when with my rmd file I click on knit to pdf or html it generates a document with various errors in the "results" section or where the various chuncks are contained.
I believe oggetto "" non trovato means object not found. My first guess would be you are referring to objects in your R Markdown document that aren't available when R Markdown knits in a fresh R session.
Make sure all of these objects are made available in the R Markdown document. When knitting, the code found in the .Rmd file are run in a clean R session and objects in your global environment are not available.
how do i make sure that all of these objects are made available in the R Markdown document?
Basically you need to ensure that any object you refer to in a code chunk is created/loaded in a preceding code chunk.
For example, the below document won't render:
---
output: html_document
---
```{r}
print(x)
```
While this document will render properly, because x is made available:
---
output: html_document
---
```{r}
x <- 1:10
```
```{r}
print(x)
```
so I have to replace the x with the name of the variables and make the chunk run in the rmd file?
for example:
output: html_document
namedataset$namevariable <- 1:10
print(namedataset$namevariable)
(I have a sample of 214 subjects and 7 variables)
My code was just meant to be a simple example. Your code will look different, I'm sure.
Just treat the R Markdown document as a self-contained script, like a normal .R script. In other words, the R Markdown should be able to run from start to end in a clean R session.
One way to manually debug your document to figure out which objects aren't properly created, open up your R Markdown file in a new R/RStudio session and try to run each code chunk one-at-a-time starting from the first code chunk and working your way down the document. Each time a code chunk fails because an object wasn't found, you will need to make sure you create that object somewhere in the document before the failed code chunk.
For example, it looks like you are using the dataset named RisposteQuestionaro_excel. You need to load this data, probably right at the beginning of the R Markdown document, so that any subsequent code chunk is able to use the data.
when I try to run chuncks in a r script the data is found but an error appears: Error: attempt to use zero-length variable name. while if I run the chuncks in the rmd document the data is found without any error.
Sorry for the confusion, I did not mean to run your code in a R script, I meant to treat the Rmd script like you would treat an R script; in the sense that all of the components need to be included in the R script to be able to run it start-to-finish in a clearn R session.
My debugging advice remains mostly the same, open up your Rmd file in a fresh R session and run it chunk-by-chunk in order. Any time an object is not found, you need to add some code that ensures the object is created in the R Markdown environment, not just the Global Environment.
To further clarify, in the top-right corner of the screenshot you just posted, there are many R objects show in the Global Environment, these objects will not be available to the Rmd document when it is knitting/rendering. Instead, these objects need to be created/codified within the Rmd itself.
Hope this is helpful.
so I should clean object from the workspace, import the dataset again and run the chunks in rmd?
thanks for your patience
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Yes, exactly. This is one way to double-check that you have created/loaded all necessary objects before referring to the objects within the Rmd file.
The more high-throughput way would be to clean the workspace, and simply try to knit the document. It will fail if objects aren't found. The knitting will produce an error indicating the object it can't find. Then you just need to make sure you create that object, try knitting again, and so forth, until the document can knit from start to end without error.
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