incpower: Power and Required Sample Size
In inctools: Incidence Estimation Tools

Description Usage Arguments Details Value Examples

Calculate power and required sample size for a given power to detect incidence change.

incpower(I1, I2, PrevH1, PrevH2, n1 = "both", n2 = "both",
  alpha = 0.05, Power = 0.8, SS = "out", CR = 1, DE_H = 1,
  DE_R = 1, BMest = "same.test", MDRI, RSE_MDRI, FRR, RSE_FRR,
  BigT = 730, Boot = FALSE, BS_Count = 1e+05, Cov.PrevH.I = c(0,
  0), debug = FALSE)

`I1`	Predicted incidence of HIV in survey 1.
`I2`	Predicted incidence of HIV in survey 2.
`PrevH1`	Predicted prevalence of HIV in survey 1.
`PrevH2`	Predicted prevalence of HIV in survey 2.
`n1`	Sample size for survey 1. If equal sample sizes for both surveys are desired at a given power level, both n1 and n2 must have value 'both', which is the default.
`n2`	Sample size for survey 2. If equal sample sizes for both surveys are desired at a given power level, both n1 and n2 must have value 'both', which is the default.
`alpha`	Significance level for test (default alpha=0.05).
`Power`	Desired power used to calculate a sample size for the surveys. Default is 0.80, meaning the function outputs the necessary sample size to achieve stated power for a test of differences in incidence. If Power is set to 'out', function will return power of detecting a difference in incidences for given sample size inputs.
`SS`	Sample size. Default is 'out', meaning the function takes a power argument and outputs a common sample size needed to achieve power level for test of differences for incidence. If power is desired for a given sample size, parameter value is irrelevant; however, values for n1 and n2 must be specified.
`CR`	Coverage rate (0-1).
`DE_H`	Design effect of HIV prevalence test (vector/integer). If a single value is specified, that value is assumed to be the value for both surveys.
`DE_R`	Design effect of recency test (vector/integer). If a single value is specified, that value is assumed to be the value for both surveys.
`BMest`	Biomarker test parameter (MDRI, FRR, and RSE) estimation by one the 3 options 'same.test'(default), 'FRR.indep', 'MDRI.FRR.indep' (string).
`MDRI`	mean duration of recent infection [days] (vector/integer). If a single value is specified, that value is assumed to be the value for both surveys.
`RSE_MDRI`	Relative standard error of MDRI [days] (vector/integer). If a single value is specified, that value is assumed to be the value for both surveys.
`FRR`	False recent rate (vector/integer). If a single value is specified, that value is assumed to be the value for both surveys.
`RSE_FRR`	Relative standard error of FRR (vector/integer). If a single value is specified, that value is assumed to be the value for both surveys.
`BigT`	Post-infection time cut-off (days). Default 730. If a single value is specified, that value is assumed to be the value for both surveys.
`Boot`	True/False variable indicating whether variance of point estimates is to be calculated by Empirical Bootstrapping (TRUE) or Delta Method (FALSE), the default setting.
`BS_Count`	Specifies number of bootstrap samples for bootstrapped confidence intervals of incidence.
`Cov.PrevH.I`	Covariance of prevalence and incidence for bootstrap resampling.
`debug`	Enable debugging mode (browser)

The package contains long form documentation in the form of vignettes that cover the use of the main fucntions. Use browseVignettes(package="inctools") to access them.

Common sample size of two surveys–or the sample size of one survey given the other has already been completed–necessary to achieve a given power level for testing a null hypothesis that the incidence rates are identical between populations; alternatively, the power of said test under a particular sample size scenario. Function also returns implied statistics from input values on paramters, confidence limits, and population counts.

incpower(I1 = 0.05, I2 = 0.03, PrevH1 = 0.20, PrevH2 = 0.20,
n1 = 5000, n2 = 5000, alpha = 0.05, Power = "out", SS = NULL,
DE_H = c(1,1.1), DE_R = 1, BMest = 'same.test', MDRI = 200,
RSE_MDRI = 0.05, FRR = 0.01, RSE_FRR = 0.20, BigT = 730)


incpower(I1 = 0.05, I2 = 0.03, PrevH1 = 0.20, PrevH2 = 0.20,
alpha = 0.05, Power = 0.80, SS = "out", DE_H = 1, DE_R = 1,
BMest = 'FRR.indep', MDRI = 200, RSE_MDRI = 0.05,
FRR = c(0.01,0.009), RSE_FRR = c(0.20,0.21), BigT = 730)

$Inc.Difference.Statistics
  deltaI_Est RSE_deltaI RSE_deltaI.infSS     Power Power.infSS      CI.low
1       0.02  0.3303751       0.05244431 0.8569912       >0.99 0.007049534
       CI.up
1 0.03295047

$Implied.Incidence.Statistics
  Survey Given.I     RSE_I     CI.low      CI.up
1      1    0.05 0.1151054 0.03871987 0.06128013
2      2    0.03 0.1469490 0.02135956 0.03864044

$Implied.MDRI.Statistics
  Given.MDRI CI.low CI.up
1        200  180.4 219.6

$Implied.FRR.Statistics
  Given.FRR CI.low CI.up
1      0.01  0.006 0.014

$Implied.Subject.Counts
                           Survey.1 Survey.2
HIV.negative                   4000     4000
HIV.positive                   1000     1000
HIV.post.tested.for.recent     1000     1000
Recency.test.pos                116       73

$Minimum.Common.SS
[1] 4297

$Inc.Difference.Statistics
  deltaI_Est RSE_deltaI RSE_deltaI.infSS     Power Power.infSS     CI.low
1       0.02  0.3569374       0.06842988 0.8000074       >0.99 0.00600831
       CI.up
1 0.03399169

$Implied.Incidence.Statistics
  Survey Given.I     RSE_I     CI.low      CI.up
1      1    0.05 0.1222911 0.03801569 0.06198431
2      2    0.03 0.1549998 0.02088618 0.03911382

$Implied.MDRI.Statistics
  Given.MDRI CI.low CI.up
1        200  180.4 219.6

$Implied.FRR.Statistics
  Given.FRR CI.low  CI.up
1     0.010 0.0061 0.0139
2     0.009 0.0053 0.0127

$Implied.Subject.Counts
                           Survey.1 Survey.2
HIV.negative                   3438     3438
HIV.positive                    859      859
HIV.post.tested.for.recent      859      859
Recency.test.pos                 99       62