PRR {PhViD} | R Documentation |
Proportional Reporting Ratio proposed by Evans et al. (2001) extended to the multiple comparison framework.
PRR(DATABASE, RR0 = 1, MIN.n11 = 1, DECISION = 1, DECISION.THRES = 0.05, RANKSTAT = 1)
DATABASE |
Object returned by the function as.PhViD . |
RR0 |
Value of the tested relative risk. By default, RR0=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(PRR). |
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 relative risks (PRR), 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.
Evans SJ, Waller PC, Davis S, Use of Proportional Reporting Ratios (PRRs) for Signal Generation from Spontaneous Adverse Drug Reaction Reports Pharmacoepidemiology and Drug Safety, 2001, 10, 483-486.
## start data(PhViDdata.frame) PhViDdata <- as.PhViD(PhViDdata.frame) res <- PRR(PhViDdata) ## end