\SweaveOpts{results=verbatim,keep.source=TRUE,include=FALSE,eps=FALSE}
%\VignetteIndexEntry{Years of life lost (YLL)}
\documentclass[a4paper,twoside,12pt]{report}

\newcommand{\Title}{Years of Life Lost (YLL)
  to disease\\Diabetes in DK as example}
\newcommand{\Tit}{YLL}
\newcommand{\Version}{February 1.2}
\newcommand{\Dates}{November 2017}
\newcommand{\Where}{SDC}
\newcommand{\Homepage}{\url{http://bendixcarstensen.com/Epi}}
\newcommand{\Faculty}{\begin{tabular}{rl}
Bendix Carstensen
  & Steno Diabetes Center, Gentofte, Denmark\\
  & {\small \& Department of Biostatistics,
               University of Copenhagen} \\
  & \texttt{b@bxc.dk}\\
  & \url{http://BendixCarstensen.com} \\[1em]
                      \end{tabular}}
\input{topreport}
<<echo=FALSE>>=
options( width=90,
         SweaveHooks=list( fig=function()
         par(mar=c(3,3,1,1),mgp=c(3,1,0)/1.6,las=1,bty="n") ) )
@ %
\renewcommand{\rwpre}{./yll}

\chapter{Theory and technicalities}

This vignette for the \texttt{Epi} package describes the
probabilistic and demographic background for and technical implementation
of the \texttt{erl} and \texttt{yll} functions that computes the
expected residual life time and years of life lost in an illness-death
model.

\section{Years of life lost (YLL)}

\ldots to diabetes or any other disease for that matter.

The general concept in calculation of ``years lost to\ldots'' is the
comparison of the expected lifetime between two groups of persons; one
with and one without disease (in this example DM). The expected
lifetime is the area under the survival curve, so basically the
exercise requires that two survival curves that are deemed relevant be
available.

The years of life lost is therefore just the area between the survival
curves for those ``Well'', $S_W(t)$, and for those ``Diseased'',
$S_D(t)$:
\[
  \YLL = \int_0^\infty S_W(t) - S_D(t) \dif t
\]
The time $t$ could of course be age, but it could also be ``time after
age 50'' and the survival curves compared would then be survival
curves \emph{conditional} on survival till age 50, and the YLL would
be the years of life lost for a 50-year old person with diabetes.

If we are referring to the expected lifetime we will more precisely use
the label expected residual lifetime, ERL.

\section{Constructing the survival curves}

YLL can be computed in two different ways, depending on the way the
survival curve and hence the expected lifetime of a person
\emph{without} diabetes is computed:
\begin{itemize}
\item Assume that the ``Well'' persons are \emph{immune} to disease
  --- using only the non-DM mortality rates throughout for calculation
  of expected life time.
\item Assume that the ``Well'' persons \emph{can} acquire the disease and
  thereby see an increased mortality, thus involving all three rates
  shown in figure \ref{fig:states}.
\end{itemize}
The former gives a higher YLL because the comparison is to persons
assumed immune to DM (and yet with the same mortality as non-immune
prior to diagnosis), the latter gives a more realistic picture of the
comparison of group of persons with and without diabetes at a given
age that can be interpreted in the real world.

The differences can be illustrated by figure \ref{fig:states}; the
immune approach corresponds to an assumption of $\lambda(t)=0$ in the
calculation of the survival curve for a person in the ``Well'' state.

Calculation of the survival of a diseased person already in the ``DM''
state is unaffected by assumptions about $\lambda$.

