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Auto-generate nif from sdtm object

Source: R/nif_auto.R
nif_auto.Rd

[Experimental]

Usage

nif_auto(
  sdtm,
  ...,
  subject_filter = "!ACTARMCD %in% c('SCRNFAIL', 'NOTTRT')",
  observation_filter = "TRUE",
  baseline_filter = NULL,
  duplicates = "resolve",
  duplicate_function = mean,
  keep = NULL,
  include_renal = TRUE,
  include_hepatic = TRUE,
  silent = NULL
)

Arguments

sdtm

A sdtm object. Needs at least the 'DM' and 'VS' domains, and the domain the observations come from.

...

Formulae to define the relationships between PCTESTCD and EXTRT.

subject_filter

The filtering to apply to the DM domain.

observation_filter

The filtering to apply to the observation source data.

baseline_filter

A filter term to identify the baseline condition, as character.

duplicates

Selection how to deal with duplicate observations with respect to the USUBJID, ANALYTE and DTC fields:

  • 'stop': Stop execution and produce error message

  • 'ignore': Include duplicates in the data set

  • 'identify': Return a list of duplicate entries

  • 'resolve': Resolve duplicates, applying the duplicate_function to the duplicate entries.

duplicate_function

Function to resolve duplicate values, defaults to mean.

keep

Columns to keep, as character.

include_renal

Add baseline creatinine, CRCL and renal function category, if possible.

include_hepatic

Add baseline hepatic function category per ODWG classification, if possible.

silent

Suppress messages, as logical. Defaults to nif_option setting if NULL.

Value

A nif object.

Details

If no mapping is provided, nif_auto() will try to find matching treatment names in EX and PCTESTCD in PC to create a basic nif object for pharmacokinetic observations. It will fail if no EXTRT and PCTESTCD with identical names are found.

If one or more mappings are provided as additional parameters, nif_auto() will create respective observations. Mappings must be provided in the form:

TESTCD ~ EXTRT

where TESTCD can be any xxTESTCD from any domain xx included in the sdtm object. See testcd() for an overview on all analytes in all domains. Formulae can also specify multiple observations to be associated with one treatment, e.g.,

RS2023 + RS2023487A ~ EXAMPLINIB.

Multiple mappings can be given, separated by commas. The analyte name in the nif object is automatically set to the respective TESTCD.

IMPORTANT: If multiple analytes are specified for a treatment, it is implicitly assumed that the first analyte corresponds to the parent analyte for the treatment, e.g., in the case above, 'RS2023' is assumed to be the analyte for the 'EXAMPLINIB' treatment parent compound.

Note that compartments (CMT) are automatically assigned. If more control over compartments, analyte names and parent assignment is desired, stepwise creation of a nif object using add_administration() and add_observation() is recommended.

See also

testcd()

add_administration()

add_observation()

