In R it has always been incorrect to call order() on a data.frame. Such a call doesn’t return a sort-order of the rows, and previously did not return an error. For example.

d <- data.frame(
  x = c(2, 2, 3, 3, 1, 1), 
  y = 6:1)

knitr::kable(d)

order(d)

##  [1]  5  6 12  1  2 11  3  4 10  9  8  7

Notice the above result has more than 12 items, so it is not a row order. It appears there is a desire to make this sort of mal-use signalling, and it is now available as an optional error-check. In fact we are starting to see packages kicked-off CRAN for not fixing this issue.

Recent CRAN package removals (from CRANberries, triggered by failing to respond when contacted to fix the order() error, (error resolves as “cannot xtfrm data frames”) include:

• ACCLMA
• ahp
• aMNLFA
• astrochron
• EasyMARK
• forestSAS
• gee4
• goeveg
• jmdl
• LncMod
• LN0SCIs
• marindicators
• McSpatial
• mcglm
• mpr
• pompom
• promotionImpact
• rodham
• rysgran
• scan
• sentometrics
• subtee
• unga

The wrapr package has supplied, for some time, the function orderv(), which is suitable for ordering the rows of data.frames.

For example, we can calculate a row order as follows.

library(wrapr)

orderv(d)

## [1] 6 5 2 1 4 3

And use such an order to sort data rows.

d[orderv(d), , drop = FALSE] %.>%
  knitr::kable(.)

Essentially orderv(d) is shorthand for do.call(base::order, as.list(d)), which places the columns of the data.frame as the ...-arguments of the order() call.

Edit: an earlier great fix can be found here.