<<states,fig=TRUE,height=5,width=5,echo=FALSE>>=
library( Epi )
TM <- matrix(NA,4,4)
rownames(TM) <-
colnames(TM) <- c("Well","DM","Dead","Dead(DM)") 
TM[1,2:3] <- TM[2,4] <- 1
zz <- boxes( TM, boxpos=list(x=c(20,80,20,80),y=c(80,80,20,20)), wm=1.5, hm=4 )
@ 
<<states,fig=TRUE,height=4,width=5,echo=FALSE>>=
zz$Arrowtext <- c( expression(lambda),   
                   expression(mu[W]),    
                   expression(mu[D][M]) )
boxes( zz )
@ %
\insfig{states}{0.7}{Illness-death model describing diabetes incidence
  and -mortality.}

\subsection{Total mortality --- a shortcut?}

A practical crude shortcut could be to compare the ERL in the diabetic
population to the ERL for the \emph{entire} population (that is use
the total mortality ignoring diabetes status).

Note however that this approach also counts the mortality of persons
that acquired the disease earlier, thus making the comparison
population on average more ill than the population we aim at, namely
those well at a given time, which only then become more gradually ill. 

How large these effects are can however be empirically explored, as we
shall do later.

\subsection{Disease duration}

In the exposition above there is no explicit provision for the effect of
disease duration, but if we were able to devise mortality rates for
any combination of age and duration, this could be taken into account.

There are however severe limitations in this as we in principle would
want to have duration effects as long as the age-effects --- in
principle for all $(a,d)$ where $d\leq A$, where $A$ is the age at
which we condition. So even if we were only to compute ERL from
age, say, 40 we would still need duration effects up to 60 years
(namely to age 100).

The incorporation of duration effects is in principle trivial from a
computational point of view, but we would be forced to entertain
models predicting duration effects way beyond what is actually
observed disease duration in any practical case.

\subsection{Computing integrals}

The practical calculations of survival curves, ERL and YLL involves
calculation of (cumulative) integrals of rates and functions of these
as we shall see below. This is easy if we have a closed form
expression of the function, so its value may be computed at any time
point --- this will be the case if we model rates by smooth parametric
functions.

Computing the (cumulative) integral of a function is done as follows: 
\begin{itemize}
\item Compute the value of the function (mortality rate for example)
  at the midpoints of a sequence of narrow equidistant intervals ---
  for example one- or three month intervals of age, say.
\item Take the cumulative sum of these values multiplied by the
  interval length --- this will be a very close approximation to the
  cumulative integral evaluated at the end of each interval.
\item If the intervals are really small (like 1/100 year), the
  distinction between the value at the middle and at the end of each
  interval becomes irrelevant.
\end{itemize}
Note that in the above it is assumed that the rates are given in units
corresponding to the interval length --- or more precisely, as the
cumulative rates over the interval.

\section{Survival functions in the illness-death model}

The survival functions for persons in the ``Well'' state can be
computed under two fundamentally different scenarios, depending on
whether persons in the ``Well'' state are assumed to be immune to the
disease ($\lambda(a)=0$) or not.

\subsection{Immune approach}

In this case both survival functions for person in the two states are
the usual simple transformation of the cumulative mortality rates:
\[
 S_W(a) = \exp\left(-\int_0^a\!\!\mu_W(u) \dif u \right), \qquad
 S_D(a) = \exp\left(-\int_0^a\!\!\mu_D(u) \dif u \right)
\]

\subsubsection{Conditional survival functions}

If we want the \emph{conditional} survival functions given survival to
age $A$, say, they are just:
\[
 S_W(a|A) = S_W(a)/S_W(A), \qquad S_D(a|A) = S_D(a)/S_D(A)
\]

\subsection{Non-immune approach}

For a diseased person, the survival function in this states is the same
as above, but the survival function for a person without disease (at
age 0) is (see figure \ref{fig:states}):
\[
S(a) = \ptxt{Well}\!(a) + \ptxt{DM}\!(a)
\]
In the appendix of the paper \cite{Carstensen.2008c} is an indication
of how to compute the probability of being in any of the four states
shown in figure \ref{fig:states}, which I shall repeat here:

