Description Usage Arguments Value Author(s) References Examples
Calculate the power for testing delta=0 based on a dataset.
1 2 3 4 5 | powerCalData(
nSubj,
triangle,
frame,
alpha = 0.05)
|
nSubj |
integer. number of subjects to be generated. Assume each subject has two observations. |
triangle |
the difference of the expected value the the extended Mann-Whitney U statistics between two prediction rules, i.e., triangle = eta^{(1)}_c - eta^{(2)}_c |
frame |
A data frame with 5 columns: cid, subuid, status, score1, and score2.
|
alpha |
type I error rate |
A list with 11 elements.
power |
the esstimated power |
rho |
rho=corr(H(Z_{ij}), H(Z_{k ell})) , where H=Phi^{-1} is the probit transformation. |
rho11 |
rho_{11}=corr(H_{ij}^{(1)}, H_{i ell}^{(1)}) , where H=Phi^{-1} is the probit transformation. |
rho22 |
rho_{22}=corr(H_{ij}^{(2)}, H_{i ell}^{(2)}) , where H=Phi^{-1} is the probit transformation. |
rho12 |
rho_{12}=corr(H_{ij}^{(1)}, H_{i ell}^{(2)}) , where H=Phi^{-1} is the probit transformation. |
p11 |
p_{11}=Pr(delta_{i1}=1 & delta_{i2}=1) , where delta_{ij}=1 if the j-th subunit of the i-th cluster has progressed. |
p10 |
p_{10}=Pr(delta_{i1}=1 & delta_{i2}=0) , where delta_{ij}=1 if the j-th subunit of the i-th cluster has progressed. |
p01 |
p_{01}=Pr(delta_{i1}=0 & delta_{i2}=1) , where delta_{ij}=1 if the j-th subunit of the i-th cluster has progressed. |
p00 |
p_{00}=Pr(delta_{i1}=0 & delta_{i2}=0) , where delta_{ij}=1 if the j-th subunit of the i-th cluster has progressed. |
mu1 |
mu_1=H(Y)-H(Y_c) is the difference between probit transformation H(Y) and probit-shift alternative H(Y_c) for the first prediction score, where Y is the prediction score of a randomly selected progressing subunit, and Y_c is the counterfactual random variable obtained if each subunit that had progressed actually had not progressed. |
mu2 |
mu_2=H(Y)-H(Y_c) is the difference between probit transformation H(Y) and probit-shift alternative H(Y_c) for the second prediction score, where Y is the prediction score of a randomly selected progressing subunit, and Y_c is the counterfactual random variable obtained if each subunit that had progressed actually had not progressed. |
Bernard Rosner <stbar@channing.harvard.edu>, Weiliang Qiu <Weiliang.Qiu@gmail.com>, Meiling Ting Lee <MLTLEE@umd.edu>
Rosner B, Qiu W, and Lee MLT. Assessing Discrimination of Risk Prediction Rules in a Clustered Data Setting. Lifetime Data Anal. 2013 Apr; 19(2): 242-256.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 | set.seed(1234567)
datFrame = genSimDataGLMEM(nSubj = 30, beta0 = -6, sd.beta0i = 1.58,
beta1 = 1.58, beta2 = -3.95, beta3 = 3.15, beta4 = 2.06,
beta5 = 0.51, beta6 = 1.47, beta7 = 3.11,
p.smkcur = 0.08, p.inieye31 = 0.44, p.inieye32 = 0.42,
p.inieye41 = 0.12, p.inieye42 = 0.11, sd.lncalorc = 0.33)
print(dim(datFrame))
print(datFrame[1:2,])
# prediction rule 1
tt1 = getScore(fmla = prog~smkcur+lncalorc+inieye3+inieye4+factor(rtotfat),
cidVar = "cid", subuidVar = "subuid", statusVar = "prog",
datFrame = datFrame, mycorstr = "exchangeable",
verbose = FALSE)
myframe1=tt1$frame
print(dim(myframe1))
print(myframe1[1:3,])
####
# prediction rule 2
tt2 = getScore(fmla = prog~smkcur+lncalorc+inieye3+inieye4,
cidVar = "cid", subuidVar = "subuid", statusVar = "prog",
datFrame = datFrame, mycorstr = "exchangeable",
verbose = FALSE)
myframe2=tt2$frame
print(dim(myframe2))
print(myframe2[1:3,])
# combine scores from two prediction rules
myframe12=myframe1[, c("cid", "subuid", "status")]
myframe12$score1=myframe1$score
myframe12$score2=myframe2$score
print(dim(myframe12))
print(myframe12[1:3,])
res = powerCalData(nSubj = 30, triangle = 0.05, frame=myframe12, alpha = 0.05)
print(res)
|
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