mexhaz function
Description
Fit an (excess) hazard regression model using different shapes for the
baseline hazard (Weibull, piecewise constant and exponential of a
Bspline), with the possibility to include timedependent and/or
nonlinear effect(s) of variable(s) and a random effect defined at the
cluster level. The timedependent effect of a covariate is modelled by
adding interaction terms between the covariate and a function of time of
the same class as the one used for the baseline hazard (in particular,
with the same knots for piecewise constant hazards; and with the same
degree and the same knots for Bspline functions). The random effect is
assumed to be normally distributed with mean 0 and standard deviation
sigma. The optimisation process uses adaptive Gaussian quadrature to
calculate the clusterspecific marginal likelihoods. The logarithm of
the full marginal likelihood, defined as the sum of the logarithms of
the clusterspecific marginal likelihoods, is then maximised using
optimisation routine such as nlm
or optim
.
Usage
1 2 3 4 5 
Arguments
formula 
a formula object, with the response on the left of the In case 
data 
a 
expected 
name of the variable (must be given in quotes) representing the
population (i.e., expected) hazard. By default, 
base 
functional form that should be used to model the baseline
hazard. Selection can be made between the following options: 
degree 
if 
knots 
if 
bo.max 
if 
n.gleg 
if 
init 
vector of initial values. By default for the baseline hazard: if if if the parameters describing the effects of the covariates are all set to 0; the parameter representing the standard deviation of the random effect is set to 0.1. 
random 
name of the variable to be entered as a random effect (must be given
between quotes), representing the cluster membership. By default,

n.aghq 
number of quadrature points to be used for estimating the
clusterspecific marginal likelihoods by adaptive GaussHermite
quadrature. By default, 
fnoptim 
name of the R optimisation procedure used to maximise the
likelihood. Selection can be made between 
verbose 
integer parameter representing the frequency at which the current state
of the optimisation process is displayed. Internally, an 'evaluation' is
defined as an estimation of the loglikelihood for a given vector of
parameters. This means that the number of evaluations is increased each
time the optimisation procedure updates the value of any of the
parameters to be estimated. If 
method 
if 
iterlim 
if 
print.level 
this argument is only used if 
... 
represents additional parameters directly passed to 
Value
An object of class mexhaz
containing the following elements:
dataset 
name of the dataset used to fit the model. 
call 
function call on which the model is based. 
formula 
formula part of the call. 
xlevels 
information concerning the levels of the categorical
variables used in the model (used by 
n.obs.tot 
total number of observations in the dataset. 
n.obs 
number of observations used to fit the model (after exclusion of missing values). 
n.events 
number of events (after exclusion of missing values). 
n.clust 
number of clusters. 
n.time.0 
number of observations for which the observed followup time was equal to 0. 
base 
function used to model the baseline hazard. 
max.time 
maximal observed time in the dataset. 
bounds 
vector of boundary values used to define the Bspline basis. 
degree 
degree of the Bspline used to model the logarithm of the baseline hazard. 
knots 
vector of interior knots used to define the Bspline basis. 
names.ph 
names of the covariables with a proportional effect. 
random 
name of the variable defining cluster membership (set to

coefficients 
a vector containing the parameter estimates. 
std.errors 
a vector containing the standard errors of the parameter estimates. 
vcov 
the variancecovariance matrix of the estimated parameters. 
mu.hat 
a 
n.par 
number of estimated parameters. 
n.gleg 
number of GaussLegendre quadrature points used to calculate the cumulative (excess) hazard (only relevant if a Bspline of degree 2 or 3 was used to model the logarithm of the baseline hazard). 
n.aghq 
number of adaptive GaussHermite quadrature points used to calculate the clusterspecific marginal likelihoods (only relevant if a multilevel model is fitted). 
fnoptim 
name of the R optimisation procedure used to maximise the likelihood. 
method 
optimisation method used by 
code 
code (integer) indicating the status of the optimisation
process (this code has a different meaning for 
loglik 
value of the loglikelihood at the end of the optimisation procedure. 
iter 
number of iterations used in the optimisation process. 
eval 
number of evaluations used in the optimisation process. 
time.elapsed 
total time required to reach convergence. 
Author(s)
Hadrien Charvat, Aurelien Belot
References
Charvat H, Remontet L, Bossard N, Roche L, Dejardin O, Rachet B, Launoy G, Belot A; CENSUR Working Survival Group. A multilevel excess hazard model to estimate net survival on hierarchical data allowing for nonlinear and nonproportional effects of covariates. Stat Med 2016. (doi: 10.1002/sim.6881)
See Also
print.mexhaz
, summary.mexhaz
, predMexhaz
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20  data(simdatn1)
## Fit of a mixedeffect excess hazard model, with the baseline hazard
## described by a Weibull distribution (without covariables)
Mod_weib_mix < mexhaz(formula=Surv(time=timesurv,
event=vstat)~1, data=simdatn1, base="weibull",
expected="popmrate", verbose=0, random="clust")
## A more complex example (not run)
## Fit of a mixedeffect excess hazard model, with the baseline hazard
## described by a cubic Bspline with two knots at 1 and 5 year and with
## effects of age (agecr), deprivation index (depindex) and sex (IsexH)
# Mod_bs3_2mix_nph < mexhaz(formula=Surv(time=timesurv,
# event=vstat)~agecr+depindex+IsexH+nph(agecr), data=simdatn1,
# base="exp.bs", degree=3, knots=c(1,5), expected="popmrate",
# random="clust", verbose=1000)

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