icpower: Study design in the presence of error-prone diagnostic tests and self-reported outcomes

Description

This function calculates the power and sample in the presence of error-prone diagnostic tests and self-reported outcomes. Two missing mechanisms can be assumed, namely MCAR and NTFP. The MCAR setting assumes that each test is subject to a constant, independent probability of missingness. The NTFP mechanism includes two types of missingness - (1) incorporates a constant, independent, probability of missing for each test prior to the first positive test result; and (2) all test results after first positive are missing.

Usage

icpower(
  HR,
  sensitivity,
  specificity,
  survivals,
  N = NULL,
  power = NULL,
  rho = 0.5,
  alpha = 0.05,
  pmiss = 0,
  pcensor = 0,
  design = "MCAR",
  negpred = 1
)

Arguments

hazard ratio under the alternative hypothesis.

sensitivity

the sensitivity of test.

specificity

the specificity of test

survivals

a vector of survival function at each test time for baseline(reference) group. Its length determines the number of tests.

a vector of sample sizes to calculate corresponding powers. If one needs to calculate sample size, then set to NULL.

power

a vector of powers to calculate corresponding sample sizes. If one needs to calculate power, then set to NULL.

rho

proportion of subjects in baseline(reference) group.

alpha

type I error.

pmiss

a value or a vector (must have same length as survivals) of the probabilities of each test being randomly missing at each test time. If pmiss is a single value, then each test is assumed to have an identical probability of missingness.

pcensor

a value or a vector (must have same length as testtimes) of the probability of censoring at each visit, assuming censoring process is independent on other missing mechanisms.

design

missing mechanism: "MCAR" or "NTFP".

negpred

baseline negative predictive value, i.e. the probability of being truely disease free for those who were tested (reported) as disease free at baseline. If baseline screening test is perfect, then negpred = 1.

Value

result: a data frame with calculated sample size and power
I1 and I2: calculated unit Fisher information matrices for each group, which can be used to calculate more values of sample size and power for the same design without the need to enumerate again

Details

To calculate sample sizes for a vector of powers, set N = NULL. To calculate powers for a vector of sample sizes, set power = NULL. One and only one of power and N should be specified, and the other set to NULL. This function uses an enumeration algorithm to calculate the expected Fisher information matrix. The expected Fisher information matrix is used to obtain the variance of the coefficient corresponding to the treatment group indicator.

Examples

Run this code

# NOT RUN {
## First specificy survivals. Assume test times are 1:8, with survival function 
## at the end time 0.9  				  
surv <- exp(log(0.9)*(1:8)/8)					  

## Obtain power vs. N					  				
pow1 <- icpower(HR = 2, sensitivity = 0.55, specificity = 0.99, survivals = surv, 
   N = seq(500, 1500, 50), power = NULL, rho = 0.5, alpha = 0.05, 
   pmiss = 0, design = "MCAR", negpred = 1)

plot(pow1$result$N, pow1$result$power, type="l", xlab="N", ylab="power")

## Calculate sample size, assuming desired power is 0.9
pow2 <- icpower(HR = 2, sensitivity = 0.55, specificity = 0.99, survivals = surv,
   N = NULL, power = 0.9, rho = 0.5, alpha = 0.05, pmiss = 0, design = "MCAR",
   negpred = 1)

## When missing test is present with MCAR
pow3 <- icpower(HR = 2, sensitivity = 0.55, specificity = 0.99, survivals = surv,
   N = NULL, power = 0.9, rho = 0.5, alpha = 0.05, pmiss = 0.4, design = "MCAR",
   negpred = 1)

## When missing test is present with NTFP
pow4 <- icpower(HR = 2, sensitivity = 0.55, specificity = 0.99, survivals = surv,
   N = NULL, power = 0.9, rho = 0.5, alpha = 0.05, pmiss = 0.4, design = "NTFP",
   negpred = 1)

## When baseline misclassification is present
pow5 <- icpower(HR = 2, sensitivity = 0.55, specificity = 0.99, survivals = surv,
   N = NULL, power = 0.9, rho = 0.5, alpha = 0.05, pmiss = 0, design = "MCAR",
   negpred = 0.98)		 

## When test is  perfect and no missing test		 
pow6 <- icpower(HR = 2, sensitivity = 1, specificity = 1, survivals = surv,
   N = NULL, power = 0.9, rho = 0.5, alpha = 0.05, pmiss = 0, design = "MCAR",
   negpred = 1)	

## Different missing probabilities at each test time
pow7 <- icpower(HR = 2, sensitivity = 0.55, specificity = 0.99, survivals = surv,
   N = NULL, power = 0.9, rho = 0.5, alpha = 0.05, pmiss = seq(0.1, 0.8, 0.1),
   design = "MCAR")	  
   
# }