first chunk of your R-markdown document do
load("myWorkSpace.RData")
but I don't recommend it. Much better to include the code that creates the objects in your R-Markdown document. That means the document is entirely selfcontained, increasing reproducibility.
I resolved the issue using this line on the top of the first chuck of the document.
knitr::opts_chunk$set(error = TRUE)
The side-effect is that the document has all log information. I am still looking for a better way to solve it!
Greetings!
I ran into this with knitr::opts_chunk$set(cache = TRUE) and tinkering too much with changing objects in the .Rmd.
Deleting the cache folders and knitting the document again seemed to work.
This error can occur if you are including multiple <> within the same code block in your .Rmd file.
I have a .Rnw document in which I include childs. The childs produce tables via the 'latex' command of the Hmisc library in R.
When I make changes in the child documents, these changes do not anymore change the pdf document. My first guess was to use the chunk option 'eval=TRUE', but this does not change anything. Then, I saw, that the tables are actually saved to a .tex file with same name as the .Rnw document. I deleted this file and after compilation with knitr I got an error:
Error: Latexmk: Could not find file documentname.tex.
I assume, this is not the way to do it. Now I am out of ideas what to do. I appreciate some help on my problem.
Best
Simon
Allright, when trying to construct a simple example, I actually found out, that neither the packages I included nor the nesting of child documents interfere with the compilation via knitr. The reason was a simple error in the low-level .Rnw document, where a Hmisc latex table had a label, that missed a closing speech mark.
This causes then the output pdf not to change - I assume, that in this case the already constructed .tex file is included instead of letting knitr recompile the .Rnw documents and this hasn't changed since the last compilation?
What I wonder about is the different format of the landscape ctable in the document. Using a simple knitr document just with \documentclass{article} produces well placed tables. In my document using a template for the JFE, I get a table that extends over the whole page and even in footnotesize it is far away from the great appearance in the simple document. There is only a margin of less than half a cm on the right and the left. Page size is the same: both US letter... Can I probably control that via knitr or only via resizebox?