Help for package surtvep

Title:

Cox Non-Proportional Hazards Model with Time-Varying Coefficients

Version:

1.0.0

URL:

https://github.com/UM-KevinHe/surtvep, https://um-kevinhe.github.io/surtvep/

BugReports:

https://github.com/UM-KevinHe/surtvep/issues

Description:

Fit Cox non-proportional hazards models with time-varying coefficients. Both unpenalized procedures (Newton and proximal Newton) and penalized procedures (P-splines and smoothing splines) are included using B-spline basis functions for estimating time-varying coefficients. For penalized procedures, cross validations, mAIC, TIC or GIC are implemented to select tuning parameters. Utilities for carrying out post-estimation visualization, summarization, point-wise confidence interval and hypothesis testing are also provided. For more information, see Wu et al. (2022) <doi:10.1007/s10985-021-09544-2> and Luo et al. (2023) <doi:10.1177/09622802231181471>.

License:

GPL-3

Encoding:

UTF-8

LazyData:

true

RoxygenNote:

7.2.3

LinkingTo:

Rcpp, RcppArmadillo

Imports:

Rcpp, splines, ggplot2, ggpubr, stats, tibble, rlang

Depends:

R (≥ 4.0)

Suggests:

knitr, rmarkdown

NeedsCompilation:

yes

Packaged:

2023-10-16 20:46:56 UTC; lingfengluo

Author:

Lingfeng Luo [aut, cre], Wenbo Wu [aut], Kevin He [aut]

Maintainer:

Lingfeng Luo <lfluo@umich.edu>

Repository:

CRAN

Date/Publication:

2023-10-17 10:00:02 UTC

example data with 2000 observations of 2 continuous variables

Description

A simulated data set containing 2 continuous variables.

Usage

data(ExampleData)

Format

A list containing the following elements:

z: simulated continuous covariates V1 and V2, with a time-independent coefficient \beta_1(t)=1 and a time-varying coefficient \beta_2(t)=sin(3\pi t/4).
event: simulated failure event response; binary variable with 0 or 1.
time: simulated observed event times; continuous variable with non-negative values.

example data with 2000 observations of 2 binary variables

Description

A simulated data set containing 2 binary variables.

Usage

data(ExampleDataBinary)

Format

A list containing the following elements:

z: simulated binary covariates V1 and V2, with a time-independent coefficient \beta_1(t)=1 and a time-varying coefficient \beta_2(t)=exp(-1.5t).
event: simulated failure event response; binary variable with 0 or 1.
time: simulated observed event times; continuous variable with non-negative values.

calculating information criteria from a `coxtp` object

Description

This function is to calculate information criteria from a coxtp object to select the penalization tuning parameter.

Usage

IC(fit, IC.prox)

Arguments

fit

model from coxtp.

IC.prox

when calculating information criteria, there might be numerical issues (e.g. the Hessian matrix is close to be singular). In such cases, warnings will be given. If IC.prox = TRUE, we modify the diagonal of the Hessian matrix following the same approach as the proximal method detailed in Wu et al. (2022), which can lead to more stable estimates. The default value is FALSE.

Details

In order to select the proper smoothing parameter, we utilize the idea of information criteria. We provide four different information criteria to select the optimal smoothing parameter \lambda. Generally, mAIC, TIC and GIC select similar parameters and the difference of resulting estimates are barely noticeable. See details in the Luo et al. (2023).

Value

model.mAIC

an object with S3 class "coxtp" using mAIC to select the tuning parameter.

model.TIC

an object with S3 class "coxtp" using TIC to select the tuning parameter.

model.GIC

an object with S3 class "coxtp" using GIC to select the tuning parameter.

mAIC

a sequence of mAIC values corresponding to each of the tuning parameter lambda from "coxtp".

TIC

a sequence of TIC values corresponding to each of the tuning parameter lambda from "coxtp".

GIC

a sequence of GIC values corresponding to each of the tuning parameter lambda from "coxtp".

References

Akaike, H. (1998) Information theory and an extension of the maximum likelihood principle. In Selected Papers of Hirotugu Akaike. 199–213.

Luo, L., He, K., Wu, W., and Taylor, J. M. (2023) Using information criteria to select smoothing parameters when analyzing survival data with time-varying coefficient hazard models. Statistical Methods in Medical Research, in press.

Takeuchi, K. (1976) Distribution of information statistics and criteria for adequacy of models. Mathematical Sciences, 153: 12–18.

Wu, W., Taylor, J. M., Brouwer, A. F., Luo, L., Kang, J., Jiang, H., and He, K. (2022) Scalable proximal methods for cause-specific hazard modeling with time-varying coefficients. Lifetime Data Analysis, 28(2): 194-218.

