aco2arm {TwoPhaseInd}R Documentation

A function to estimate parameters in augmented case-only designs, the genotype is ascertained for a random subcohort from both the active treatment arm and the placebo arm

Description

This function estimates parameters of proportional hazards model with gene-treatment interaction. It employs case-cohort estimation incorporating the case-only estimators. The method was published in Dai et al. (2015) Biometrics.

Usage

aco2arm(data, svtime, event, treatment, BaselineMarker, id, 
subcohort, esttype = 1, extra)

Arguments

data

A data frame used to access the following data.

svtime

A character string of column name, corresponds to one column of the data frame, which is used to store the failure time variable (numeric).

event

A character string of column name, corresponds to one column of the data frame,which is used to store the indicator of failure event (1: failure, 0: not failure).

treatment

A character string of column name, corresponds to one column of the data frame, which is used to store the binary vector of treatment variable (1: treatment, 0: placebo).

BaselineMarker

A character string of column name, corresponds to one column of the data frame, which is used to store a vector of biomarker.

id

A character string of column name, corresponds to one column of the data frame, which is used to store the sample identifier.

subcohort

A character string of column name, corresponds to one column of the data frame, which is used to store the indicator of sub-cohort (1: sample belong to the sub-cohort, 0: not belong to the sub-cohort)

esttype

The option of estimation methods (1: Self-Prentice estimator, 0: Lin-Ying estimator).

extra

A string vector of column name(s), corresponds to more or more column(s) of the data frame, which is/are used to store the extra baseline covariate(s) to be adjusted for in addition to treatment and biomarker.

Details

The function returns estimates of the proportional hazards model, and variance of the estimates. The method was published in Dai et al. (2015) Biometrics.

Value

beta

Estimated parameter

stder

Standard error

pVal

p value

Author(s)

James Y. Dai

References

J. Y. Dai, X. C. Zhang,C. Y. Wang, and C. Kooperberg. Augmented case-only designs for randomized clinical trials with failure time endpoints. Biometrics, DOI: 10.1111/biom.12392, 2016.

See Also

aco1arm

Examples

## Load the example data
data(acodata)
## Case-cohort + case-only estimators
rfit1 <- aco2arm(data=acodata,
                 svtime="vacc1_evinf",
                 event="f_evinf",
                 treatment="f_treat",
                 BaselineMarker="fcgr2a.3",
                 id="ptid",
                 subcohort="subcoh",
                 esttype=1,
                 extra=c("f_agele30","f_hsv_2","f_ad5gt18","f_crcm",
                 "any_drug","num_male_part_cat","uias","uras")) 
rfit1

[Package TwoPhaseInd version 1.1.1 Index]