Refactor nm_input

[kylebaron]

Examples

library(yspec)

spek <- ys_help$spec() 
spec <- ys_select(spek, ID, NUM,  EVID, RF, ALT, BMI, PHASE, STUDY, AMT, DV)

Default, wide

nm_input(spek)
#> $INPUT
#> C NUM ID SUBJ=DROP TIME SEQ CMT EVID AMT DV AGE WT CRCL ALB BMI
#> AAG SCR AST ALT HT CP TAFD TAD LDOS MDV BLQ PHASE STUDY RF=DROP

Drop

nm_input(spec, .drop = "PHASE")
#> $INPUT
#> ID NUM EVID RF=DROP ALT BMI PHASE=DROP STUDY AMT DV

Rename

nm_input(spec, DOSE = AMT)
#> $INPUT
#> ID NUM EVID RF=DROP ALT BMI PHASE STUDY DOSE=AMT DV

Long

nm_input(spec, .long = TRUE)
#> $INPUT
#> ID      ; subject identifier
#> NUM     ; record number
#> EVID    ; event ID
#> RF=DROP ; renal function stage
#> ALT     ; alanine aminotransferase
#> BMI     ; BMI
#> PHASE   ; study phase indicator
#> STUDY   ; study number
#> AMT     ; dose amount
#> DV      ; dependent variable

Long, with decodes

nm_input(spec, .long = TRUE, .decodes = TRUE)
#> $INPUT
#> ID      ; subject identifier
#> NUM     ; record number
#> EVID    ; event ID 
#>         ; [0 = observation, 1 = dose]
#> RF=DROP ; renal function stage
#> ALT     ; alanine aminotransferase
#> BMI     ; BMI
#> PHASE   ; study phase indicator 
#>         ; [values: 1]
#> STUDY   ; study number 
#>         ; [1 = SAD, 2 = MAD, 3 = Renal, 4 = Hepatic]
#> AMT     ; dose amount
#> DV      ; dependent variable

^{Created on 2024-05-11 with reprex v2.0.2}

Summary

This is a breaking change.

• Users can still get the old, long, verbose output. But we'll default with the more standard, wide format going forward. I have never seen anyone using the long format.
• This also re-names some arguments; I don't have any special handling for that at the moment; if this were in use, I think the most likely result would be an error in selecting columns called cat or width.

[kylebaron]

Thanks @kyleam. I'm going to stick with the breaking change on this one just because I like the name and $INPUT almost always looks like the new default. With larger, more complicated data sets, the long output is unwieldy.