PhViD (version 1.0.1)

ROR: Reporting Odds Ratio

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).

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 ($n1. \times n.1 / N$, 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.

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.

References

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.

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