mexhaz-package | R Documentation |
Fit an (excess) hazard regression model using different shapes for the
baseline hazard (Weibull, piecewise constant, exponential of a B-spline
of degree 1 to 3, exponential of a restricted cubic spline), with the
possibility to include time-dependent effects of variable(s) and a
random effect defined at the cluster level. Follow-up time can be
entered in the right-censored or counting process input style. The
latter allows the modelling of survival data with delayed entries. The
time-dependent effect of a covariable is modelled by adding interaction
terms between the covariable 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 B-spline or restricted cubic spline 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 cluster-specific marginal likelihoods. The
logarithm of the full marginal likelihood, defined as the sum of the
logarithms of the cluster-specific marginal likelihoods, is then
maximised using an optimisation routine such as nlm
(default) or
optim
. Functions to compute and plot the predicted (excess)
hazard and (net) survival (possibly with marginal or cluster-specific predictions in
the case of a random effect model) are provided.
Package: | mexhaz |
Type: | Package |
Version: | 2.2 |
Date: | 2022-01-19 |
License: | GPL (>=2) |
Hadrien Charvat, Aurelien Belot
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 non-linear and non-proportional effects of covariates. Stat Med 2016;35(18):3066-3084 (doi: 10.1002/sim.6881)
Charvat H, Belot A. An R package for fitting flexible hazard-based regression models for overall and excess mortality with a random effect. J Stat Softw 2021;98(14):1-36 (doi: 10.18637/jss.v098.i14)
data(simdatn1) ## Fit of a mixed-effect 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") ## Examples of syntax for various models (not run) ## Fit of a fixed-effect excess hazard model, with the baseline hazard ## described by a Weibull distribution and with effects of age (agecr), ## deprivation index (depindex) and sex (IsexH) using the optim ## procedure and the BFGS method (see help of optim). # Mod_weib <- mexhaz(formula=Surv(time=timesurv, # event=vstat)~agecr+depindex+IsexH, data=simdatn1, base="weibull", # expected="popmrate", verbose=1000, fnoptim="optim", # method="BFGS") ## Fit of a mixed-effect excess hazard model, with the baseline hazard ## described by a cubic B-spline with two knots at 1 and 5 year and with ## effects of age (agecr), deprivation index (depindex) and sex (IsexH) # Mod_bs3_2mix <- mexhaz(formula=Surv(time=timesurv, # event=vstat)~agecr+depindex+IsexH, data=simdatn1, base="exp.bs", # degree=3, knots=c(1,5), expected="popmrate", random="clust", # verbose=1000) ## Fit of a fixed-effect overall hazard model, with the baseline hazard ## described by a piecewise constant function with the following vector ## of knots (defining the endpoints of the intervals on which the hazard ## is constant): (1,3,5,8), and with effects of age (agecr), deprivation ## index (depindex) and sex (IsexH) # Mod_pw <- mexhaz(formula=Surv(time=timesurv, event=vstat)~ # agecr+depindex+IsexH, data= simdatn1, base="pw.cst", knots=c(1,3,5,8), # verbose=1000) ## Fit of a fixed-effect excess hazard model, with the baseline hazard ## described by a cubic B-spline with two knots at 1 and 5 year and with ## effects of age (agecr), deprivation index (depindex) and sex (IsexH) # Mod_bs3_2 <- mexhaz(formula=Surv(time=timesurv, # event=vstat)~agecr+depindex+IsexH, data=simdatn1, base="exp.bs", # degree=3, knots=c(1,5), expected="popmrate", verbose=1000) ## Fit of a mixed-effect excess hazard model, with the baseline hazard ## described by a cubic B-spline with two knots at 1 and 5 year and with ## effects of age (agecr), deprivation index (depindex) and sex (IsexH) # Mod_bs3_2mix <- mexhaz(formula=Surv(time=timesurv, # event=vstat)~agecr+depindex+IsexH, data=simdatn1, base="exp.bs", # degree=3, knots=c(1,5), expected="popmrate", random="clust", # verbose=1000) ## Fit of a mixed-effect excess hazard model, with the baseline hazard ## described by a cubic B-spline with two knots at 1 and 5 year, with ## effects of age (agecr), deprivation index (depindex) and sex (IsexH) ## and with a time-dependent effect for age (agecr) and sex (IsexH). # Mod_bs3_2mixnph <- mexhaz(formula=Surv(time=timesurv, # event=vstat)~agecr+depindex+IsexH + nph(agecr+IsexH), data=simdatn1, # base="exp.bs", degree=3, knots=c(1,5), expected="popmrate", # random="clust", verbose=1000)
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