Nothing
## ---- echo=TRUE, warning=FALSE, message=FALSE---------------------------------
library(popEpi)
library(Epi)
## -----------------------------------------------------------------------------
data(sire)
data(popmort)
c <- lexpand( sire, status = status, birth = bi_date, exit = ex_date, entry = dg_date,
breaks = list(per = 1950:2013, age = 1:100, fot = c(0,10,20,Inf)),
aggre = list(fot, agegroup = age, year = per, sex) )
se <- sir( coh.data = c, coh.obs = 'from0to2', coh.pyrs = 'pyrs',
ref.data = popmort, ref.rate = 'haz',
adjust = c('agegroup','year','sex'), print ='fot')
se
## -----------------------------------------------------------------------------
c <- lexpand( sire, status = status %in% 1:2, birth = bi_date, exit = ex_date, entry = dg_date,
breaks = list(per = 1950:2013, age = 1:100, fot = c(0,10,20,Inf)),
aggre = list(fot, agegroup = age, year = per, sex) )
se <- sir( coh.data = c, coh.obs = 'from0to1', coh.pyrs = 'pyrs',
ref.data = popmort, ref.rate = 'haz',
adjust = c('agegroup','year','sex'), print ='fot')
se
## ---- fig.height=3, fig.width=6-----------------------------------------------
plot(se, col = 2:3)
title('SMR for follow-up categories')
## ---- fig.height=5, fig.width=6-----------------------------------------------
c <- lexpand( sire, status = status %in% 1:2, birth = bi_date, exit = ex_date, entry = dg_date,
breaks = list(per = 1950:2013, age = 1:100, fot = 0:50),
aggre = list(fot, agegroup = age, year = per, sex) )
sf <- sirspline( coh.data = c, coh.obs = 'from0to1', coh.pyrs = 'pyrs',
ref.data = popmort, ref.rate = 'haz',
adjust = c('agegroup','year','sex'),
spline = c('agegroup','fot'), dependent.splines=FALSE)
st <- sirspline( coh.data = c, coh.obs = 'from0to1', coh.pyrs = 'pyrs',
ref.data = popmort, ref.rate = 'haz',
adjust = c('agegroup','year','sex'),
spline = c('agegroup','fot'), dependent.splines = TRUE)
plot(sf, col=2, log=TRUE)
title('Splines fitted in different models')
plot(st, col=4, log=TRUE)
title('Splines are dependent')
## ---- results='hide', fig.height=5, fig.width=6-------------------------------
c$year.cat <- ifelse(c$year < 2002, 1, 2)
sy <- sirspline( coh.data = c, coh.obs = 'from0to1', coh.pyrs = 'pyrs',
ref.data = popmort, ref.rate = 'haz',
adjust = c('agegroup','year','sex'),
spline = c('agegroup'), print = 'year.cat')
plot(sy, log=TRUE)
legend('topright', c('before 2002','after 2002'), lty=1, col=c(1,2))
## -----------------------------------------------------------------------------
print(sy)
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