In terms of the rates, the probability of being in the ``Well'' box is
simply the probability of escaping both death (at a rate of $\mu_W(a)$)
and diabetes (at a rate of $\lambda(a)$):
\[  
   \ptxt{Well}(a)  = \exp\left(\!-\int_0^a\!\!\mu_W(u)+\lambda(u) \right) \dif u
\]
The probability of being alive with diabetes at age $a$, is computed given that
 diabetes occurred at age $s$ ($s<a$) and then integrated over $s$ from $0$
 to $a$:
\begin{align*}
 \ptxt{DM}(a) = \int_0^a\!\! & \ptxt{survive to $s$, DM diagnosed at $s$} \\
                & \times \ptxt{survive with DM from $s$ to $a$} \dif s \\
              = \int_0^a\!\! & \lambda(s) 
                           \exp\left(\!-\int_0^s\!\!\mu_W(u)+\lambda(u) \dif u \right) \\
                & \times \exp\left(\!-\int_s^a\!\!\mu_D(u) \dif u \right) \dif s
\end{align*}
Sometimes we will use a version where the mortality among diabetes
patients depend both on age $a$ and duration of diabetes, $d$,
$\mu_D(a,d)$, in which case we get:
\begin{align*}
 \ptxt{DM}(a) = \int_0^a \! & \lambda(s) 
                           \exp\left(-\int_0^s\!\mu_W(u)+\lambda(u) \dif u \right) \\
                & \times \exp\left(-\int_s^a\!\mu_D(u,u-s) \dif u \right) \dif s
\end{align*}
because the integration variable $u$ is the age-scale and the second
integral refers to mortality among persons diagnosed at age $s$, that
is, with duration $u-s$ at age $u$.

The option of using duration-dependent mortality rates among diseased
individuals is not implemented yet.

\subsubsection{Conditional survival functions}

Unlike the immune approach, the conditional survival function in the
more realistic case is not just a ratio of the unconditional to the
value at the conditioning age, $A$, say. This would amount to
conditioning on being merely \emph{alive} at age $A$, but what we want
is to condition on being in the ``Well'' state at age $A$.

The formulae for the conditional probabilities of being either in
``Well'' or ``DM'', given being in ``Well'' at age $A$ are basically
replicates of the unconditional, albeit with changes in integration
limits:
\begin{align*}
\ptxt{Well|Well at $A$}(a) &= \exp\left(-\int_A^a \! \mu_W(u)+\lambda(u) \right) \dif u \\
  \ptxt{DM|Well at $A$}(a) &= \int_A^a \! \lambda(s) 
                               \exp\left(-\int_A^s\!\mu_W(u)+\lambda(u) \dif u \right) \\
                           & \qquad \times \exp\left(-\int_s^a\!\mu_D(u,u-s) \dif u \right) \dif s
\end{align*}
The calculation of these conditional survival functions is implemented
but not allowing for duration-dependence. Thus it is only implemented
assuming $\mu_D(a,d)=\mu_D(a)$.

\chapter{Analyses for DM in Denmark}

The rates we use as basis for the following calculations are derived
from the NDR, where we have omitted the blood-glucose criteria,
because there is compelling evidence that these have quite a low
specificity (particularly in the younger ages among women), and do
not substantially contribute to the sensitivity.

As noted above the calculations of YLL requires access to
(age-specific) rates of incidence of DM and mortality for persons with
and without DM.

\section{Modeling mortality and incidence data}

We read in the dataset of DM and population mortality and incidence, \texttt{DMepi}:
<<>>=
data( DMepi )
@ % 
The dataset \texttt{DMepi} contains diabetes events, deaths and
person-years for persons without diabetes and deaths and person-years
for persons with diabetes:
<<>>=
str( DMepi )
head( DMepi )
@ %
For each combination of sex, age, period and date of birth in 1 year
age groups, we have the person-years in the ``Well'' (\texttt{Y.nD})
and the ``DM'' (\texttt{Y.DM}) states, as well as the number of deaths
from these (\texttt{D.nD}, \texttt{D.DM}) and the number of incident
diabetes cases from the ``Well'' state (\texttt{X}).

