inst/doc/nordpred.R

In haraldwf/nordpred: Prediction of cancer incidence (as used in the Nordpred project)

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library(nordpred)

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knitr::kable(inpop1)

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knitr::kable(inpop2)

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knitr::kable(inpop2)

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inpop <- cbind(inpop1, inpop2)

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est <- nordpred.estimate(cases=indata, pyr = inpop, noperiod = 4, startestage = 5)

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res <- nordpred.prediction(est, startuseage = 6, cuttrend = c(0,.25,.5,.75,.75), recent=TRUE)

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res <- nordpred(cases = indata, pyr = inpop, startestage = 5, startuseage = 6, 
                noperiods = 4, cuttrend = c(0, .25, .5, .75, .75))

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res <- nordpred(indata, inpop, startestage = 5, startuseage = 6, noperiods = 4:6,
                cuttrend=c(0, .25, .5, .75, .75))


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est2 <- nordpred.estimate(indata, inpop, 4, 5, linkfunc = "poisson")
res2 <- nordpred.prediction(est2, startuseage = 6, cuttrend = c(0, .25, .5, .75, .75), recent = TRUE)

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print(res)
nordpred.getpred(res)
summary(res, printpred = FALSE)

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## World population standard
wstand <- c(0.12, 0.1, 0.09, 0.09, 0.08, 0.08, 0.06, 0.06, 0.06, 0.06,0.05, 
            0.04, 0.04, 0.03, 0.02, 0.01, 0.005, 0.005)
            
round(nordpred.getpred(res, incidence = TRUE, standpop = NULL), 2)
round(nordpred.getpred(res, incidence = TRUE, standpop = wstand), 2)


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plot(res, standpop = wstand)

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plot(res2, standpop = wstand)
plot(res, new = FALSE, lty = c(1, 2), standpop = wstand)

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plot(nordpred.prediction(est, startuseage = 6, cuttrend = c(0, 0, 0, 0, 0), 
    recent = FALSE), standpop = wstand, new = TRUE)
plot(nordpred.prediction(est, startuseage = 6, cuttrend = c(1, 1, 1, 1, 1), 
    recent = FALSE), standpop = wstand, new = FALSE, lty = c(1, 2))
plot(nordpred.prediction(est, startuseage = 6, cuttrend = c(0, .25, .5, .75, .75), 
    recent = FALSE), standpop = wstand, new = FALSE, lty = c(1, 4))