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I am currently working on an analysis and it all runs great, but now I am working on putting it into an R Markdown to make it presentable and am running into an issue. It seems the R Markdown is not recognizing the loaded dataframes but the other R window is. Please see below. I am so lost on why it is working in one not the other. For context this is all within the same session of R Studio desktop and I am a beginner.

R-studio screen shot

I have tried redoing the code and refreshing the imported data. Everything seems structurally fine.

kjetil b halvorsen
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Jayna Rubich
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  • Rmarkdown files are compiled in a fresh R session. Objects in your global environment are not available in the document. Your document needs to stand alone and create all the data objects it needs to compile. – MrFlick Feb 24 '23 at 02:19
  • ok, how? When I attempt to load the dataframes into the R Markdown it keeps saying they are corrupted but I can load and use them just fine outside of R Markdown. – Jayna Rubich Feb 24 '23 at 15:55
  • How are you loading them outside of R Markdown? What is the exact error message? – MrFlick Feb 24 '23 at 16:23

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