In order to compute the years of life lost to diabetes and how this
has changed over time, we fit models for the mortality and incidence
of both groups (and of course, separately for men and women). The
models we use will be age-period-cohort models \cite{Carstensen.2007a}
providing estimated mortality rates for ages 0--99 and dates
1.1.1996--1.1.2016.

First we transform the age and period variables to reflect the mean
age and period in each of the Lexis triangles. We also compute the
total number of deaths and amount of risk time, as we are going to
model the total mortality as well. Finally we restrict the dataset to
ages over 30 only:
<<>>=
DMepi <- transform( subset( DMepi, A>30 ),
                    D.T = D.nD + D.DM, 
                    Y.T = Y.nD + Y.DM )
head(DMepi)
@ %
With the correct age and period coding in the Lexis triangles, we fit
models for the mortalities and incidences. Note that we for
comparative purposes also fit a model for the \emph{total} mortality,
ignoring the 
<<>>=
# Knots used in all models
( a.kn <- seq(40,95,,6) )
( p.kn <- seq(1997,2015,,4) )
( c.kn <- seq(1910,1976,,6) )
# Check the number of events between knots
ae <- xtabs( cbind(D.nD,D.DM,X) ~ cut(A,c(30,a.kn,Inf)) + sex, data=DMepi )
ftable( addmargins(ae,1), col.vars=3:2 )
pe <- xtabs( cbind(D.nD,D.DM,X) ~ cut(P,c(1990,p.kn,Inf)) + sex, data=DMepi )
ftable( addmargins(pe,1), col.vars=3:2 )
ce <- xtabs( cbind(D.nD,D.DM,X) ~ cut(P-A,c(-Inf,c.kn,Inf)) + sex, data=DMepi )
ftable( addmargins(ce,1), col.vars=3:2 )
# Fit an APC-model for all transitions, seperately for men and women
mW.m <- glm( D.nD ~ -1 + Ns(A  ,knots=a.kn,int=TRUE) +
                         Ns(  P,knots=p.kn,ref=2005) +
                         Ns(P-A,knots=c.kn,ref=1950), 
           offset = log(Y.nD),
           family = poisson,
             data = subset( DMepi, sex=="M" ) )
mD.m <- update( mW.m,  D.DM ~ . , offset=log(Y.DM) )
mT.m <- update( mW.m,  D.T  ~ . , offset=log(Y.T ) )
lW.m <- update( mW.m,  X ~ . )
# Model for women
mW.f <- update( mW.m, data = subset( DMepi, sex=="F" ) )
mD.f <- update( mD.m, data = subset( DMepi, sex=="F" ) )
mT.f <- update( mT.m, data = subset( DMepi, sex=="F" ) )
lW.f <- update( lW.m, data = subset( DMepi, sex=="F" ) )
@ % 

