kable output is suboptimal for data.tables with list columns that contain functions

[sebffischer]

The knitr::kable output is suboptimal for data.tables with list columns that contain functions (see reprex below).

dt = data.table::data.table(list(help))
print(knitr::kable(dt))
#> 
The `knitr::kable()` output is suboptimal for data.tables with list columns that contain functions, see the reprex below. 

#> 
#> |V1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
#> |:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
#> |function (topic, package = NULL, lib.loc = NULL, verbose = getOption("verbose"), ,     try.all.packages = getOption("help.try.all.packages"), help_type = getOption("help_type")) , {,     types <- c("text", "html", "pdf"),     help_type <- if (!length(help_type)) ,         "text",     else match.arg(tolower(help_type), types),     if (!missing(package)) ,         if (is.name(y <- substitute(package))) ,             package <- as.character(y),     if (missing(topic)) {,         if (!is.null(package)) {,             if (interactive() && help_type == "html") {,                 port <- tools::startDynamicHelp(NA),                 if (port <= 0L) ,                   return(library(help = package, lib.loc = lib.loc, ,                     character.only = TRUE)),                 browser <- if (.Platform$GUI == "AQUA") {,                   get("aqua.browser", envir = as.environment("tools:RGUI")),                 },                 else getOption("browser"),                 browseURL(paste0("http://127.0.0.1:", port, "/library/", ,                   package, "/html/00Index.html"), browser),                 return(invisible()),             },             else return(library(help = package, lib.loc = lib.loc, ,                 character.only = TRUE)),         },         if (!is.null(lib.loc)) ,             return(library(lib.loc = lib.loc)),         topic <- "help",         package <- "utils",         lib.loc <- .Library,     },     ischar <- tryCatch(is.character(topic) && length(topic) == ,         1L, error = function(e) FALSE),     if (!ischar) {,         reserved <- c("TRUE", "FALSE", "NULL", "Inf", "NaN", ,             "NA", "NA_integer_", "NA_real_", "NA_complex_", "NA_character_"),         stopic <- deparse1(substitute(topic)),         if (!is.name(substitute(topic)) && !stopic %in% reserved) ,             stop("'topic' should be a name, length-one character vector or reserved word"),         topic <- stopic,     },     paths <- index.search(topic, find.package(if (is.null(package)) ,         loadedNamespaces(),     else package, lib.loc, verbose = verbose)),     try.all.packages <- !length(paths) && is.logical(try.all.packages) && ,         !is.na(try.all.packages) && try.all.packages && is.null(package) && ,         is.null(lib.loc),     if (try.all.packages) {,         for (lib in .libPaths()) {,             packages <- .packages(TRUE, lib),             packages <- packages[is.na(match(packages, .packages()))],             paths <- c(paths, index.search(topic, file.path(lib, ,                 packages))),         },         paths <- paths[nzchar(paths)],     },     structure(unique(paths), call = match.call(), topic = topic, ,         tried_all_packages = try.all.packages, type = help_type, ,         class = "help_files_with_topic"), } |

^{Created on 2021-11-17 by the reprex package (v2.0.1)}

[cderv]

Thanks for the report.

This is not an issue with data.table specifically but with list column in structure that supports it.

> knitr::kable(tibble::tibble(a = list(head)))

|a                                     |
|:-------------------------------------|
|function (x, ...) , UseMethod("head") |

I don't think knitr::kable() was designed for those type of structure.

Printing list column is not something easy to do generically. What should be printed for such cells exactly ?

I don't see a use case where using kable() or any other table formatting tool would be useful. 🤔
Why not just print them as in the console ? which will use the printing method that usually supports it ?

---
title: "Test"
output: html_document
---

```{r}
tibble::tibble(a = list(head))
```

```{r}
data.table::data.table(a = list(head))
```

Is that expectation to have a markdown table containing the same information as the console printed version ?

Thanks.

[sebffischer]

Thanks for the quick answer,
I agree that there is probably nothing to print that is particularly useful. Nonetheless
the suggestion you made below is imo a way better default behaviour than is currently implemented.

[cderv]

the suggestion you made below

Which suggestion exactly ? Just to be sure I got it right.

[sebffischer]

I understood it as you suggesting to e.g. represent the function head as <function[1]>.
Or maybe simply use the class of the object?

[sebffischer]

Maybe in general something like sprintf("<%s>", class(obj)[1]) ?

[cderv]

I wanted to confirm that this would be your expectation as a result of a kable() call on such table.

This could be a way to output the content without creating those long unreadable contents. We would need process the table and transform the content before printing it a table. Seems something that could be considered.

I still think that when this happens, one should prevent from using knitr::kable() on table with list column. But maybe I am wrong...

I'll add this as a feature request. Thanks for the suggestion.

I think this is related to rstudio/rmarkdown#1822 (comment) where were paged_table() in rmarkdown kind of detect list content to write a summary and not the content.

[atusy]

I think the optimal outputs depend on users.
For example, head may become

• function (x, ...) UseMethod("head")
• function
• head
• function<head>

and so on...

I would rather suggest define own format methods.

format.list = function(x, ...) vapply(x, function(x) class(x)[[1L]], NA_character_)
knitr::kable(tibble::tibble(
  x = list(head, rnorm)
))

[cderv]

Yes I agree - It is what I meant by "Printing list column is not something easy to do generically. What should be printed for such cells exactly ?" 😄

Regarding format method, that is a nice solution ! thanks for sharing.

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