xhaz {xhaz}

xhaz function

Description

Fits the excess hazard models proposed by Esteve et al. (1990) doi:10.1002/sim.4780090506, with the possibility to account for time dependent covariates. Fits also the non-proportional excess hazard model proposed by Giorgi et al. (2005) doi:10.1002/sim.2400. In addition, fits excess hazard models with possibility to rescale (Goungounga et al. (2019) doi:10.1186/s12874-019-0747-3) or to correct the background mortality with a proportional (Touraine et al. (2020) doi:10.1177/0962280218823234) or non-proportional (Mba et al. (2020) doi:10.1186/s12874-020-01139-z) effect.

Usage

xhaz(
  formula = formula(data),
  data = sys.parent(),
  ratetable,
  rmap = list(age = NULL, sex = NULL, year = NULL),
  baseline = c("constant", "bsplines"),
  pophaz = c("classic", "rescaled", "corrected"),
  only_ehazard = FALSE,
  add.rmap = NULL,
  add.rmap.cut = list(breakpoint = FALSE, cut = NA, probs = NULL, criterion = "BIC",
    print_stepwise = FALSE),
  interval,
  ratedata = sys.parent(),
  subset,
  na.action,
  init,
  control = list(eps = 1e-04, iter.max = 800, level = 0.95),
  optim = TRUE,
  scale = 365.2425,
  trace = 0,
  speedy = FALSE,
  nghq = 12,
  ...
)

Arguments

formula

a formula object of the function with the response on the left of a ~ operator and the terms on the right. The response must be a survival object as returned by the Surv function (time in first and status in second).

data

a data frame in which to interpret the variables named in the formula

ratetable

a rate table stratified by age, sex, year (if missing, ratedata is used)

rmap

a list that maps data set names to the ratetable names.

baseline

an argument to specify the baseline hazard: if it follows a piecewise constant, baseline = "constant" is used and corresponds to the baseline in Esteve et al. model; if the baseline follows a quadratic b-splines, baseline = "bsplines" is used, corresponding to the baseline excess hazard in Giorgi et al model.

pophaz

indicates three possibles arguments in character: classic or rescaled and corrected. If pophaz = "classic" chosen, fits the model that do not require to rescale or to correct the background mortality (i.e. the Esteve et al. model or Giorgi et al. model); if pophaz = "rescaled" or pophaz = "corrected" chosen, fits the models that require to rescale or to correct the background mortality.

only_ehazard

a boolean argument (by default, only_ehazard=FALSE). If only_ehazard = TRUE, pophaz = "classic" must be provided and the total value of the log-likelihood will not account for the cumulative population hazard.

add.rmap

character that indicates the name in character of the additional demographic variable from data to be used for correction of the life table, in particular when one is in the presence of an insufficiently stratified life table (see Touraine et al. model). This argument is not used if pophaz = "classic" or pophaz = "rescaled".

add.rmap.cut

a list containing arguments to specify the modeling strategy for breakpoint positions, which allows a non-proportional effect of the correction term acting on the background mortality. By default list(breakpoint = FALSE), i.e. a proportional effect of the correction term acting on the background mortality is needed; in this case, all the other argument of the list are not working for the model specification;

if list(breakpoint = TRUE, cut = c(70)), the chosen cut-point(s) is (are) the numeric value(s) proposed. If list(breakpoint = TRUE, cut = NA), there is the same number of breakpoints as the number of NA, with their possible positions specified as here by probs, i.e. list(breakpoint = TRUE, cut = NA, probs = seq(0, 1, 0.25)). That corresponds to a numeric vector of probabilities with values between 0 and 1 as in quantile function. criterion is used to choose the best model, using the AIC or the BIC (the default criterion). If needed, all the fitted models are printed by the user by adding in the list print_stepwise = FALSE.

interval

a vector indicating either the location of the year-scale time intervals for models with piecewise constant function, or the location of the knots for models with B-splines functions for their baseline hazard (see the appropriate specification in baseline argument). The first component of the vector is 0, and the last one corresponds to the maximum time fellow-up of the study.

ratedata

a data frame of the hazards mortality in general population.

subset

an expression indicating which subset of the data should be used in the modeling. All observations are included by default

na.action

as in the coxph function, a missing-data filter function.

