Table R Markdown qwraps2 and knitr::kable. Column missing

Question

I have the following dummy data.frame

set.seed(12345)
df<-data.frame(var1=floor(runif(10,1000000,5000000)),  group=rep(c("A","B"),5), event=rep(c("Yes","No"),5))

And would like to create a summary table of it. I tried to use qwraps2

As follows:

summary<-list("VAlue1" =
          list("min" = ~ min(.data$var1),
              "max" = ~ max(.data$var1),
              "mean (sd)" = ~ qwraps2::mean_sd(.data$var1)),

       "Group" =
         list("Yes" = ~ qwraps2::n_perc0(.data$group == "A"),
              "No"  = ~ qwraps2::n_perc0(.data$group == "B")))
knitr::kable(
  qwraps2::summary_table(dplyr::group_by(df, event),summary )
)

The output is unfortunately missing the variable to look at:

|          |event: No (N = 5)                |event: Yes (N = 5)                 |
|:---------|:--------------------------------|:----------------------------------|
|min       |2591303                          |1315253                            |
|max       |4232714                          |4711820                            |
|mean (sd) |3,456,579.40 ± 672,665.35 |3,029,844.00 ± 1,572,709.32 |
|Yes       |0 (0)                            |5 (100)                            |
|No        |5 (100)                          |0 (0)                              |

How do I incorporate the category "Value1" and "Group"?

Thank you!

suggestions for other packages are welcome, too.

Answer 1

The object returned by summary_table is a character matrix with the additional S3 class qwraps2_summary_table. The rowgroup names Value1 and Group are not part of the character matrix explicitly, they are part attributes. The print method for the qwraps2_summary_table object builds the table as need for the appropriate markup language, LaTeX or markdown.

Two edits the the example posted to get the table you are looking for:

1. Add options(qwraps2_markup = "markdown") to your script. The default mark up language is LaTeX, setting this option changes the default to markdown.

2. Do not wrap summary_table inside of knitr::kable: this prevents the needed print method from being called.

options(qwraps2_markup = "markdown")

set.seed(12345)
df <- data.frame(var1  = floor(runif(10,1000000,5000000)),
                 group = rep(c("A","B"),5),
                 event = rep(c("Yes","No"),5))


summary <- list("Value1" =
                list("min" = ~ min(var1),
                     "max" = ~ max(var1),
                     "mean (sd)" = ~ qwraps2::mean_sd(var1)),
                "Group" =
                  list("Yes" = ~ qwraps2::n_perc0(group == "A"),
                       "No"  = ~ qwraps2::n_perc0(group == "B")))


tab <- qwraps2::summary_table(df, summaries = summary, by = "event")
str(tab)
#>  'qwraps2_summary_table' chr [1:5, 1:2] "1665487" "4958947" ...
#>  - attr(*, "dimnames")=List of 2
#>   ..$ : chr [1:5] "min" "max" "mean (sd)" "Yes" ...
#>   ..$ : chr [1:2] "No (N = 5)" "Yes (N = 5)"
#>  - attr(*, "rgroups")= Named int [1:2] 3 2
#>   ..- attr(*, "names")= chr [1:2] "Value1" "Group"

tab
#> 
#> 
#> |                       |No (N = 5)                         |Yes (N = 5)                      |
#> |:----------------------|:----------------------------------|:--------------------------------|
#> |**Value1**             |&nbsp;&nbsp;                       |&nbsp;&nbsp;                     |
#> |&nbsp;&nbsp; min       |1665487                            |2300381                          |
#> |&nbsp;&nbsp; max       |4958947                            |4043929                          |
#> |&nbsp;&nbsp; mean (sd) |3,741,784.20 &plusmn; 1,370,520.00 |3,392,933.80 &plusmn; 782,295.15 |
#> |**Group**              |&nbsp;&nbsp;                       |&nbsp;&nbsp;                     |
#> |&nbsp;&nbsp; Yes       |0 (0)                              |5 (100)                          |
#> |&nbsp;&nbsp; No        |5 (100)                            |0 (0)                            |

^{Created on 2020-09-15 by the reprex package (v0.3.0)}

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