Title: | Correcting AUC for Measurement Error |
---|---|
Description: | Correcting area under ROC (AUC) for measurement error based on probit-shift model. |
Authors: | Bernard Rosner, Shelley Tworoger, Weiliang Qiu |
Maintainer: | Weiliang Qiu <[email protected]> |
License: | GPL (>= 2) |
Version: | 0.0.3 |
Built: | 2025-02-13 04:11:56 UTC |
Source: | https://github.com/cran/correctedAUC |
Calculate AUC corrected for measurement error based on Reiser's (2000) method.
AUCest.Reiser( datFrame, sidVar = "subjID", obsVar = "y", grpVar = "grp", repVar = "myrep", alpha = 0.05)
AUCest.Reiser( datFrame, sidVar = "subjID", obsVar = "y", grpVar = "grp", repVar = "myrep", alpha = 0.05)
datFrame |
a data frame with at least the following columns:
|
sidVar |
character. variable name for subject id in the data frame |
obsVar |
character. variable name for observations in the data frame |
grpVar |
character. variable name for group indictor in the data frame |
repVar |
character. variable name for replication indictor in the data frame |
alpha |
confidence interval level |
A list of 4 elements
AUC.c |
AUC corrected for measurement error based on Reiser's (2000) method. |
sd.AUC.c |
standard error of the estimated AUC corrected for measurement error based on Reiser's (2000) method. |
AUC.c.low |
lower bound of the |
AUC.c.upp |
upper bound of the |
Bernard Rosner <[email protected]>, Shelley Tworoger <[email protected]>, Weiliang Qiu <[email protected]>
Rosner B, Tworoger S, Qiu W (2015) Correcting AUC for Measurement Error. J Biom Biostat 6:270. doi:10.4172/2155-6180.1000270
set.seed(1234567) tt=genSimDataReiser( nX = 100, nY = 100, sigma.X2 = 1, mu.X = 0.25, sigma.Y2 = 1, mu.Y = 0, sigma.epsilon2 = 0.5, sigma.eta2 = 0.5) print(dim(tt$datFrame)) print(tt$datFrame[1:2,1:3]) print(tt$theta2) print(tt$mu.true) print(tt$AUC.true) res = AUCest.Reiser( datFrame = tt$datFrame, sidVar = "subjID", obsVar = "y", grpVar = "grp", repVar = "myrep", alpha = 0.05) print(res)
set.seed(1234567) tt=genSimDataReiser( nX = 100, nY = 100, sigma.X2 = 1, mu.X = 0.25, sigma.Y2 = 1, mu.Y = 0, sigma.epsilon2 = 0.5, sigma.eta2 = 0.5) print(dim(tt$datFrame)) print(tt$datFrame[1:2,1:3]) print(tt$theta2) print(tt$mu.true) print(tt$AUC.true) res = AUCest.Reiser( datFrame = tt$datFrame, sidVar = "subjID", obsVar = "y", grpVar = "grp", repVar = "myrep", alpha = 0.05) print(res)
Calculate AUC.c for measurement error based on probit-shift model.
