knitr: object cannot be found when converting markdown file into html

Question

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!

I believe knit opens its own R session, it's best for reproducibility — baptiste
– baptiste, Commented Dec 4, 2013 at 0:24
if you want to knit based on the objects in the current session (a possibly bad idea as @baptiste suggests), just library(knitr); knit2html("<filename>") in the console. — Ben Bolker
– Ben Bolker, Commented Dec 4, 2013 at 0:44
I think I face today a similar problem as @AleksandrBlekh. How to debug further this one? — Nikos Alexandris
– Nikos Alexandris, Commented Jul 14, 2016 at 11:14
@AleksandrBlekh when you load/read an object, even in-line, how do you check if it's there? Can you str(object) and/or else, like summary(object)? — Nikos Alexandris
– Nikos Alexandris, Commented Jul 14, 2016 at 11:32

agstudy · Accepted Answer · 2013-12-04 01:03:42Z

3

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")

edited Dec 4, 2013 at 1:03

answered Dec 4, 2013 at 0:49

agstudy

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Comments

lawyeR · Accepted Answer · 2013-12-04 01:59:04Z

0

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.

answered Dec 4, 2013 at 1:59

lawyeR

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