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Add baseline and change from baseline fields

Source: R/nif_class.R
add_cfb.Rd

Add baseline and change from baseline fields

Usage

add_cfb(
  obj,
  baseline_filter = "TIME <= 0",
  summary_function = median,
  silent = NULL
)

Arguments

obj

A NIF object.

baseline_filter

A filter term to identify the baseline condition.

summary_function

The function to derive the baseline. This function is applied over the DV values identified by the 'baseline_filter' term. The default function is median. Alternatively, mean, min or max can be considered.

silent

Suppress messages, defaults to nif_option setting if NULL.

Value

A NIF object

Details

Output fields:

  • DVBL Baseline value for the dependent variable DV.

  • DVCFB Change from baseline for the dependent variable DV.

The Baseline is calculated as the median (or the summary function output) of the DV field for all time points identified by the baseline_filter' term.

Examples

head(add_cfb(examplinib_poc_nif))
#>   REF ID    STUDYID           USUBJID AGE SEX  RACE HEIGHT WEIGHT      BMI
#> 1   1  1 2023000022 20230000221010001  58   1 WHITE  185.3   91.4 26.61922
#> 2   2  1 2023000022 20230000221010001  58   1 WHITE  185.3   91.4 26.61922
#> 3   3  1 2023000022 20230000221010001  58   1 WHITE  185.3   91.4 26.61922
#> 4   4  1 2023000022 20230000221010001  58   1 WHITE  185.3   91.4 26.61922
#> 5   5  1 2023000022 20230000221010001  58   1 WHITE  185.3   91.4 26.61922
#> 6   6  1 2023000022 20230000221010001  58   1 WHITE  185.3   91.4 26.61922
#>                   DTC  TIME NTIME  TAFD   TAD PCELTM EVID AMT    ANALYTE CMT
#> 1 2001-01-13 10:36:00 0.000   0.0 0.000 0.000   <NA>    1 500     RS2023   1
#> 2 2001-01-13 10:36:00 0.000   0.0 0.000 0.000   PT0H    0   0     RS2023   2
#> 3 2001-01-13 10:36:00 0.000   0.0 0.000 0.000   PT0H    0   0 RS2023487A   3
#> 4 2001-01-13 11:36:00 1.000   0.5 1.000 1.000 PT0.5H    0   0     RS2023   2
#> 5 2001-01-13 11:36:00 1.000   0.5 1.000 1.000 PT0.5H    0   0 RS2023487A   3
#> 6 2001-01-13 12:04:00 1.467   1.0 1.467 1.467   PT1H    0   0     RS2023   2
#>   PARENT TRTDY METABOLITE DOSE MDV  ACTARMCD                       IMPUTATION
#> 1 RS2023     1      FALSE  500   1 TREATMENT admin time imputed from PCRFTDTC
#> 2 RS2023     1      FALSE  500   0 TREATMENT                                 
#> 3 RS2023     1      FALSE  500   0 TREATMENT                                 
#> 4 RS2023     1      FALSE  500   0 TREATMENT                                 
#> 5 RS2023     1      FALSE  500   0 TREATMENT                                 
#> 6 RS2023     1      FALSE  500   0 TREATMENT                                 
#>          DV BL_CREAT  BL_CRCL DVBL     DVCFB
#> 1        NA 72.78062 107.4689    0        NA
#> 2    0.0000 72.78062 107.4689    0    0.0000
#> 3    0.0000 72.78062 107.4689    0    0.0000
#> 4  636.6833 72.78062 107.4689    0  636.6833
#> 5  135.1259 72.78062 107.4689    0  135.1259
#> 6 1844.8225 72.78062 107.4689    0 1844.8225
head(add_cfb(examplinib_poc_min_nif))
#>   ID  TIME EVID AMT ANALYTE CMT MDV RATE       DV DVBL    DVCFB
#> 1  1 0.000    1 500       1   1   1    0       NA   NA       NA
#> 2  1 0.000    0   0       2   2   0    0 0.000000    0 0.000000
#> 3  1 0.000    0   0       3   3   0    0 0.000000    0 0.000000
#> 4  1 2.167    0   0       2   2   0    0 3.380265    0 3.380265
#> 5  1 2.167    0   0       3   3   0    0 3.453869    0 3.453869
#> 6  1 4.633    0   0       2   2   0    0 1.477397    0 1.477397