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Is there any way to export tables in a academic article using R?

enter image description here

I have a data frame of observation, and I want to export the data frame to a docx file in the format like the picture. I can do this but in a hard way. Is there any more convenient way? Here are the packages I know that may help:knitr printr bookdown. Say I have a data frame mydata like this:

Group CRP PCT
pos   1   7
pos   2   8
pos   3   9
neg   4   10
neg   5   11
neg   6   12

I want the output like this:

Group   CRP     PCT
pos     2(1~3)  8(7~9)
neg     5(4~6)  11(10~12)
p-value 0.00    0.00

I think the question is:

  1. Given the mydata above, how can I transform it easily to output?
  2. After I got the output, how can I export it to docx same as the format in the picture ?
Solution

  • You can use dplyr to transform your data and tableHTML to create a table like the one in your question.

    library(dplyr)

    This function is used to summarise the CRP and PCT by GROUP. 

    fun <- function(x) {
  paste0(x[! x %in% c(min(x), max(x)) ], 
         "(",
         min(x),
         "~",
         max(x),
         ")")
}

    Use that function in summarise_all() on mydata grouped by Group and sort the data by Group:

    output <- mydata %>% 
  group_by(Group) %>% 
  summarise_all(.funs = fun) %>% 
  arrange(desc(Group))

    Then use tableHTML on output to create a scientific table:

    library(tableHTML)
output %>% 
  tableHTML(rownames = FALSE,
            widths = rep(100, 3), 
            theme = 'scientific')

    The result looks like this:

    tableHTML