| Type: | Package |
| Title: | Multiple Imputation Method in Survival Analysis |
| Version: | 0.1.0 |
| Depends: | R(≥ 3.4.0) |
| Imports: | survival (≥ 3.1.11), zoo, stats, graphics, base |
| Maintainer: | Yiming Chen <yimingc1208@gmail.com> |
| Description: | In clinical trials, endpoints are sometimes evaluated with uncertainty. Adjudication is commonly adopted to ensure the study integrity. We propose to use multiple imputation (MI) introduced by Robin (1987) <doi:10.1002/9780470316696> to incorporate these uncertainties if reasonable event probabilities were provided. The method has been applied to Cox Proportional Hazard (PH) model, Kaplan-Meier (KM) estimation and Log-rank test in this package. Moreover, weighted estimations discussed in Cook (2004) <doi:10.1016/S0197-2456(00)00053-2> were also implemented with weights calculated from event probabilities. In conclusion, this package can handle time-to-event analysis if events presented with uncertainty by different methods. |
| License: | GPL-2 |
| Encoding: | UTF-8 |
| LazyData: | TRUE |
| RoxygenNote: | 7.1.1 |
| NeedsCompilation: | no |
| Packaged: | 2020-07-10 16:15:25 UTC; Yiming.Chen |
| Author: | Yiming Chen [aut, cre], John Lawrence [ctb] |
| Repository: | CRAN |
| Date/Publication: | 2020-07-13 08:50:03 UTC |
Cox PH model with MI method
Description
CoxMI function estimated Cox model with uncertain endpoints by using MI method. Users have to provide survival data in a long format with rows for all potential events, together with corresponding event probabilities. The long format data should be transformed by the uc_data_transform function into a data list before feed into the function.
Usage
CoxMI(data_list,nMI=1000,covariates=NULL,id=NULL,...)
Arguments
data_list |
The data list which has been transformed from the long format by the uc_data_transform function. |
nMI |
Number of imputations (>1). |
covariates |
Vector of covariates on the RHS of Cox model. Categorical variables need to be encoded as factor variables before entering the model. This encoding has to be done before the data transform step. |
id |
Vector of id variable if Andersen-Gill model is required. |
... |
Other arguments passed on to coxph(). |
Details
Calculates the estimated parameters as in the usual Cox proportional hazards model when event uncertainties present. The data are assumed to consist of potential event times with probabilities or weights between 0 and 1 corresponding to the probability that an event occurred at each time.
Value
est |
Estimated vector of coefficients in the model |
var |
Estimated variance of the coefficients |
betamat |
Matrix containing estimate of coefficient from each imputed dataset |
Var_mat |
Array containing variances for each imputed dataset |
Between Var |
Between imputation variance |
Within Var |
Mean within imputed dataset variance |
nMI |
Number of imputed datasets |
pvalue |
Estimated two-sided p-value |
en |
Expected events count - mean event count of imputed datasets |
Author(s)
Yiming Chen, John Lawrence
References
[1] Rubin DB. Multiple Imputation for Nonresponse in Surveys. New York: Wiley; 1987
See Also
Examples
set.seed(128)
df_x<-data_sim(n=500,true_hr=0.8,haz_c=0.5/365)
df_x$f.trt<-as.factor(df_x$trt_long)
data_intrim<-uc_data_transform(data=df_x,
var_list=c("id_long","f.trt"),
var_list_new=c("id","trt"),
time="time_long",
prob="prob_long")
#nMI=10 used in the example below to reduce the time needed
#but a large number as nMI=1000 is recommended in practice
fit<-CoxMI(data_list=data_intrim,nMI=10,covariates=c("trt"))
CoxMI.summ(fit)
fit<-CoxMI(data_list=data_intrim,nMI=1000,covariates=c("trt"),id=c("id"))
CoxMI.summ(fit)
Summary function for the Cox MI model
Description
Prints the fitting results from the CoxMI function.
Usage
CoxMI.summ(x,digits=3)
Arguments
x |
An object returned by the CoxMI function. |
digits |
Digits of output |
Details
Print a summary table of Cox regression result with MI implemented.
Value
A summary table of Cox regression result with MI implemented.
Author(s)
Yiming Chen
See Also
Weighted Cox PH model estimation
Description
Estimate the Cox PH model by weighted partial likelihood. Event weights are calcualted with respect to event probabilities.
Usage
Coxwt(data_list,covariates,init=NULL,BS=FALSE,nBS=1000)
Arguments
data_list |
The data list which has been transformed from the long format by the uc_data_transform function. |
covariates |
The vector of varaible on the RHS of the Cox model. |
init |
The initial value of covariates vector in the likelihood, length matches the length of covariates. |
BS |
T/F, whether conduct estimation via the Bootstrap method. |
nBS |
Number of BS, only effective if BS=TRUE. |
Value
coefficients |
Estimated vector of coefficients in the model |
var |
Estimated variance of the coefficients |
hr |
Estimated hazard ratios in the model |
z |
Wald test statistics |
pvalue |
Estimated two-sided p-value |
coefficients_bs |
Bootstrapped coefficient estimation |
var_bs |
Bootstrapped variance estimation |
column_name |
Column name |
Author(s)
Yiming Chen, John Lawrence
References
[1]Cook TD. Adjusting survival analysis for the presence of unadjudicated study events. Controlled clinical trials. 2000;21(3):208-222.
