Output a series of crosstabs using sjPlot into an RMarkdown document using knitr

Question

I'm trying to use purrr::imap() to output a series of crosstab tables into a Flexdashboard. However, no matter what I try to output from the mapped function, all I get is an escaped HTML string instead of actual raw HTML.

I'm pretty new to R and RMarkdown.

Here's a minimal working example of what I'm talking about:

---
title: "Multiple Crosstabs Example"
output: 
  flexdashboard::flex_dashboard:
    orientation: columns
    vertical_layout: fill
---

```{r setup, include=FALSE}
library(dplyr)
library(purrr)
library(flexdashboard)
library(sjPlot)
```

Column {data-width=650}
-----------------------------------------------------------------------

### Crosstabs

```{r}
# Converting several mtcars values to factors for sake of an easily reproducible example
mycars <- mtcars
mycars$cyl <- as.factor(mycars$cyl)
mycars$vs <- as.factor(mycars$vs)
mycars$am <- as.factor(mycars$am)
mycars$gear <- as.factor(mycars$gear)
mycars$carb <- as.factor(mycars$carb)

# THIS is the part I'm having trouble with
mycars %>%
  select_if(is.factor) %>%
  select(-cyl) %>%
  imap(\(x, cname) {
    xt <-tab_xtab(
      mycars$cyl,
      x,
      var.labels=c("Cylinders", cname),
      show.row.prc = TRUE,
      show.summary=TRUE,
      show.na=TRUE
    )
    xt$knitr
  })
```

And the output I get looks something like:

$vs
[1] "<table style=\"border-collapse:collapse; border:none;\">\n <tr>\n <th style=\"border-top:double; text-align:center; font-style:italic; font-weight:normal; border-bottom:1px solid;\" rowspan=\"2\">Cylinders</th>\n <th style=\"border-top:double; text-align:center; font-style:italic; font-weight:normal;\" colspan=\"3\">vs</th>\n <th style=\"border-top:double; text-align:center; font-style:italic; font-weight:normal; font-weight:bolder; font-style:italic; border-bottom:1px solid; \" rowspan=\"2\">Total</th>\n </tr>\n \n<tr>\n <td style=\"border-bottom:1px solid; text-align:center; padding:0.2cm;\">0</td>\n <td style=\"border-bottom:1px solid; text-align:center; padding:0.2cm;\">1</td>\n <td style=\"border-bottom:1px solid; text-align:center; padding:0.2cm;\">NA</td>\n </tr>\n \n<tr> \n<td style=\"padding:0.2cm;...

Notice that instead of just plain HTML, which is what I'm hoping for, it wraps the whole thing in double quotes and escapes all of the internal double quotes.

I've tried a number of permutations including:

Just outputting the table without assigning it to a variable
Using purrr::iwalk() and including a print(xt$knitr) inside the function
And probably a variety of iterations on that

The package author wrote a blog post related to this, but I can't figure out how my version is different.

Here's a screenshot of the above example after knitting:

System Environment

Windows 11 x64
R v4.3.1
flexdashboard v0.6.2
dplyr v1.1.2
purrr v1.0.2
sjPlot v2.8.15

If you're viewing HTML by printing it to the console then this is what you'd expect: it's a character variable, hence the quotes and escaped quotes. What happens when you try to output the variable in your Flex dashboard? — neilfws, Aug 28 '23 at 00:37
yeah, it outputs the escaped string as content. If I don't capture the output of the function in a variable, then it just outputs the column name as if it were running on the console. — morphatic, Aug 28 '23 at 00:50
I think a reproducible example using Flex or at least RMarkdown would help, with full code including libraries (_e.g._ `sjPlot`). — neilfws, Aug 28 '23 at 01:03
Ok, now the example I provided is the entire content of the `.Rmd` file that reproduces the issue. — morphatic, Aug 28 '23 at 01:44
It knits fine on my machine and pops up a documemt with a table and plot. — IRTFM, Aug 28 '23 at 06:11

score 0 · Answer 1 · answered Aug 28 '23 at 15:16

I found a solution, although it was a little counterintuitive to me and I'm not sure it's the best one. I'd like to see a cleaner/better one. The solution was to pipe everything to htmltools::knit_print.html(). Here's what I ended up with:

---
title: "Multiple Crosstabs Example"
output:
  flexdashboard::flex_dashboard:
    orientation: columns
    vertical_layout: fill
---

```{r setup, include=FALSE}
library(dplyr)
library(purrr)
library(flexdashboard)
library(sjPlot)
```

Column {data-width=650}
-----------------------------------------------------------------------

### Crosstabs

```{r}
# Converting several mtcars values to factors for sake of an easily reproducible example
mycars <- mtcars
mycars$cyl <- as.factor(mycars$cyl)
mycars$vs <- as.factor(mycars$vs)
mycars$am <- as.factor(mycars$am)
mycars$gear <- as.factor(mycars$gear)
mycars$carb <- as.factor(mycars$carb)

# THIS is the part I'm having trouble with
mycars %>%
  select_if(is.factor) %>%
  select(-cyl) %>%
  imap(\(x, cname) {
    xt <- tab_xtab(
      mycars$cyl,
      x,
      var.labels=c("Cylinders", cname),
      show.row.prc = TRUE,
      show.summary=TRUE,
      show.na=TRUE
    )
    xt$knitr
  }) %>% htmltools::knit_print.html() # <- THIS IS WHAT I ADDED
```

Output a series of crosstabs using sjPlot into an RMarkdown document using knitr

System Environment

1 Answers1