| Type: | Package |
| Title: | Fit Semiparametric Mixture Cure Models |
| Version: | 2.1 |
| Date: | 2022-05-04 |
| Author: | Chao Cai, Yubo Zou, Yingwei Peng, Jiajia Zhang |
| Maintainer: | Chao Cai <caic@email.sc.edu> |
| Description: | An R-package for Estimating Semiparametric PH and AFT Mixture Cure Models. |
| Depends: | survival, stats, graphics |
| License: | GPL-2 |
| LazyLoad: | yes |
| RoxygenNote: | 7.1.2 |
| Encoding: | UTF-8 |
| NeedsCompilation: | no |
| Packaged: | 2022-05-06 11:51:08 UTC; CAIC |
| Repository: | CRAN |
| Date/Publication: | 2022-05-09 08:30:02 UTC |
Bone marrow transplant study
Description
Bone marrow transplant study which is widely used in the AFTMC model
Usage
data(bmt)Format
There were 46 patients in the allogeneic treatment and 44 patients in the autologous treatment group
Timetime to event
Statuscensor indicator, 0 for censored and 1 for uncensored
TRT1 for autologous treatment group; 0 for allogeneic treatment group
Retrieves the estimated coefficients from object
Description
Retrieving coefficients, printing method, and summary mthod for a smcure object.
Usage
coefsmcure(x,...)
Arguments
x |
an object from smcure function |
... |
Further arguments to be passed to the printsmcure function. |
Eastern Cooperative Oncology Group (ECOG) data
Description
Eastern Cooperative Oncology Group (ECOG) data used for modeling PH semicure model
Usage
data(e1684)Format
A data frame with 284 observations on the following 5 variables.
TRT0=control group, 1=IFN treatment group
FAILTIMEobserved relapse-free time
FAILCENSrelapse-free censor indicator
AGEcontinuous variable, which is centered to the mean
SEX0 for male, 1 fopr female
EM algorithm
Description
EM algorithm used in the mixture cure model by assuming a latent indicator of uncure. Detailed estimation methods can be found in the reference section
Usage
em(Time, Status, X, Z, offsetvar, b, beta, model, link, emmax, eps)
Arguments
Time |
time to event of interest |
Status |
status indicator, 0=alive, 1=dead |
X |
a vector or matrix of covariates corresponding to latency part |
Z |
a vector or matrix of covariates corresponding to incidence part |
offsetvar |
offset variable |
b |
initial value for parameter b |
beta |
initial value for parameter beta |
model |
either "ph" or "aft" |
link |
specifies the link in incidence part. The "logit", "probit" or complementary loglog ("cloglog") links are available. By default link = "logit". |
emmax |
specifies the maximum iteration number. If the convergence criterion is not met, the EM iteration will be stopped after emmax iterations and the estimates will be based on the last maximum likelihood iteration. The default emmax = 100. |
eps |
sets the convergence criterion. The default is eps = 1e-7. The iterations are considered to be converged when the maximum relative change in the parameters and likelihood estimates between iterations is less than the value specified. |
Plot predicted smcure object
Description
plot predicted survival curve(s) from the estimated mixture cure model
Usage
plotpredictsmcure(object, type = "S", xlab = "Time",
ylab = "Predicted Survival Probability",
model = c("ph", "aft"), ...)
Arguments
object |
an object of the predictsmcure function |
type |
type of plot. "S" means steps plot. |
xlab |
a label for the x axis |
ylab |
a label for the y axis |
model |
either "ph" or "aft" |
... |
Further options in plotfunction can be passed to the plotpredictsmcure function |
prediction of semicure model
Description
Prediction of semicure model
Usage
predictsmcure(object, newX, newZ, model = c("ph", "aft"), ...)
Arguments
object |
an object of smcure |
newX |
new value(s) of X |
newZ |
new value(s) of Z |
model |
either 'ph' or 'aft' |
... |
further arguments to be passed to the predictsmcure function |
Details
Predicted population survival function can be calculated by the following equation
S_{pop}(t)=\pi+(1-\pi)*S(t)
Print smcure object
Description
Output of smcure object
Usage
printsmcure(x, Var, ...)
Arguments
x |
an object of smcure |
Var |
If it is TRUE, the program returns standard error by bootstrap method. If set to False, the program only returns estimators of coefficients. By default, Var = TRUE |
... |
Further arguments to be passed to the printsmcure function. |
Title
Description
Title
Usage
smcure(
formula,
cureform,
offset = NULL,
data,
na.action = na.omit,
model = c("aft", "ph"),
link = "logit",
Var = TRUE,
emmax = 50,
eps = 1e-07,
nboot = 100
)
Arguments
formula |
a formula object |
cureform |
specifies the variables in the incidence |
offset |
variable(s) with coefficient 1 in PH model or AFT model |
data |
a data.frame in which to interpret the variables named in the formula and cureform |
na.action |
a missing-data filter function. By default na.action = na.omit |
model |
specifies your model ph or aft |
link |
incidence part |
Var |
By default Var = TRUE |
emmax |
maximum iteration number |
eps |
convergence criterion |
nboot |
number of bootstrap sampling |
Value
a smcure object
Examples
data(e1684)
pd <- smcure(Surv(FAILTIME,FAILCENS)~TRT+SEX+AGE,
cureform=~TRT+SEX+AGE,data=e1684,model="ph",
Var = FALSE)
printsmcure(pd,Var = FALSE)
Estimation of the baseline survival
Description
This R-program uses the Breslow method to estimate baseline survival of PH mixture cure model and AFT mixture cure model.
Usage
smsurv(Time, Status, X, beta, w, model)
Arguments
Time |
this is the follow up time for "ph" model. If model is "aft", then this is residual. |
Status |
The status indicator, normally 0=alive, 1=dead |
X |
effects of covariates of uncured patients |
beta |
initial beta from coxph |
w |
conditional probability of the ith individual remains uncured at the mth iteration. We use Status as initial value |
model |
specifies your model, it can be "ph" or "aft" |