tables() from data.table

[jaredlander]

I've noticed some issues in other posts about data.table and environments and stumbled upon an one of my own. The tables() argument depends on the environment and works fine if it is in the same chunk as where the data.table was created, but if it is in its own chunk it will not work. This has something to do with caching as setting cache=FALSE takes care of the issue. It does not, however, affect just accessing the tables. A reproducible example is below.

data.table issue

opts_chunk$set(cache=TRUE,cache.path="dtCache/")

If we call tables() in the same chunk where the tables were created it works, if we call it in its own chunk it does not work.

require(data.table)
theDT <- data.table(A=1:10, B=letters[1:10], C=LETTERS[11:20])
theDT
nrow(theDT)
carsDT <- data.table(cars)
head(carsDT)
nrow(carsDT)
tables()

Now we look at the tables command in its own chunk.

tables()

Here tables will only recognize the tables from this chunk and not the previous ones.

secondDT <- data.table(First=10:1, Second=1:10)
secondDT
tables()

We can still access all the previous data.tables though.

theDT
secondDT
head(carsDT)

If you turn off caching, everything works fine.

Sorry that GitHub is incorrectly interpreting the code but pasting all of it into a Rmd file should make things clear.

[yihui]

tables() has an env argument, and you can pass knitr's environment to it; with the current devel version, you can tables(env = knit_global())

[jaredlander]

Perfect, I knew it was be an environment issue, didn't realize there was a special knitr environment. Is there a way to set that globally so that I can hide the env from the reader and not have it each time?

[yihui]

This is actually a very tricky problem. I need to use the special (empty) environment in order to know which objects are created in a chunk. At best I can say tables(env = globalenv()) which looks less confusing.

The fundamental fix requires the author of data.table to make a change in tables():

> tables
function (mb = TRUE, order.col = "NAME", width = 80, env = parent.frame(), 
    silent = FALSE) 
{
    tt = objects(envir = env, all.names = TRUE)
....

For tt, it can also take object names from the enclosing environment: c(objects(envir = env, all.names = TRUE), objects(envir = parent.env(env), all.names = TRUE))

The other way is to add an argument to allow users to specify the object names.

function (mb = TRUE, order.col = "NAME", width = 80, env = parent.frame(), 
    silent = FALSE, objects = ls(env, all.names = TRUE)) 

and you can call data.tables(objects = c('carsDT', ...))

[jaredlander]

This is a perfect excuse to allow me to eval according to line (#383).

Right now to get around this and not confuse the user by specifying the environment I am doing

# show tables
tables()

# show tables
tables(env=knit_global())

It would be so much better to do

# show tables
tables()
tables(env=knit_global())

[yihui]

The problem should be gone now.

[github-actions]

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