CODEWITHSUNDEEP
rr-markdown
ceallac
ceallac

Reputation: 107

RMarkdown Error plot rendered but would not knit - noob

Question: Plot appears in rmarkdown but does not knit. Two errors appear. no other issues with the file.

  1. Error window Error while opening file "The system cannot find the file specified"
  2. I get the message shown below in Render after trying to knit to pdf

Line 239 Error in parse(text = x, scrfile = src) : ,text>:4:16: unexpected ' , '

3: alpha = 0.9, width = 7) + theme_minimal(base_size = 8) + #Note minimal theme alpha

4: alpha = 0.9

Calls: ... -> parse_all -> parse_all.character -> parse

I have changed a lot to make it work, including alpha and confirmed the code is linked correctly to its dependencies. I have made sure dplyr is in library (read it in other solution that did not work for me). I cannot see the issue as the plot works in rstudio and shows in rmarkdown and it did not knit

This is the chunk that is in rmarkdown linked to the error

#next line is line 239
ONE1 <- ggplot(Italy,  aes(Date, as.numeric(FirstDosePC))) +
  geom_col(fill = "red", alpha = .9, width = 7) +  theme_minimal(base_size = 8) + 
#Note minimal theme
  xlab(NULL) + ylab(NULL) + scale_x_date(date_labels = "%Y/%m/%d")
OneTwo <- ONE1 + geom_col(data=Ireland,  aes(Date, 
    as.numeric(FirstDosePC)),  
    fill="Green",  alpha = .9,width = 5)
OneTwoThree <- OneTwo + geom_col(data=Latvia,  aes(Date, 
    as.numeric(FirstDosePC)),  
    fill="black",  alpha = .9, width = 2)
OneTwoThree + labs(title="Ireland, Italy, & Latvia - First Dose comparision",
    subtitle="ITALY = RED, IRELAND = GREEN, LATVIA = BLACK",              
    caption = "(ECDC, 2021)",
    x="Date Administered",
   y="% Population treated")

Upvotes: 0

Views: 283

Answers (1)

ceallac
ceallac

Reputation: 107

Noob mistake. I had a comment in the first piece of the chunk that allowed the plot to be built in both rmarkdown and the r workspace.

BUT the comment # was stopping the knitting process.

Removed comment - knitting happened (removed #Note minimal theme ... to help you see the solution)

BEFORE

ONE1 <- ggplot(Italy,  aes(Date, as.numeric(FirstDosePC))) +
  geom_col(fill = "red", alpha = .9, width = 7) +  theme_minimal(base_size = 8) + 
#Note minimal theme
  xlab(NULL) + ylab(NULL) + scale_x_date(date_labels = "%Y/%m/%d")

AFTER

ONE1 <- ggplot(Italy,  aes(Date, as.numeric(FirstDosePC))) +
  geom_col(fill = "red", alpha = .9, width = 7) +  theme_minimal(base_size = 8) + 

  xlab(NULL) + ylab(NULL) + scale_x_date(date_labels = "%Y/%m/%d")

Upvotes: 1

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