Examples

data(ExampleData)
z <- ExampleData$z
time <- ExampleData$time
event <- ExampleData$event
fit <- coxtp(event = event, z = z, time = time)
IC  <- IC(fit)

example data for stratified model illustration

Description

A simulated data set containing 2 binary variables from 10 distinct stratums.

Usage

data(StrataExample)

Format

A list containing the following elements:

z: simulated binary covariates V1 and V2, with a time-independent coefficient \beta_1(t)=1 and a time-varying coefficient \beta_2(t)=sin(3\pi t/4).
event: simulated failure event response; binary variable with 0 or 1.
time: simulated observed event times; continuous variable with non-negative values.
strata: simulated strata variable; patients in different stratums have different baseline hazards.

calculating baseline hazard and baseline cumulative hazard using the result from a `coxtv` or `coxtp` object

Description

The baseline estimation is the baseline hazard at each observed failure time when holding all the covariates to be zero.

Usage

baseline(fit)

Arguments

fit

model from coxtv or coxtp.

Value

A list with three components:

time

the unique observed failure times.

hazard

the baseline hazard corresponding to each unique failure time point.

cumulHaz

the cumulative baseline hazard corresponding to each unique failure time point.

Examples

data(ExampleData)
z <- ExampleData$z
time  <- ExampleData$time
event <- ExampleData$event

fit   <- coxtv(event = event, z = z, time = time)
base.est <- baseline(fit)

get confidence intervals of time-varying coefficients from a fitted object

Description

Get confidence intervals of time-varying coefficients from a fitted coxtv or coxtp object.

Usage

## S3 method for class 'coxtp'
confint(object, parm, level = 0.95, time, ...)

## S3 method for class 'coxtv'
confint(object, parm, level = 0.95, time, ...)

Arguments

object

fitted "coxtv" model.

parm

the names of parameters.

level

the confidence level. The default value is 0.95.

time

the time points for which the confidence intervals to be estimated. The default value is the unique observed event times in the dataset fitting the time-varying effects model.

...

other parameters to function

Value

A list where each element corresponds to one of the parameters specified in parm. Each element in the list is a matrix, with rows corresponding to the specified time points and three columns representing the estimated values of the parameter, and the lower and upper bounds of the confidence interval at the specified confidence level. The length of the list is determined by the number of parameters in parm, and each matrix has rows equal to the number of specified time points.

Examples


data(ExampleData)
z <- ExampleData$z
time <- ExampleData$time
event <- ExampleData$event
fit <- coxtp(event = event, z = z, time = time)
IC  <- IC(fit)
confint(IC$model.mAIC)


data(ExampleData)
z <- ExampleData$z
time <- ExampleData$time
event <- ExampleData$event
fit <- coxtv(event = event, z = z, time = time)
confint <- confint(fit)

fit a Cox non-proportional hazards model with P-spline or Smoothing-spline, with penalization tuning parameter chosen by information criteria or cross-validation

Description

Fit a Cox non-proportional hazards model via penalized maximum likelihood.

Usage

coxtp(
  event,
  z,
  time,
  strata = NULL,
  penalty = "Smooth-spline",
  nsplines = 8,
  lambda = c(0.1, 1, 10),
  degree = 3L,
  knots = NULL,
  ties = "Breslow",
  tol = 1e-06,
  iter.max = 20L,
  method = "ProxN",
  gamma = 1e+08,
  btr = "dynamic",
  tau = 0.5,
  stop = "ratch",
  parallel = FALSE,
  threads = 2L,
  fixedstep = FALSE
)

Arguments

event

failure event response variable of length nobs, where nobs denotes the number of observations. It should be a vector containing 0 or 1.

z

input covariate matrix, with nobs rows and nvars columns; each row is an observation.

time

observed event times, which should be a vector with non-negative values.

strata

a vector of indicators for stratification. Default = NULL (i.e. no stratification group in the data), an unstratified model is implemented.

penalty

a character string specifying the spline term for the penalized Newton method. This term is added to the log-partial likelihood, and the penalized log-partial likelihood serves as the new objective function to control the smoothness of the time-varying coefficients. Default is P-spline. Three options are P-spline, Smooth-spline and NULL. If NULL, the method will be the same as coxtv (unpenalized time-varying effects models) and lambda (defined below) will be set as 0.

P-spline stands for Penalized B-spline. It combines the B-spline basis with a discrete quadratic penalty on the difference of basis coefficients between adjacent knots. When lambda goes to infinity, the time-varying effects are reduced to be constant.

Smooth-spline refers to the Smoothing-spline, the derivative-based penalties combined with B-splines. See degree for different choices. When degree=3, we use the cubic B-spline penalizing the second-order derivative, which reduces the time-varying effect to a linear term when lambda goes to infinity. When degree=2, we use the quadratic B-spline penalizing first-order derivative, which reduces the time-varying effect to a constant when lambda goes to infinity. See Wood (2017) for details.