[2]Cook TD, Kosorok MR. Analysis of time-to-event data with incomplete event adjudication. Journal of the american statistical association. 2004;99(468):1140-1152.
[3]Snapinn SM. Survival analysis with uncertain endpoints. Biometrics. 1998;54(1):209-218.
See Also
Examples
df_x<-data_sim(n=500,0.8,haz_c=0.5/365)
data_intrim<-uc_data_transform(data=df_x,
var_list=c("id_long","trt_long"),
var_list_new=c("id","trt"),
time="time_long",
prob="prob_long")
fit<-Coxwt(data_list=data_intrim,covariates=c("trt"),init=c(1),BS=FALSE)
Coxwt.summ(fit)
##an example if we would like to check the BS variance
fit2<-Coxwt(data_list=data_intrim,covariates=c("trt"),init=c(1),BS=TRUE, nBS = 100)
Coxwt.summ(fit2)
Summary function for the weighted Cox model
Description
Print the fitting results from the weighted Cox regression.
Usage
Coxwt.summ(x,digits=3)
Arguments
x |
An object returned by the Coxwt function |
digits |
Digits of output |
Value
A summary table of weighted Cox regression result.
Author(s)
Yiming Chen
See Also
Kaplan-Meier estimation with event uncertainty
Description
KM estimation for survival data when event uncertainty presents. KM plot will be output if plot=TRUE specfied.
Usage
KMMI(data_list,nMI,covariates,data_orig = NULL,plot = TRUE,
time_var=NULL,event_var=NULL)
Arguments
data_list |
The data list which has been transformed from the long format by uc_data_transform function. |
nMI |
Number of imputations (>1). If missing, weighted statistics would be output instead. |
covariates |
The grouping varaible, no need to be factorized. If missing then the overall KM is returned. |
plot |
T/F, whether output a KM plot, the plot potentially contains KM curves from original dataset and imputed/weighted dataset. |
data_orig |
The original data without any uncertain events. If supplies then user can compare results from certain events only and all possible events. |
time_var |
Time variable in data_orig. If user provides the orig dataset then user need to specify the time and event indicator variable in the orignal dataset. |
event_var |
Event indicator variable in the original data set. |
Value
KM_mi |
A dataset contains MI estimation and variance at all potential event time |
KM_cook |
A dataset contains weighted KM estimation and variance at all potential event time |
ngroup |
Number of groups |
cate_level |
Values of the categorical variable |
nMI |
Number of imputed datasets |
Author(s)
Yiming Chen
References
[1]Cook TD. Adjusting survival analysis for the presence of unadjudicated study events. Controlled clinical trials. 2000;21(3):208-222.
[2]Cook TD, Kosorok MR. Analysis of time-to-event data with incomplete event adjudication. Journal of the american statistical association. 2004;99(468):1140-1152.
[3]Klein JP, Moeschberger ML. Survival Analysis : Techniques for Censored and Truncated Data. New York: Springer; 1997.
[4]Rubin DB. Multiple Imputation for Nonresponse in Surveys. New York: Wiley; 1987
See Also
Examples
##an example with more potential event case
##data_orig was created as keeping the event with largest weights for individuals
df_x<-data_sim(n=500,0.8,haz_c=0.5/365)
data_intrim<-uc_data_transform(data=df_x,
var_list=c("id_long","trt_long"),
var_list_new=c("id","trt"),
time="time_long",
prob="prob_long")
df_y<-data_sim2(data_list=data_intrim,covariates=c("trt"),percentage=1)
data_orig<-df_y[df_y$prob==0|df_y$prob==1,]
data_orig<-data_orig[!duplicated(data_orig$id),]
data_orig$cens<-data_orig$prob
##weighted estimation
KM_res<-KMMI(data_list=data_intrim,nMI=NULL,covariates=c("trt"),plot=TRUE,data_orig=NULL)
##MI estimation
KMMI(data_list=data_intrim,nMI=1000,covariates=c("trt"),plot=TRUE,data_orig=NULL)
data_intrim2<-uc_data_transform(data=df_y, var_list=c("id","trt"),
var_list_new=NULL,time="time", prob="prob")
KMMI(data_list=data_intrim2,nMI=1000,covariates=c("trt"),plot=TRUE,data_orig=data_orig,
time_var=c("time"),event_var=c("cens"))
Log-rank test with events uncertainty
Description
This function conducts the Log-rank test with respect to uncertain endpoints, by MI or weighted method.
Usage
LRMI(data_list, nMI, covariates, strata = NULL,...)
