analyse_realdata: Analysis of the the real data (retrospective) according to...

In svetlanache/caden: What the Package Does (One Line, Title Case)

Analysis of the the real data (retrospective) according to the cross-validate adaptive enrichment risk scores (CADEN) design

Description

The design has two stages. At the end of stage 1, an interim analysis is performed to test the efficacy of the treatment compared to the control in the overall trial population. If the test in the overall population is significanct, the trial proceeds into stage 2 by analysing all patients (the "unselected" strategy). If the test in the overall population is not significant then the trial proceeds by testing whether there is a subgroup of patients (sensitive group) that show a promising treatment effect. Depending on the results of the test in the sensitive group, the design proceeds into stage 2 according to one of the mutually exclusive strategies "stop" or "enrichment".

Usage

analyse_realdata(
  datalist_stage1,
  datalist_stage2,
  threshold_overall,
  threshold_group,
  seed,
  standardise_cvrs = TRUE,
  full_model = TRUE
)

Arguments

threshold_overall	P-value threshold for the test for the differences in the treatment effect in the overall trial population
threshold_group	P-value threshold for the test for the treatment effect in the sensitive group
seed	A seed for random number generating
standardise_cvrs	A logical flag for the standardisation of the risk scores. Default is 'standardise_cvrs=TRUE'. The standardisation is performed with respect to the training data sets, per cross-validation fold.
full_model	A logical flag for the full model (treatment effect, covariate effect and the interaction effect). Default is 1full_model = TRUE. When 'full_model = FALSE', only interaction effect is included in the model
realdata_stage1	A list with two data frames (patients, covar) and two vectors (resp.rate, response) patients: a data frame with one row per patient and the following columns: FID (family ID), IID (individual ID), treat (1 for treatment and 0 for control), sens_status (true sensitivity status), stage (1) covar: a data frame with covariate data response: a vector of simulated binary responses
realdata_stage2	A list with two data frames with the same structure as realdata_stage1

Value

An object of class "caden".

decision: Enrichment, stop or unselected.

cvrs: A vector of the risk scores

sens_status_predicted: A vector of the predicted sensitivity status.

noneligible: Number of patients non-eligible for the trial (for the enrichment strategy).

pval_overall: P-value for the difference between the arm in the overall trial population.

pval_sens_group: P-value for the difference between the arms in the sensitive group (as assessed using Fisher exact test).

Author(s)

Svetlana Cherlin, James Wason

See Also

simulate_data, function.

Examples

data(realdata_stage1)
data(realdata_stage2)
threshold_overall = 0.04
threshold_group = 0.1
seed = 123
standardise_cvrs = 0
full_model = 0
real_res <- analyse_realdata(realdata_stage1, realdata_stage2, threshold_overall, threshold_group, seed, standardise_cvrs, full_model)

svetlanache/caden documentation built on Aug. 27, 2023, 3:36 p.m.