Examples

nif_auto(examplinib_sad, RS2023 ~ EXAMPLINIB, silent = TRUE) |> head()
#>   REF ID    STUDYID           USUBJID AGE SEX  RACE HEIGHT WEIGHT     BMI
#> 1   1  1 2023000001 20230000011010001  43   0 WHITE  187.4     77 21.9256
#> 2   2  1 2023000001 20230000011010001  43   0 WHITE  187.4     77 21.9256
#> 3   3  1 2023000001 20230000011010001  43   0 WHITE  187.4     77 21.9256
#> 4   4  1 2023000001 20230000011010001  43   0 WHITE  187.4     77 21.9256
#> 5   5  1 2023000001 20230000011010001  43   0 WHITE  187.4     77 21.9256
#> 6   6  1 2023000001 20230000011010001  43   0 WHITE  187.4     77 21.9256
#>                   DTC TIME NTIME TAFD TAD EVID AMT ANALYTE CMT PARENT TRTDY
#> 1 2000-12-31 10:18:00  0.0   0.0  0.0 0.0    1   5  RS2023   1 RS2023     1
#> 2 2000-12-31 10:18:00  0.0   0.0  0.0 0.0    0   0  RS2023   2 RS2023     1
#> 3 2000-12-31 10:48:00  0.5   0.5  0.5 0.5    0   0  RS2023   2 RS2023     1
#> 4 2000-12-31 11:18:00  1.0   1.0  1.0 1.0    0   0  RS2023   2 RS2023     1
#> 5 2000-12-31 11:48:00  1.5   1.5  1.5 1.5    0   0  RS2023   2 RS2023     1
#> 6 2000-12-31 12:18:00  2.0   2.0  2.0 2.0    0   0  RS2023   2 RS2023     1
#>   METABOLITE DOSE MDV ACTARMCD                 IMPUTATION      DV BL_CREAT
#> 1      FALSE    5   1       C1 time imputed from PCRFTDTC      NA  67.4825
#> 2      FALSE    5   0       C1                             0.0000  67.4825
#> 3      FALSE    5   0       C1                            40.7852  67.4825
#> 4      FALSE    5   0       C1                            48.5530  67.4825
#> 5      FALSE    5   0       C1                            44.0391  67.4825
#> 6      FALSE    5   0       C1                            34.0729  67.4825
#>    BL_CRCL BL_RENAL
#> 1 135.8911   normal
#> 2 135.8911   normal
#> 3 135.8911   normal
#> 4 135.8911   normal
#> 5 135.8911   normal
#> 6 135.8911   normal
nif_auto(examplinib_sad, RS2023 + RS2023487A ~ EXAMPLINIB, silent = TRUE) |>
head()
#>   REF ID    STUDYID           USUBJID AGE SEX  RACE HEIGHT WEIGHT     BMI
#> 1   1  1 2023000001 20230000011010001  43   0 WHITE  187.4     77 21.9256
#> 2   2  1 2023000001 20230000011010001  43   0 WHITE  187.4     77 21.9256
#> 3   3  1 2023000001 20230000011010001  43   0 WHITE  187.4     77 21.9256
#> 4   4  1 2023000001 20230000011010001  43   0 WHITE  187.4     77 21.9256
#> 5   5  1 2023000001 20230000011010001  43   0 WHITE  187.4     77 21.9256
#> 6   6  1 2023000001 20230000011010001  43   0 WHITE  187.4     77 21.9256
#>                   DTC TIME NTIME TAFD TAD EVID AMT    ANALYTE CMT PARENT TRTDY
#> 1 2000-12-31 10:18:00  0.0   0.0  0.0 0.0    1   5     RS2023   1 RS2023     1
#> 2 2000-12-31 10:18:00  0.0   0.0  0.0 0.0    0   0     RS2023   2 RS2023     1
#> 3 2000-12-31 10:18:00  0.0   0.0  0.0 0.0    0   0 RS2023487A   3 RS2023     1
#> 4 2000-12-31 10:48:00  0.5   0.5  0.5 0.5    0   0     RS2023   2 RS2023     1
#> 5 2000-12-31 10:48:00  0.5   0.5  0.5 0.5    0   0 RS2023487A   3 RS2023     1
#> 6 2000-12-31 11:18:00  1.0   1.0  1.0 1.0    0   0     RS2023   2 RS2023     1
#>   METABOLITE DOSE MDV ACTARMCD                 IMPUTATION      DV BL_CREAT
#> 1      FALSE    5   1       C1 time imputed from PCRFTDTC      NA  67.4825
#> 2      FALSE    5   0       C1                             0.0000  67.4825
#> 3       TRUE    5   0       C1                             0.0000  67.4825
#> 4      FALSE    5   0       C1                            40.7852  67.4825
#> 5       TRUE    5   0       C1                            13.8228  67.4825
#> 6      FALSE    5   0       C1                            48.5530  67.4825
#>    BL_CRCL BL_RENAL
#> 1 135.8911   normal
#> 2 135.8911   normal
#> 3 135.8911   normal
#> 4 135.8911   normal
#> 5 135.8911   normal
#> 6 135.8911   normal