Nothing
.setUp <- function(){
#data(respWutzler10)
.setUpDf <- within( list(),{
rde <- subset(respWutzler10, suite == "Face" & experiment == 3 )
})
attach(.setUpDf)
}
.tearDown <- function(){
detach()
}
test.fitKinrespExperiment <- function(){
plot( resp ~ time, data=rde, col=as.numeric(rde$rep) )
#mtrace(kinrespGrowthphaseExperiment)
res4 <- kinrespGrowthphaseExperiment(rde, weights=varPower(fixed=0.5) )
# extract the dataset of unlimited growth
rde.e <- getUnlimitedGrowthData(res4)
# get the initial values (microbial parameters of replicate fits)
coefRep <- coefKinresp(res4)
# fit the mixed model
#mtrace(fitKinrespExperiment)
res5 <- fitKinrespExperiment( rde.e, coefRep )
summary(res5$model)
coefKinresp(fixef(res5$model))
confintKinresp(confint(res5$model))
#mtrace(momentsLogitnorm)
(pars <- kinrespParDist(res5$model))
iPar="x0"
xGrid <- seq( pars[iPar,"cf025"]*0.8, pars[iPar,"cf975"]*1.2, length.out=80)
fx <- dlnorm(xGrid, meanlog=pars[iPar,"mu"],sdlog=pars[iPar,"sigma"])
plot( fx ~ xGrid, type="l" )
abline(v=pars[iPar,c("mle","median","mean","cf025","cf975")], col=c("red","green","blue","gray","gray"))
iPar="r0"
xGrid <- seq( pars[iPar,"cf025"]*0.8, pars[iPar,"cf975"]*1.2, length.out=80)
fx <- dlogitnorm(xGrid, mean=pars[iPar,"mu"],sd=pars[iPar,"sigma"])
plot( fx ~ xGrid, type="l" )
abline(v=pars[iPar,c("mle","median","mean","cf025","cf975")], col=c("red","green","blue","gray","gray"))
}
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