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

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:
Add options(qwraps2_markup = "markdown") to your script. The default
mark up language is LaTeX, setting this option changes the default to
markdown.
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** | | |
#> | min |1665487 |2300381 |
#> | max |4958947 |4043929 |
#> | mean (sd) |3,741,784.20 ± 1,370,520.00 |3,392,933.80 ± 782,295.15 |
#> |**Group** | | |
#> | Yes |0 (0) |5 (100) |
#> | No |5 (100) |0 (0) |
Created on 2020-09-15 by the reprex package (v0.3.0)
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