Description Usage Arguments Details Value Examples

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

1 2 3 4 5 |

`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.

1 2 3 4 5 6 7 8 9 10 | ```
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
```

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