Arguments
data_list |
The data list which has been transformed from the long format by uc_data_transform function. |
nMI |
Number of imputation (>1). If missing, weighted statistics would be output instead. |
covariates |
The categorical variable used in the Log-rank test. No need to factorlize numeric variables. |
strata |
Strata variable may required by the Log-rank test |
... |
Other arguments passed on to survdiff(). |
Value
est |
Estimated LR statistics, either from the MI method or weighted method |
var |
Estimated variance matrix |
est_mat |
Matrix containing estimate of statistics from each imputed dataset |
Var_mat |
Array containing variances for each imputed dataset |
Between Var |
Between imputation variance |
Within Var |
Mean within imputed dataset variance |
nMI |
Number of imputed datasets |
pvalue |
Estimated two-sided Chi-square test p-value |
df |
Degree of freedom |
covariates |
covariates |
ngroup |
Number of groups |
obsmean |
Mean of observed events count across imputations |
expmean |
Mean of expected events count across imputations |
Author(s)
Yiming Chen
References
[1]Cook TD. Adjusting survival analysis for the presence of unadjudicated study events. Controlled clinical trials. 2000;21(3):208-222.
[2]Cook TD, Kosorok MR. Analysis of time-to-event data with incomplete event adjudication. Journal of the american statistical association. 2004;99(468):1140-1152.
[3]Klein JP, Moeschberger ML. Survival Analysis : Techniques for Censored and Truncated Data. New York: Springer; 1997.
[4]Rubin DB. Multiple Imputation for Nonresponse in Surveys. New York: Wiley; 1987
See Also
Examples
df_x<-data_sim(n=500,0.8,haz_c=0.5/365)
data_intrim<-uc_data_transform(data=df_x,
var_list=c("id_long","trt_long"),
var_list_new=c("id","trt"),
time="time_long",
prob="prob_long")
#nMI=10 used in the example below to reduce the time needed
#but a large number as nMI=1000 is recommended in practice
fit<-LRMI(data_list=data_intrim,nMI=10,covariates=c("trt"),strata=NULL)
LRMI.summ(fit)
Prints the test results output by the LRMI function
Description
Summary function for the Log-rank test either by the MI method or the weighted method.
Usage
LRMI.summ(x,digits=3)
Arguments
x |
An object returned by the LRMI function. |
digits |
Digits of output |
Value
A summary table of LR test result with MI implemented.
Author(s)
Yiming Chen
See Also
Simulated survival data with uncertain endpoints from exponential distribution.
Description
data_sim function simulates data from a hypothetic 1:1 two-arms clinical trial, with one year uniform accrual period and three years follow-up.
data_sim2 function simplifies data list generated from above function to a more events only case. Note this function is only used for demonstration purpose.
Usage
data_sim(n=200,true_hr=0.8,haz_c=1/365)
data_sim2(data_list,covariates,percentage)
Arguments
n |
Total number of subject. |
true_hr |
True hazard ratio between trt and control. |
haz_c |
True event rate in the control arm. |
data_list |
The data list which has been transformed from the long format by uc_data_transform function. |
covariates |
The covariate we pose the true HR. |
percentage |
The percentage of censored subjects with potential events we would like to ultilize in the analysis. Ideally, with more potential events added, more power gain of imputation. |
Value
Dataframe. Simulated datasets with event probabilities and potential event date.
Author(s)
Yiming Chen, John Lawrence
Examples
df_x<-data_sim(n=500,true_hr=0.8,haz_c=1/365)
data_intrim<-uc_data_transform(data=df_x,
var_list=c("id_long","trt_long"),
var_list_new=c("id","trt"),
time="time_long",
prob="prob_long")
df_y<-data_sim2(data_list=data_intrim,covariates=c("trt"),percentage=0.2)
Transform long formatted time-to-event data into a data list
Description
This function transforms data from long format (one record per event) to a datalist with length as unique subject number. The transformation is required before fitting other models from the package.
Usage
uc_data_transform(data,var_list,var_list_new,time,prob)
Arguments
data |
The dataset in long format with a row for each potential event. For ceonsoring record, the event prob should be 0. It should include id, time and prob variables at a minimum. If any covariates are included in the call to the function, then these variables should also be included. A censoring record is required for each subject. Categorical variables need to be encoded as factor varaible before transformationif they are expected to be in the Cox model. |
var_list |
The list of identification variables, such as: c("id_long","trt_long"). |
time |
The time variable need to be transofirmed, e.g. time_long. |
prob |
The prob variable need to be transformed, e.g. prob_long. |
var_list_new |
The character vector contains the new names for the id variables defined in the var_list, if missing, previous variable names would be used. |
Value
time |
The list of all potential event time |
prob |
The list of all potential event probabilities |
weights |
The list of all potential event weights |
e |
The list of individual potential event count |
s |
The list of all survival probabilities |
data_uc |
The dataset contains unique information of each subject |
data_long |
The dataset contains the original data in long format |
Author(s)
Yiming Chen
Examples
df_x<-data_sim(n=1000,true_hr=0.8,haz_c=0.5/365)
df_x$f.trt<-as.factor(df_x$trt_long)
data_intrim<-uc_data_transform(data=df_x,
var_list=c("id_long","f.trt"),
var_list_new=c("id","trt"),
time="time_long",
prob="prob_long")