PhViD (version 1.0.3)

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.

encoding

UTF-8

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, Broët{Broet} P, Tubert-Bitter P. False discovery rate estimation for frequentist pharmacovigilance signal detection methods. Biometrics. 2010 Mar;66(1):301-309.

Dalmasso C, Broët{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