Hi I am using R studio and the "knitHTML" button to convert my Rmd file into a html file. However, even thought the code runs fine, when using knitHTML it cannot find any of my objects previously created:
## Error: object 'cbt_2010' not found
however if I type cbt_2010 at the terminal - it is there. Bascially knit cannot find any of the objects in the workspace.
what am I doing wrong? it just seems any data produced in each chunk is lost in memory when using knit!
As already mentioned by #BenBolker , you can use knit2html( Note that it is different from the Rstudio button, Rstudio use its own function to process document) from knitr:
x <- 10
writeLines(c("# hello markdown",
"```{r hello-random, echo=TRUE}",
"rnorm(x)", "```"), ## note the use of x
"test.Rmd")
library(knitr)
knit2html("test.Rmd")
Maybe I am missing something in your question, but if you create object 'cbt_2010' in your .Rmd file, knitr will have that object to work with.
Stated differently, you can find it when you type object 'cbt_2010' at the console because you created that object and it is available to R. You need to do the same in the .Rmd file.
Related
I'm using RStudio Cloud. I'm running an RMarkdown doc, when I run the code chunks in the doc they work fine, but when I'm trying to knit I get errors. Before I used the code "knitr::opts_chunk$set(error = TRUE)" the doc wouldn't knit at all (error message was saying objects couldn't be found); now it knits BUT I get the error message "## Error in .External2(C_dataviewer, x, title): unable to start data viewer" when I try to View(dataframes) that I've created (the data frames I created show up in the global environment but not in my file path directory, which is /cloud/project). I'm guessing that RMarkdown can't find these since they are in a different file path? I'm also assuming that files in the global directory aren't available for RMarkdown to knit, so how do I get them to be available for RMarkdown to knit? Thank you!
Instead of doing View you can just do this.
```{r}
df # assuming df is your data.frame object name
```
this will print your whole dataframe df in the knitted document.
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 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 wonder whether I can use knitr markdown to just create a report on the fly with objects stemming from my current workspace. Reproducibility is not the issue here. I also read this very fine thread here.
But still I get an error message complaining that the particular object could not be found.
1) Suppose I open a fresh markdown document and save it.
2) write a chunk that refers to some lm object in my workspace. call summary(mylmobject)
3) knitr it.
Unfortunately the report is generated but the regression output cannot be shown because the object could not be found. Note, it works in general if i just save the object to .Rdata and then load it directly from the markdown file.
Is there a way to use objects in R markdown that are in the current workspace?
This would be really nice to show non R people some output while still working.
RStudio opens a new R session to knit() your R Markdown file, so the objects in your current working space will not be available to that session (they are two separate sessions). Two solutions:
file a feature request to RStudio, asking them to support knitting in the current R session instead of forcibly starting a new session;
knit manually by yourself: library(knitr); knit('your_file.Rmd') (or knit2html() if you want HTML output in one step, or rmarkdown::render() if you are using R Markdown v2)
Might be easier to save you data from your other session using:
save.image("C:/Users/Desktop/example_candelete.RData")
and then load it into your MD file:
load("C:/Users/Desktop/example_candelete.RData")
The Markdownreports package is exactly designed for parsing a markdown document on the fly.
As Julien Colomb commented, I've found the best thing to do in this situation is to save the large objects and then load them explicitly while I'm tailoring the markdown. This is a must if your data is coming through an ODBC and you don't want to run the entire queries repeatedly as you tinker with fonts and themes.