Description Usage Arguments Value References See Also Examples
Fit an integrative Cox model proposed by Wang et al. (2020) for rightcensored survival data with uncertain event times due to imperfect data integration.
1 2 3 4 5 6 7 8 9 10 
formula 

data 
An optional data frame, list, or environment that contains the
covariates and response variables included in the model. If not found in
data, the variables are taken from 
subset 
An optional logical vector specifying a subset of observations to be used in the fitting process. 
na.action 
An optional function that indicates what should the
procedure do if the data contains 
contrasts 
An optional list, whose entries are values (numeric
matrices or character strings naming functions) to be used as
replacement values for the contrasts replacement function and whose
names are the names of columns of data containing factors. See

start 
A list returned by function 
control 
A list returned by function 
... 
Other arguments for future usage. A warning will be thrown if any invalid argument is specified. 
An iCoxphclass
object, whose slots include
call
: Function call.
formula
: Formula used in the model fitting.
data
: A processed data frame used for model fitting.
nObs
: Number of observation.
estimates
:
beta
: Coefficient estimates.
pi
: Estimated parameters in prior multinomial
distribution indicating the probabilities of corresponding
record being true.
baseline
: A data frame that contains estimated
baseline hazard function with columns named time
and
h0
.
start
: The initial guesses beta_mat
and
pi_mat
specified for the parameters to be estimated,
and the set of initial guess beta_start
and pi_start
that resulted in the largest objective function, i.e.,
the observeddata likelihood function.
control
: The control list specified for model fitting.
na.action
: The procedure specified to deal with
missing values in the covariate.
xlevels
: A list that records the levels in
each factor variable.
contrasts
: Contrasts specified and used for each
factor variable.
convergeCode
: code
returned by function
nlm
, which is an integer indicating why the
optimization process terminated. help(nlm)
for details.
logL
: A numeric vector containing the observeddata
loglikelihood over iterations.
Wang, W., Aseltine, R. H., Chen, K., & Yan, J. (2020). Integrative Survival Analysis with Uncertain Event Times in Application to A Suicide Risk Study. Annals of Applied Statistics, 14(1), 51–73.
iCoxph.start
and iCoxph.control
, respectively,
for starting and controlling iCoxph fitting;
summary,iCoxphmethod
for summary of fitted model;
coef,iCoxphmethod
for estimated covariate coefficients;
bootSe
for SE estimates from bootstrap methods.
1 2 3 4 5 6 7 8 9 10 11 12 13 14  library(intsurv)
## generate simulated survival data with uncertain records
set.seed(123)
simuDat < simData4iCoxph(nSubject = 200)
## fit the integertive Cox model
fit < iCoxph(Survi(ID, time, event) ~ x1 + x2 + x3 + x4,
data = simuDat, start = iCoxph.start(methods = "nearest"),
control = iCoxph.control(tol_beta = 1e5))
## estimated covariate coefficients
coef(fit)
## get SE estimates by bootstrap
fit < bootSe(fit, B = 30)
## summary of the fitted model
summary(fit)

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