gen.exp: Generate covariates for drug-exposure follow-up from drug purchase records.

Description

From records of drug purchase and possibly known treatment intensity, the time since first drug use and cumulative dose at prespecified times is computed. Optionally, lagged exposures are computed too, i.e. cumulative exposure a prespecified time ago.

Usage

gen.exp(purchase, id = "id", dop = "dop", amt = "amt", dpt = "dpt",
              fu, doe = "doe", dox = "dox",
          breaks,
         use.dpt = ( dpt %in% names(purchase) ),
            lags = NULL,
        push.max = Inf,
        pred.win = Inf,
         lag.dec = 1 )

Arguments

purchase

Data frame with columns id-person id, dop - date of purchase, amt - amount purchased, and optionally dpt - (dose per time) ("defined daily dose", DDD, that is), how much is assume to be ingested per unit time. The units used for dpt is assumed to be units of amt per units of dop.

Character. Name of the id variable in the data frame.

dop

Character. Name of the date of purchase variable in the data frame.

amt

Character. Name of the amount purchased variable in the data frame.

dpt

Character. Name of the dose-per-time variable in the data frame.

Data frame with follow-up period for each person, the person id variable must have the same name as in the purchase data frame.

doe

Character. Name of the date of entry variable.

dox

Character. Name of the date of exit variable.

use.dpt

Logical: should we use information on dose per time.

breaks

Numerical vector of dates at which the time since first exposure, cumulative dose etc. are computed.

lags

Numerical vector of lag-times used in computing lagged cumulative doses.

push.max

Numerical. How much can purchases maximally be pushed forward in time. See details.

pred.win

The length of the window used for constructing the average dose per time used to compute the duration of the last purchase

lag.dec

How many decimals to use in the construction of names for the lagged exposure variables

Value

A data frame with one record per follow-up interval between breaks, with columns:

id: person id.
dof: date of follow up, i.e. start of interval. Apart from possibly the first interval for each person, this will assume values in the set of the values in breaks.
Y: the length of interval.
tfi: time from first initiation of drug.
tfc: time from latest cessation of drug.
cdur: cumulative duration of the drug.
cdos: cumulative dose.
ldos: suffixed with one value per element in lags, the latter giving the cumulative doses lags before dof.

Details

Each purchase record is converted into a time-interval of exposure.

If use.dpt is TRUE then the dose per time information is used to compute the exposure interval associated with each purchase. Exposure intervals are stacked, that is each interval is put after any previous. This means that the start of exposure to a given purchase can be pushed into the future. The parameter push.max indicates the maximally tolerated push. If this is reached by a person, the assumption is that some of the purchased drug is not counted in the exposure calculations.

The dpt can either be a constant, basically translating the purchased amount into exposure time the same way for all persons, or it can be a vector with different treatment intensities for each purchase. In any case the cumulative dose is computed taking this into account.

If use.dpt is FALSE then the exposure from one purchase is assumed to stretch over the time to the next purchase, so we are effectively assuming different rates of dose per time between any two adjacent purchases. Moreover, with this approach, periods of non-exposure does not exist. Formally this approach conditions on the future, because the rate of consumption (the accumulation of cumulative exposure) is computed based on knowledge of when next purchase is made.

The intention of this function is to generate covariates for a particular drug for the entire follow-up of each person. The reason that the follow-up prior to drug purchase and post-exposure is included is that the covariates must be defined for these periods too, in order to be useful for analysis of disease outcomes.

This function is described in terme of calendar time as underlying time scale, because this will normally be the time scale for drug purchases and for entry and exit for persons. In principle the variables termed as dates might equally well refer to say the age scale, but this would then have to be true both for the purchase data and the follow-up data.

Examples

Run this code

# NOT RUN {
# Construct a simple data frame of purchases for 3 persons
# The purchase units (in variable dose) correspond to
n <- c( 10, 17, 8 )
dop <- c( 1995.2+cumsum(sample(1:4/10,n[1],replace=TRUE)),
          1997.3+cumsum(sample(1:4/10,n[2],replace=TRUE)),
          1997.3+cumsum(sample(1:4/10,n[3],replace=TRUE)) )
amt <- sample(   1:3/15, sum(n), replace=TRUE )
dpt <- sample( 15:20/25, sum(n), replace=TRUE )
dfr <- data.frame( id = rep(1:3,n),
                  dop,
                  amt = amt,
                  dpt = dpt )
round( dfr, 3 )
# Construct a simple dataframe for follow-up periods for these 3 persons
fu  <- data.frame( id = 1:3,
                  doe = c(1995,1997,1996)+1:3/4,
                  dox = c(2001,2003,2002)+1:3/5 )
round( fu, 3 )
( dpos <- gen.exp( dfr,
                    fu = fu,
                breaks = seq(1990,2015,0.5),
                  lags = 2:3/5 ) )
( xpos <- gen.exp( dfr,
                    fu = fu,
               use.dpt = FALSE,
                breaks = seq(1990,2015,0.5),
                  lags = 2:3/5 ) )

# How many relevant columns
nvar <- ncol(xpos)-3
clrs <- rainbow(nvar)

# Show how the variables relate to the follow-up time
par( mfrow=c(3,1), mar=c(3,3,1,1), mgp=c(3,1,0)/1.6, bty="n" )
for( i in unique(xpos$id) )
matplot( xpos[xpos$id==i,"dof"],
         xpos[xpos$id==i,-(1:3)],
         xlim=range(xpos$dof), ylim=range(xpos[,-(1:3)]),
         type="l", lwd=2, lty=1, col=clrs,
         ylab="", xlab="Date of follow-up" )
ytxt <- par("usr")[3:4]
ytxt <- ytxt[1] + (nvar:1)*diff(ytxt)/(nvar+2)
xtxt <- rep( sum(par("usr")[1:2]*c(0.98,0.02)), nvar )
text( xtxt, ytxt, colnames(xpos)[-(1:3)], font=2,
                  col=clrs, cex=1.5, adj=0 )
# }