ROR: Reporting Odds Ratio

In PhViD: PharmacoVigilance Signal Detection

Description

Reporting Odds Ratio proposed by van Puijenbroak et al. (2002) extended to the multiple comparison framework.

Usage

ROR(DATABASE, OR0 = 1, MIN.n11 = 1, DECISION = 1, 
DECISION.THRES = 0.05, RANKSTAT = 1)

Arguments

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).

Details

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.

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.

Author(s)

Ismaïl Ahmed & Antoine Poncet

References

Ahmed I, Dalmasso C, Haramburu F, Thiessard F, Broët P, Tubert-Bitter P. False discovery rate estimation for frequentist pharmacovigilance signal detection methods. Biometrics. 2010 Mar;66(1):301-309.

Dalmasso C, Broët 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.

Examples

## 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

Example output

Loading required package: LBE
Loading required package: MCMCpack
Loading required package: coda
Loading required package: MASS
##
## Markov Chain Monte Carlo Package (MCMCpack)
## Copyright (C) 2003-2020 Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
##
## Support provided by the U.S. National Science Foundation
## (Grants SES-0350646 and SES-0350613)
##

PhViD documentation built on May 2, 2019, 11:37 a.m.