init

a list of initial values for the parameters to estimate. For each elements of the list, give the name of the covariate followed by the vector of the fixed initials values

control

a list of control values used to control the optimization process. In this list, eps, is a convergence criteria (by default, eps=10^-4), iter.max is the maximum number of iteration (by default, iter.max=15), and level, is the level used for the confidence intervals (by default, level=0.95).

optim

a Boolean argument (by default, optim = FALSE). If optim = TRUE), the maximization algorithm uses the optim function

scale

a numeric argument to specify whether the life table contains death rates per day (default scale = 365.2425) or death rates per year (scale = 1).

trace

a Boolean argument, if trace = TRUE), tracing information on the progress of the optimization is produced

speedy

a Boolean argument, if speedy = TRUE, optimization is done in a parallel mode

nghq

number of nodes and weights for Gaussian quadrature

...

other parameters used with the xhaz function

Details

Use the Surv(time_start, time_stop, status) notation for time dependent covariate with the appropriate organization of the data set (see the help page of the Surv function)

Only two interior knots are possible for the model with B-splines functions to fit the baseline (excess) hazard. Determination of the intervals might be user's defined or automatically computed according to the quantile of the distribution of deaths. Use NA for an automatic determination (for example, interval = c(0, NA, NA, 5)).

Value

An object of class xhaz.constant or xhaz.bsplines, according to the type of functions chosen to fit the baseline hazard of model (see details for argument baseline). This object is a list containing the following components:

coefficients

estimates found for the model

varcov

the variance-covariance matrix

loglik

for the Estève et al. model: the log-likelihood of the null model, i.e without covariate, and the log-likelihood of the full model, i.e with all the covariates declared in the formula; for the Giorgi et al. model: the log-likelihood of the full model

cov.test

for the Esteve et al.model: the log-likelihood of the null model, i.e without covariate, and the log-likelihood of the full model, i.e with all the covariates declared in the formula; for the Giorgi et al. model: the log-likelihood of the full model

message

a character string returned by the optimizer see details in optim help page

convergence

an integer code as in optim when "L-BFGS-B" method is used.

n

the number of individuals in the dataset

n.events

the number of events in the dataset. Event are considered as death whatever the cause

level

the confidence level used

interval

the intervals used to split time for piecewise baseline excess hazard, or knots positions for Bsplines baseline

terms

the representation of the terms in the model

call

the function call based on model

pophaz

the assumption considered for the life table used in the excess hazard model

add.rmap

the additional variable for which the life table is not stratified

ehazardInt

the cumulative hazard of each individuals calculated from the ratetable used in the model

ehazard

the individual expected hazard values from the ratetable used to fit the model

data

the dataset used to run the model

time_elapsed

the time to run the model

Note

time is OBLIGATORY in YEARS.

Author(s)

Juste Goungounga, Darlin Robert Mba, Nathalie Graffeo, Roch Giorgi

References

Goungounga JA, Touraine C, Grafféo N, Giorgi R; CENSUR working survival group. Correcting for misclassification and selection effects in estimating net survival in clinical trials. BMC Med Res Methodol. 2019 May 16;19(1):104. doi: 10.1186/s12874-019-0747-3. PMID: 31096911; PMCID: PMC6524224. (PubMed)

Touraine C, Grafféo N, Giorgi R; CENSUR working survival group. More accurate cancer-related excess mortality through correcting background mortality for extra variables. Stat Methods Med Res. 2020 Jan;29(1):122-136. doi: 10.1177/0962280218823234. Epub 2019 Jan 23. PMID: 30674229. (PubMed)

Mba RD, Goungounga JA, Grafféo N, Giorgi R; CENSUR working survival group. Correcting inaccurate background mortality in excess hazard models through breakpoints. BMC Med Res Methodol. 2020 Oct 29;20(1):268. doi: 10.1186/s12874-020-01139-z. PMID: 33121436; PMCID: PMC7596976. (PubMed)

Giorgi R, Abrahamowicz M, Quantin C, Bolard P, Esteve J, Gouvernet J, Faivre J. A relative survival regression model using B-spline functions to model non-proportional hazards. Statistics in Medicine 2003; 22: 2767-84. (PubMed)

Examples

library("numDeriv")
library("survexp.fr")
library("splines")
library("statmod")
data("simuData","rescaledData", "dataCancer")
# load the data sets 'simuData', 'rescaledData' and 'dataCancer'.