AUCest.Rosner( datFrame, sidVar = "subjID", obsVar = "y", grpVar = "grp", repVar = "myrep", alpha = 0.05)
AUCest.Rosner( datFrame, sidVar = "subjID", obsVar = "y", grpVar = "grp", repVar = "myrep", alpha = 0.05)
datFrame |
a data frame with at least the following columns:
|
sidVar |
character. variable name for subject id in the data frame |
obsVar |
character. variable name for observations in the data frame |
grpVar |
character. variable name for group indictor in the data frame |
repVar |
character. variable name for replication indictor in the data frame |
alpha |
confidence interval level |
A list of 9 elements:
AUC.obs |
AUC estimated based on the Mann-Whitney statistic. |
AUC.c |
AUC corrected for measurement error based on the probit-shift model. |
ICC.x |
intra-class correlation for cases. |
ICC.y |
intra-class correlation for controls |
mu.mle |
maximum likelihood estimate of |
AUC.obs.low |
lower bound of the |
AUC.obs.upp |
upper bound of the |
AUC.c.low |
lower bound of the |
AUC.c.upp |
upper bound of the |
Bernard Rosner <[email protected]>, Shelley Tworoger <[email protected]>, Weiliang Qiu <[email protected]>
Rosner B, Tworoger S, Qiu W (2015) Correcting AUC for Measurement Error. J Biom Biostat 6:270. doi:10.4172/2155-6180.1000270
set.seed(1234567) tt=genSimDataModelIII( nX = 100, nY = 100, mu = 0.25, lambda = 0, sigma.X2 = 1, sigma.Y2 = 1, sigma.e.X = 1, sigma.e.Y = 1) print(dim(tt$datFrame)) print(tt$datFrame[1:2,1:3]) print(tt$AUC.true) res = AUCest.Rosner( datFrame = tt$datFrame, sidVar = "subjID", obsVar = "y", grpVar = "grp", repVar = "myrep", alpha = 0.05) print(res)
set.seed(1234567) tt=genSimDataModelIII( nX = 100, nY = 100, mu = 0.25, lambda = 0, sigma.X2 = 1, sigma.Y2 = 1, sigma.e.X = 1, sigma.e.Y = 1) print(dim(tt$datFrame)) print(tt$datFrame[1:2,1:3]) print(tt$AUC.true) res = AUCest.Rosner( datFrame = tt$datFrame, sidVar = "subjID", obsVar = "y", grpVar = "grp", repVar = "myrep", alpha = 0.05) print(res)
Generate one simulated data set based on Model II in Rosner et al's (2015) manuscript.
genSimDataModelII( nX, nY, mu, lambda, sigma.X2, sigma.Y2, sigma.e.X, sigma.e.Y)
genSimDataModelII( nX, nY, mu, lambda, sigma.X2, sigma.Y2, sigma.e.X, sigma.e.Y)
nX |
integer. number of cases. |
nY |
integer. number of controls. |
mu |
difference of means between the case distribution and control distribution. |
lambda |
mean for controls. |
sigma.X2 |
variance of the true value for cases. |
sigma.Y2 |
variance of the true value for controls. |
sigma.e.X |
variance of the random error term for cases. |
sigma.e.Y |
variance of the random error term for controls. |
The Model II in Rosner et al.'s (2005) manuscript:
A list of 2 elements:
datFrame |
A data frame with 4 elements:
|
AUC.true |
true AUC value |
Bernard Rosner <[email protected]>, Shelley Tworoger <[email protected]>, Weiliang Qiu <[email protected]>
Rosner B, Tworoger S, Qiu W (2015) Correcting AUC for Measurement Error. J Biom Biostat 6:270. doi:10.4172/2155-6180.1000270
set.seed(1234567) tt=genSimDataModelII( nX = 100, nY = 100, mu = 0.25, lambda = 0, sigma.X2 = 1, sigma.Y2 = 1, sigma.e.X = 1, sigma.e.Y = 1) print(dim(tt$datFrame)) print(tt$datFrame[1:2,1:3]) print(tt$AUC.true)
set.seed(1234567) tt=genSimDataModelII( nX = 100, nY = 100, mu = 0.25, lambda = 0, sigma.X2 = 1, sigma.Y2 = 1, sigma.e.X = 1, sigma.e.Y = 1) print(dim(tt$datFrame)) print(tt$datFrame[1:2,1:3]) print(tt$AUC.true)
Generate one simulated data set based on Model III in Rosner et al's (2015) manuscript.
