ROR {PhViD} | R Documentation |
Reporting Odds Ratio proposed by van Puijenbroak et al. (2002) extended to the multiple comparison framework.
ROR(DATABASE, OR0 = 1, MIN.n11 = 1, DECISION = 1, DECISION.THRES = 0.05, RANKSTAT = 1)
DATABASE |
Object returned by the function as.PhViD . |
OR0 |
Value of the tested odds ratio. By default, OR0=1 . |
MIN.n11 |
Minimum number of notifications for a couple to be potentially considered as a signal. By default, MIN.n11 = 1 . |
DECISION |
Decision rule for the signal generation based on
1 = FDR (Default value) 2 = Number of signals 3 = Ranking statistic. See RANKSTAT |
DECISION.THRES |
Threshold for DECISION . Ex 0.05 for FDR (DECISION =1). |
RANKSTAT |
Statistic used for ranking the couples:
1 = P-value 2 = Lower bound of the 95% two sided confidence interval of log(ROR). |
The FDR is estimated with the LBE procedure proposed by Dalmasso et al. (2005). Note that the FDR can only be estimated if the statistic of interest is the P-value.
ALLSIGNALS |
Data.frame summarizing the results of all couples with at least MIN.n11 notifications ordered by RANKSTAT . It contains notably the labels, the cell counts, the expected counts (n1. * n.1 / N, see as.PhViD ), RANKSTAT , the observed odds ratios (ROR), the marginal counts and the estimations of FDR (when
RANKSTAT=1 .) |
SIGNALS |
Same Data.frame as ALLSIGNALS but restricted to the list of generated signals. |
NB.SIGNALS |
Number of generated signals. |
INPUT.PARAM |
Parameters entered in the function. |
Ismail Ahmed & Antoine Poncet
Ahmed I, Dalmasso C, Haramburu F, Thiessard F, Broet P, Tubert-Bitter P, False Discovery Rate Estimation for Frequentist Pharmacovigilance Signal Detection Methods, Biometrics, accepted.
Dalmasso C, Broet P, Moreau T (2005), A simple procedure for estimating the false discovery rate, Bioinformatics, Bioinformatics, 21: 660 - 668.
van Puijenbroek EP, Bate A, Leufkens HG, Lindquist M, Orre R, Egberts AC, A Comparison of Measures of Disproportionality for Signal Detection in Spontaneous Reporting Systems for Adverse Drug Reactions Pharmacoepidemiology and Drug Safety, 2002, 11, 3-1.
## start data(PhViDdata.frame) PhViDdata <- as.PhViD(PhViDdata.frame) res <- ROR(PhViDdata, MIN.n11 = 3) # Decision rule proposed by van Puijenbroek et al. (2002) res2 <- ROR(PhViDdata, MIN.n11 = 1, DECISION=3, DECISION.THRES=0, RANKSTAT=2) ## end