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# ------------------------------------------------------------------------------
# Copyright (C) 2019 University of Liège
# <penPHcure is an R package for for estimation, variable selection and
# simulation of the semiparametric proportional-hazards (PH) cure model with
# time-varying covariates.>
# Authors: Alessandro Beretta & Cédric Heuchenne
# Contact: a.beretta@uliege.be
#
# Licence as published by the Free Software Foundation, either version 3 of the
# Licence, or any later version. This program is distributed in the hope that it
# will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public Licence for more details. You should have received a copy of the GNU
# General Public Licence along with this program.
# If not, see <http://www.gnu.org/licenses/>.
# ------------------------------------------------------------------------------
penPHcure.stdfit <- function(init){
SV <- init$SV
# Fit standard cure model
fit <- fit_cure_cpp(SV$b,SV$beta,SV$base_hazard,
init$tstart,init$tstop,
init$sort1,init$sort2,
init$status,init$fail_times,
init$nfails,init$nobs_i,
init$status_FIX,init$X_FIX,
init$Z,init$ties,
init$warnings,init$maxIterNR,
init$maxIterEM,init$tol,
init$constraint)
# If covariates were standardized, rescale the estimated coefficients
if (init$standardize){
Z_mean <- attr(init$Z,"scaled:center")
Z_sd <- attr(init$Z,"scaled:scale")
X_mean <- attr(init$X_FIX,"scaled:center")
X_sd <- attr(init$X_FIX,"scaled:scale")
fit$beta <- fit$beta/Z_sd
temp <- fit$b[1] - sum(fit$b*X_mean/X_sd)
fit$b <- fit$b/X_sd
fit$b[1] <- temp
fit$cumhaz <- fit$cumhaz/exp(sum(Z_mean*fit$beta))
}
fit$b <- as.vector(fit$b)
names(fit$b) <- colnames(init$X_FIX)
fit$beta <- as.vector(fit$beta)
names(fit$beta) <- colnames(init$Z)
fit$cumhaz <- as.vector(fit$cumhaz)
attr(fit$cumhaz,"time") <- init$fail_times
fit$which.X <- init$which.X
fit$survform <- init$survform
fit$cureform <- init$cureform
class(fit) <- 'PHcure'
return(fit)
}
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