## ----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)