# Esteve et al. model: baseline excess hazard is a piecewise function
#                      linear and proportional effects for the covariates on
#                      baseline excess hazard.

levels(simuData$sex) <- c("male", "female")

fit.estv1 <- xhaz(formula = Surv(time_year, status) ~ agec + race,
                  data = simuData,
                  ratetable = survexp.us,
                  interval = c(0, NA, NA, NA, NA, NA, 6),
                  rmap = list(age = 'age', sex = 'sex', year = 'date'),
                  baseline = "constant", pophaz = "classic")


fit.estv1


# Touraine et al. model: baseline excess hazard is a piecewise function
#                        with a linear and proportional effects for the
#                        covariates on the baseline excess hazard.
# An additionnal cavariate (here race) missing in the life table is
# considered by the model.


fit.corrected1 <- xhaz(formula = Surv(time_year, status) ~ agec + race,
                       data = simuData,
                       ratetable = survexp.us,
                       interval = c(0, NA, NA, NA, NA, NA, 6),
                       rmap = list(age = 'age', sex = 'sex', year = 'date'),
                       baseline = "constant", pophaz = "corrected",
                       add.rmap = "race")



fit.corrected1

# extension of Touraine et al model: baseline excess hazard is a piecewise
# constant function with a linear and proportional effects for the covariates
# on the baseline excess hazard.

# An additionnal cavariate (here race) missing in the life table is
# considered by the model with a breakpoint at 75 years

fit.corrected2 <- xhaz(formula = Surv(time_year, status) ~ agec + race,
                       data = simuData,
                       ratetable = survexp.us,
                       interval = c(0, NA, NA, NA, NA, NA, 6),
                       rmap = list(age = 'age', sex = 'sex', year = 'date'),
                       baseline = "constant", pophaz = "corrected",
                       add.rmap = "race",
                        add.rmap.cut = list(breakpoint = TRUE, cut = 75))



fit.corrected2


#Giorgi et al model: baseline excess hazard is a quadratic Bsplines
#                    function with two interior knots and allow here a
#                    linear and proportional effects for the covariates on
#                    baseline excess hazard.


fitphBS <- xhaz(formula = Surv(time_year, status) ~ agec + race,
                data = simuData,
                ratetable = survexp.us,
                interval = c(0, NA, NA, 6),
                rmap = list(age = 'age', sex = 'sex', year = 'date'),
                baseline = "bsplines", pophaz = "classic")

fitphBS





# Application on `dataCancer`.
#Giorgi et al model: baseline excess hazard is a quadratic Bspline
#                    function with two interior knots and allow here a
#                    linear and proportional effect for the variable
#                    "immuno_trt" plus a non-proportional effect
#                    for the variable "ageCentre" on baseline excess hazard.


fittdphBS <- xhaz(formula = Surv(obs_time_year, event) ~ qbs(ageCentre) + immuno_trt,
                  data = dataCancer,
                  ratetable = survexp.fr,
                  interval = c(0, 0.5, 12, 15),
                  rmap = list(age = 'age', sex = 'sexx', year = 'year_date'),
                  baseline = "bsplines", pophaz = "classic")

fittdphBS




# Application on `rescaledData`.
# rescaled model: baseline excess hazard is a piecewise function with a
# linear and proportional effects for the covariates on baseline excess hazard.

# A scale parameter on the expected mortality of general population is
# considered to account for the non-comparability source of bias.

rescaledData$timeyear <- rescaledData$time/12
rescaledData$agecr <- scale(rescaledData$age, TRUE, TRUE)

fit.res <- xhaz(formula = Surv(timeyear, status) ~ agecr + hormTh,
                data = rescaledData,
                ratetable = survexp.fr,
                interval = c(0, NA, NA, NA, NA, NA, max(rescaledData$timeyear)),
                rmap = list(age = 'age', sex = 'sex', year = 'date'),
                baseline = "constant", pophaz = "rescaled")

 fit.res