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Wrapper for P-value calculations

Source: R/by_strata_across_trt.R
p_val.Rd

Ensures the input to the statistical function is in the proper format, and enruse the output is formated to the need of the AMNOG workflow.

Usage

p_val(
  dat,
  event_index,
  cell_index,
  treatment_var,
  treatment_refval,
  subjectid_var,
  safe_mode = FALSE,
  threshold_lower = 5,
  threshold_upper = 200,
  ...
)

Arguments

dat

data.table. The analysis data set.

event_index

vector of integers that index the rows in dat that match the definition of an 'event'. Matching is done via the INDEX_ column in dat.

cell_index

A vector of integers referencing the rows of dat (as specified by the INDEX_ column in dat) that match the population to be analyzed. See the "Endpoint Events" vignette in ramnog for more information.

treatment_var

character. The name of the treatment variable in the data.

treatment_refval

character. The reference value of the treatment variable in the data.

subjectid_var

character. Name of the subject identifier variable in the data (default is "USUBJID").

safe_mode

Boolean determing if the function should fail when given input that cannot be calculated (safe_mode = TRUE), or if it should silently return a NA value (default).

threshold_lower

numeric. Lower threshold limit for selecting Fischer vs. Barnard.

threshold_upper

numeric. Upper threshold limit for selecting Fischer vs. Barnard.

...

Optional parameters.

Value

A data.table containing p-value statistics.

Examples

dat <- data.table::data.table(
  USUBJID = c("S1", "S2", "S3", "S4", "S5", "S6"),
  TRT     = c("Active", "Active", "Active", "Placebo", "Placebo", "Placebo")
)
dat[, INDEX_ := .I]
#>    USUBJID     TRT INDEX_
#>     <char>  <char>  <int>
#> 1:      S1  Active      1
#> 2:      S2  Active      2
#> 3:      S3  Active      3
#> 4:      S4 Placebo      4
#> 5:      S5 Placebo      5
#> 6:      S6 Placebo      6
data.table::setkey(dat, INDEX_)
p_val(dat, event_index = c(1L, 2L, 4L), cell_index = dat[["INDEX_"]],
      treatment_var = "TRT", treatment_refval = "Placebo",
      subjectid_var = "USUBJID")
#> ----- Calculating Barnards test - this may take a minute 
#>      label    description qualifiers  value
#>     <char>         <char>     <char>  <num>
#> 1: p-value Barnard's test       <NA> 0.6875