\section{Residual life time and years lost to DM}

We now collect the estimated years of life lost classified by method
(immune assumption or not), sex, age and calendar time:
<<>>=
a.ref <- 30:90
p.ref <- 1996:2016
aYLL <- NArray( list( type = c("Imm","Tot","Sus"),
                       sex = levels( DMepi$sex ),
                       age = a.ref,
                      date = p.ref ) )
str( aYLL )
system.time(
for( ip in p.ref )
   {
   nd <- data.frame( A = seq(30,90,0.2)+0.1,
                     P = ip,
                  Y.nD = 1,
                  Y.DM = 1,
                  Y.T  = 1 )
   muW.m <- ci.pred( mW.m, nd )[,1]
   muD.m <- ci.pred( mD.m, nd )[,1]
   muT.m <- ci.pred( mT.m, nd )[,1]
   lam.m <- ci.pred( lW.m, nd )[,1]
   muW.f <- ci.pred( mW.f, nd )[,1]
   muD.f <- ci.pred( mD.f, nd )[,1]
   muT.f <- ci.pred( mT.f, nd )[,1]
   lam.f <- ci.pred( lW.f, nd )[,1]
   aYLL["Imm","M",,paste(ip)] <- yll( int=0.2, muW.m, muD.m, lam=NULL, 
                                      A=a.ref, age.in=30, note=FALSE )[-1]
   aYLL["Imm","F",,paste(ip)] <- yll( int=0.2, muW.f, muD.f, lam=NULL,  
                                      A=a.ref, age.in=30, note=FALSE )[-1]
   aYLL["Tot","M",,paste(ip)] <- yll( int=0.2, muT.m, muD.m, lam=NULL,  
                                      A=a.ref, age.in=30, note=FALSE )[-1]
   aYLL["Tot","F",,paste(ip)] <- yll( int=0.2, muT.f, muD.f, lam=NULL,  
                                      A=a.ref, age.in=30, note=FALSE )[-1]
   aYLL["Sus","M",,paste(ip)] <- yll( int=0.2, muW.m, muD.m, lam=lam.m, 
                                      A=a.ref, age.in=30, note=FALSE )[-1]
   aYLL["Sus","F",,paste(ip)] <- yll( int=0.2, muW.f, muD.f, lam=lam.f, 
                                      A=a.ref, age.in=30, note=FALSE )[-1]
   } )
round( ftable( aYLL[,,seq(1,61,10),], col.vars=c(3,2) ), 1 )
@ %
We now have the relevant points for the graph showing YLL to diabetes
for men and women by age, and calendar year, both under the immunity
and susceptibility models for the calculation of YLL.
<<imm,fig=TRUE,width=8,height=5>>=
plyll <- function(wh){
par( mfrow=c(1,2), mar=c(3,3,1,1), mgp=c(3,1,0)/1.6, bty="n", las=1 )

matplot( a.ref, aYLL[wh,"M",,],
         type="l", lty=1, col="blue", lwd=1:2,
         ylim=c(0,12), xlab="Age",
         ylab="Years lost to DM", yaxs="i" )
abline(v=50,h=1:10,col=gray(0.7))
text( 90, 11, "Men", col="blue", adj=1 )
text( 40, aYLL[wh,"M","40","1996"], "1996", adj=c(0,0), col="blue" )
text( 43, aYLL[wh,"M","44","2016"], "2016", adj=c(1,1), col="blue" )

matplot( a.ref, aYLL[wh,"F",,],
         type="l", lty=1, col="red", lwd=1:2,
         ylim=c(0,12), xlab="Age",
         ylab="Years lost to DM", yaxs="i" )
abline(v=50,h=1:10,col=gray(0.7))
text( 90, 11, "Women", col="red", adj=1 )
text( 40, aYLL[wh,"F","40","1996"], "1996", adj=c(0,0), col="red" )
text( 43, aYLL[wh,"F","44","2016"], "2016", adj=c(1,1), col="red" )
}
plyll("Imm")
@ %
<<tot,fig=TRUE,width=8,height=5>>=
plyll("Tot")
@ %
<<sus,fig=TRUE,width=8,height=5>>=
plyll("Sus")
@ %
\begin{figure}[h]
  \centering
  \includegraphics[width=\textwidth]{yll-imm}
  \caption{Years of life lost to DM: the difference in expected
    residual life time at different ages between persons with and
    without diabetes, assuming the persons without diabetes at a given
    age remain free from diabetes (immunity assumption --- not
    reasonable). The lines refer to date of evaluation; the top lines
    refer to 1.1.1996 the bottom ones to 1.1.2016. Blue curves are
    men, red women.}
  \label{fig:imm}
\end{figure}

