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Calculates case fatality ratio from incomplete epidemic data

casefat[ifexp] [inrange] ,dead(deathvar)rec(recvar)t(eventtime)[gen(prefix)replacegreenwooduntransorigin(originvar)cens(censtime)]

Description

casefatestimates the case fatality ratio (CFR), the proportion of cases who ultimately die of the disease, using incomplete data such as would be available part-way through an epidemic: some patients are observed to have died or recovered, but others are still ill.

Options

dead(deathvar)andrec(recvar)are indicator variables for death and recovery respectively. Both options are required.deathvar= 1 means death,recvar= 1 means recovery, and both equal to 0 means that the subject is censored.

t(eventtime)is required. It records the time of death, recovery or censoring for each subject. If the optionorigin(originvar)is not specified, theneventtimeis the time since the patient became at risk of death or recovery, which would normally be the time since infection. Iforigin(originvar)is specified thenoriginvaris the calendar time the subject became at risk andeventtimeis the calendar time of death, recovery or censoring

gen(prefix)creates three new variables,prefix0,prefix1 andprefixt.prefix0 andprefix1 are the estimated cumulative incidence functions for death and recovery at timeprefixt. Ifreplaceis also specified, then any existing variables with these names are replaced.

greenwoodrequests that the variance-covariance matrix of the survivor function be calculated using Greenwood's formula.

untransrequests that confidence intervals be calculated on the untransformed scale. The default is to use the logit scale.

cens(censtime)specifies a calendar time at which the data are to be censored, to illustrate what the estimates would have been if the analysis had been carried out then. This option only makes sense ift(eventtime)refers to calendar time.

RemarksThe data should be in the form of one record per person. The Kaplan-Meier-like estimate of the CFR, its standard error, and theta0 and 1-theta1, the estimated lower and upper bounds of the CFR, are calculated according to the formulae given in: Ghani, A. C. et al. Methods for estimating the case fatality ratio for a novel emerging infectious disease. American Journal of Epidemiology September 2005 Vol 162 No 5 In addition, two more simple estimates of the CFR are calculated. These are: E1=D/C and E2=D/(D+R) where C, D and R are the numbers of cases, deaths and recoveries observed so far. Jeffreys binomial confidence intervals are calculated for these two statistics.

Examples

. casefat, t(t) dead(dead) rec(rec). casefat, t(t) dead(dead) rec(rec) gen(theta) replace

Jamie Griffin and Azra Ghani Imperial College, London jamie.griffin@imperial.ac.uk Updated 7th May 2009Authors