power.calc: Generate the power to detect the difference between two...

In jsnwyse/simvitD: Simulation Tools for Planning Vitamin D Studies

Generate the power to detect the difference between two groups

Description

generates a value for the power between two groups

Usage

  power.calc( n, ratio=1, N = 500, test.type, sig.level = 0.05,
    vitdcurves.placebo = NULL, vitdcurves.treatment = NULL,
  	baseline = 0.03, RR = 3, rate = 1, intensity.func = intensity.function(), 
  	holding.time = 2, lohi.vit = c(10,70), clt = NULL, mc.error = 1, boot.rep = 500, 
  	parallel = FALSE, num.cores = NULL, verbose=FALSE )

Arguments

n	Numeric, the number of participants in the control group.
ratio	Ratio greater than or equal to 1 giving size of treatment group as a multiple of n. Defaults to groups of equal size.
N	Number of simulations of the study to run.
test.type	Type of test to calculate the power, one of "count" or "proportions".
sig.level	Significance level used to test for a statistically significant difference between the groups.
vitdcurves.placebo	An object of class vitd.curve.
vitdcurves.treatment	An object of class vitd.curve.
baseline	Baseline prevalence of getting diseased at any exposure time. Probability of getting diseased when a participant has sufficient vitamin D levels.
RR	Fold risk difference between getting infection between the most deficient and most sufficient vitamin D levels.
rate	Expected number of exposures per week, the rate at which exposures occur in the equivalent homogeneous Poisson process.
intensity.func	Function taking time as sole argument and returns value between 0 and 1, input to nhpp function see poisson package.
holding.time	Expected number of weeks for the holding time.
lohi.vit	Inflection points of the relative risk curve used in infection.count.
clt	Vector or single logical variable indicating whether Central Limit Theorem should be used to approximate the p-value.
mc.error	Number of times to repeat the experiment at each n value to explore Monte Carlo error.
boot.rep	Number of bootstrap samples to carry out non-parametric tests of hypotheses.
parallel	Use parallel processing to carry out the simulations. This will parallelise over mc.error.
num.cores	Number of cores to exploit in parallel mode. Defaults to (cores available) - 1.
verbose	If TRUE print out regular updates on progression. Not available when parallel is set to TRUE.

Value

power.calc returns an object of class power.calc that is a list. The list has the following slots.

test.type	The type of study the power has been calculated on.
baseline	The baseline prevalence for disease.
RR	The relative risk of the study.
npergroup	The number of participants per group in the study.
mc.error	Number of repetitions of experiment to approximate Monte Carlo error.
power	A length(RR) x mc.error x length(npergroup) array of estimated power values.
eff.size	A length(RR) x mc.error x length(npergroup) array of estimated treatment effects (differences between groups).

Author(s)

Rebecca Mangan and Jason Wyse

Examples

# simulate placebo group
placebo <- vitd.curve( n = 10, type = "placebo" )

# simulate treatment group
treatment <- vitd.curve( n = 10, type = "dynamic-dose" )

# intensity function for exposures to infection
intensfun <- intensity.function( summer.rate = 0, winter.rate = 1 )
  
# calculate power: example only- run for much larger num.sims
pow <- power.calc( n = c(10,20,30), 
        N = 10,  test.type = 'count', 
        vitdcurves.placebo = placebo, vitdcurves.treatment = treatment,
        baseline = 0.03, RR = c(2,3,4), rate = 1, intensity.func = intensfun )
            
### NOT RUN ###            
# approximate the Monte Carlo error in estimation of the power-- takes longer to run
#pow <- power.calc( n = c(10,20,30), 
#         N = 100, test.type = 'count', 
#         vitdcurves.placebo = placebo, vitdcurves.treatment = treatment,
#         baseline = 0.03, RR = c(2,3,4), rate = 1, 
#         intensity.func = intensfun, mc.error = 10 )

# plot power curves
plot( pow, xlab = "n", x.legend = 10, y.legend = 1, main.legend = "Relative Risk" )

jsnwyse/simvitD documentation built on April 21, 2022, 6:59 a.m.