\begin{figure}[h]
  \centering
  \includegraphics[width=\textwidth]{yll-sus}
  \caption{Years of life lost to DM: the difference in expected
    residual life time at different ages between persons with and
    without diabetes, allowing the persons without diabetes at a given
    to contract diabetes and thus be subject to higher mortality. The
    lines refer to date of evaluation; the top lines refer to 1.1.1996
    the bottom ones to 1.1.2016. Blue curves are men, red women.}
  \label{fig:sus}
\end{figure}

\begin{figure}[h]
  \centering
  \includegraphics[width=\textwidth]{yll-tot}
  \caption{Years of life lost to DM: the difference in expected
    residual life time at different ages between persons with and
    without diabetes. Allowance for susceptibility is approximated by
    using the total population mortality instead of non-DM
    mortality. The lines refer to date of evaluation; the top lines
    refer to 1.1.1996 the bottom ones to 1.1.2016. Blue curves are
    men, red women.}
  \label{fig:tot}
\end{figure}

From figure \ref{fig:sus} we see that for men aged 50 the years lost to
diabetes has decreased from a bit over 8 to a bit less than 6 years,
and for women from 8.5 to 5 years; so a greater improvement for women.

\chapter{Practical implementation}

We have devised functions that wraps these formulae up for practical
use.

\section{Function definitions}

% The following code sources the originally formatted code in erl.R in
% order to make it printable with all the formatting and comments in
% it. However the sourcing does not work when compiling the vignettes
% in R CMD build. So when checking the code we comment this out by
% putting eval=FALSE. So depending on whether we actually construct
% the pdf for the inst/doc folder or test (upload) the package, one of
% the following two chunks are run with eval=FALSE and the other with
% eval=TRUE.
<<CHANGE1,echo=FALSE,results=hide,eval=FALSE>>=
source( "../R/erl.R", keep.source=TRUE )
@ %
% When checking the package
<<CHANGE2,echo=FALSE,results=hide,eval=TRUE>>=
surv1 <- Epi::surv1
surv2 <- Epi::surv2
erl1 <- Epi::erl1
erl <- Epi::erl
yll <- Epi::yll
@ %
When using the functions it is assumed that the functions $\mu_W$,
$\mu_D$ and $\lambda$ are given as vectors corresponding to
equidistantly (usually tightly) spaced ages from 0 to $K$ where K is
the age where everyone can safely be assumed dead.

\texttt{surv1} is a simple function that computes the survival
function from a vector of mortality rates, and optionally the
conditional survival given being alive at prespecified ages:
<<>>=
surv1
@ %
\texttt{erl1} basically just expands the result of \texttt{surv1} with
a column of expected residual life times:
<<>>=
erl1
@ %
We also define a function, \texttt{surv2}, that computes the survival
function for a non-diseased person that may become diseased with rate
\texttt{lam} and after that die at a rate of \texttt{muD}
(corresponding to the formulae above). This is the sane way of
handling years of life lost to a particular illness:
<<>>=
surv2
@ %
Finally we devised a function using these to compute the expected
residual lifetime at select ages:
<<>>=
erl
@ %
\ldots and a wrapper for this if we only want the years of life lost
returned:
<<>>=
yll
@ %

\bibliographystyle{plain}

\begin{thebibliography}{1}

\bibitem{Carstensen.2007a}
B~Carstensen.
\newblock Age-{P}eriod-{C}ohort models for the {L}exis diagram.
\newblock {\em Statistics in Medicine}, 26(15):3018--3045, 2007.

\bibitem{Carstensen.2008c}
B~Carstensen, JK~Kristensen, P~Ottosen, and K~Borch-Johnsen.
\newblock The {D}anish {N}ational {D}iabetes {R}egister: {T}rends in incidence,
  prevalence and mortality.
\newblock {\em Diabetologia}, 51:2187--2196, 2008.

\end{thebibliography}

\addcontentsline{toc}{chapter}{References}

\end{document}