genSimDataModelIII( nX, nY, mu, lambda, sigma.X2, sigma.Y2, sigma.e.X, sigma.e.Y)
genSimDataModelIII( nX, nY, mu, lambda, sigma.X2, sigma.Y2, sigma.e.X, sigma.e.Y)
nX |
integer. number of cases. |
nY |
integer. number of controls. |
mu |
difference of means between the case distribution and control distribution. |
lambda |
mean for controls. |
sigma.X2 |
variance of the true value for cases. |
sigma.Y2 |
variance of the true value for controls. |
sigma.e.X |
variance of the random error term for cases. |
sigma.e.Y |
variance of the random error term for controls. |
The Model III in Rosner et al.'s (2005) manuscript:
A list of 2 elements:
datFrame |
A data frame with 4 elements:
|
AUC.true |
true AUC value |
Bernard Rosner <[email protected]>, Shelley Tworoger <[email protected]>, Weiliang Qiu <[email protected]>
Rosner B, Tworoger S, Qiu W (2015) Correcting AUC for Measurement Error. J Biom Biostat 6:270. doi:10.4172/2155-6180.1000270
set.seed(1234567) tt=genSimDataModelIII( nX = 100, nY = 100, mu = 0.25, lambda = 0, sigma.X2 = 1, sigma.Y2 = 1, sigma.e.X = 1, sigma.e.Y = 1) print(dim(tt$datFrame)) print(tt$datFrame[1:2,1:3]) print(tt$AUC.true)
set.seed(1234567) tt=genSimDataModelIII( nX = 100, nY = 100, mu = 0.25, lambda = 0, sigma.X2 = 1, sigma.Y2 = 1, sigma.e.X = 1, sigma.e.Y = 1) print(dim(tt$datFrame)) print(tt$datFrame[1:2,1:3]) print(tt$AUC.true)
Generate one simulated data set based on Reiser's (2000) model. The true AUC will also be calculated.
genSimDataReiser( nX = 100, nY = 100, sigma.X2 = 1, mu.X = 0.25, sigma.Y2 = 1, mu.Y = 0, sigma.epsilon2 = 0.5, sigma.eta2 = 0.5)
genSimDataReiser( nX = 100, nY = 100, sigma.X2 = 1, mu.X = 0.25, sigma.Y2 = 1, mu.Y = 0, sigma.epsilon2 = 0.5, sigma.eta2 = 0.5)
nX |
integer. number of cases. |
nY |
integer. number of controls. |
sigma.X2 |
variance of the true value for cases. |
mu.X |
mean of the true value for cases. |
sigma.Y2 |
variance of the true value for controls. |
mu.Y |
mean of the true value for controls. |
sigma.epsilon2 |
variance of the random error term for cases. |
sigma.eta2 |
variance of the random error term for controls. |
Reiser's (2000) measurement error model is:
A list of 4 elements:
datFrame |
A data frame with 4 elements:
|
theta2 |
|
mu.true |
|
AUC.true |
true AUC value |
Bernard Rosner <[email protected]>, Shelley Tworoger <[email protected]>, Weiliang Qiu <[email protected]>
Rosner B, Tworoger S, Qiu W (2015) Correcting AUC for Measurement Error. J Biom Biostat 6:270. doi:10.4172/2155-6180.1000270
set.seed(1234567) tt=genSimDataReiser( nX = 100, nY = 100, sigma.X2 = 1, mu.X = 0.25, sigma.Y2 = 1, mu.Y = 0, sigma.epsilon2 = 0.5, sigma.eta2 = 0.5) print(dim(tt$datFrame)) print(tt$datFrame[1:2,1:3]) print(tt$theta2) print(tt$mu.true) print(tt$AUC.true)
set.seed(1234567) tt=genSimDataReiser( nX = 100, nY = 100, sigma.X2 = 1, mu.X = 0.25, sigma.Y2 = 1, mu.Y = 0, sigma.epsilon2 = 0.5, sigma.eta2 = 0.5) print(dim(tt$datFrame)) print(tt$datFrame[1:2,1:3]) print(tt$theta2) print(tt$mu.true) print(tt$AUC.true)