If P-spline or Smooth-spline, then lambda is initialized as a sequence (0.1, 1, 10). Users can modify lambda. See details in lambda.

nsplines

number of basis functions in the splines to span the time-varying effects. The default value is 8. We use the R function splines::bs to generate the B-splines.

lambda

a user-specified lambda sequence as the penalization coefficients in front of the spline term specified by penalty. This is the tuning parameter for penalization. The function IC can be used to select the best tuning parameter based on the information criteria. Alternatively, cross-validation can be used via the cv.coxtp function. When lambda is 0, Newton method without penalization is fitted.

degree

degree of the piecewise polynomial for generating the B-spline basis functions—default is 3 for cubic splines. degree = 2 results in the quadratic B-spline basis functions.

If the penalty is P-spline or NULL, degree's default value is 3.

If the penalty is Smooth-spline, degree's default value is 2.

knots

the internal knot locations (breakpoints) that define the B-splines. The number of the internal knots should be nsplines-degree-1. If NULL, the locations of knots are chosen as quantiles of distinct failure time points. This choice leads to more stable results in most cases. Users can specify the internal knot locations by themselves.

ties

a character string specifying the method for tie handling. If there are no tied events, the methods are equivalent. By default "Breslow" uses the Breslow approximation, which can be faster when many ties are present. If ties = "none", no approximation will be used to handle ties.

tol

tolerance used for stopping the algorithm. See details in stop below. The default value is 1e-6.

iter.max

maximum iteration number if the stopping criterion specified by stop is not satisfied. The default value is 20.

method

a character string specifying whether to use Newton method or proximal Newton method. If Newton then Hessian is used, while the default method "ProxN" implements the proximal Newton which can be faster and more stable when there exists ill-conditioned second-order information of the log-partial likelihood. See details in Wu et al. (2022).

gamma

parameter for proximal Newton method "ProxN". The default value is 1e8.

btr

a character string specifying the backtracking line-search approach. "dynamic" is a typical way to perform backtracking line-search. See details in Convex Optimization by Boyd and Vandenberghe (2004). "static" limits Newton's increment and can achieve more stable results in some extreme cases, such as ill-conditioned second-order information of the log-partial likelihood, which usually occurs when some predictors are categorical with low frequency for some categories. Users should be careful with static, as this may lead to under-fitting.

tau

a positive scalar used to control the step size inside the backtracking line-search. The default value is 0.5.

stop

a character string specifying the stopping rule to determine convergence. "incre" means we stop the algorithm when Newton's increment is less than the tol. See details in Convex Optimization (Chapter 10) by Boyd and Vandenberghe (2004). "relch" means we stop the algorithm when the (loglik(m)-loglik(m-1))/(loglik(m)) is less than the tol, where loglik(m) denotes the log-partial likelihood at iteration step m. "ratch" means we stop the algorithm when (loglik(m)-loglik(m-1))/(loglik(m)-loglik(0)) is less than the tol. "all" means we stop the algorithm when all the stopping rules ("incre", "relch", "ratch") are met. The default value is ratch. If iter.max is achieved, it overrides any stop rule for algorithm termination.

parallel

if TRUE, then the parallel computation is enabled. The number of threads in use is determined by threads.

threads

an integer indicating the number of threads to be used for parallel computation. The default value is 2. If parallel is false, then the value of threads has no effect.

fixedstep

if TRUE, the algorithm will be forced to run iter.max steps regardless of the stopping criterion specified.

Details

The sequence of models implied by lambda.spline is fit by the (proximal) Newton method. The objective function is

loglik - P_{\lambda},

where P_{\lambda} is a penalty matrix for P-spline or Smooth-spline. The \lambda is the tuning parameter (See details in lambda). Users can define the initial sequence. The function IC below provides different information criteria to choose the tuning parameter \lambda. Another function cv.coxtp uses the cross-validation to choose the tuning parameter.

Value

A list of objects with S3 class "coxtp". The length is the same as that of lambda; each represents the model output with each value of the tuning parameter lambda.

call

the call that produced this object.

beta

the estimated time-varying coefficient for each predictor at each unique time. It is a matrix of dimension len_unique_t by nvars, where len_unique_t is the length of unique observed event times.

bases

the basis matrix used in model fitting. If ties="none", the dimension of the basis matrix is nvars by nsplines; if ties="Breslow", the dimension is len_unique_t by nsplines. The matrix is constructed using the bs::splines function.

ctrl.pts

estimated coefficient of the basis matrix of dimension nvars by nsplines. Each row represents a covariate's coefficient on the nsplines-dimensional basis functions.

Hessian

the Hessian matrix of the log-partial likelihood, of which the dimension is nsplines * nvars by nsplines * nvars.

internal.knots

the internal knot locations (breakpoints) that define the B-splines.

nobs

number of observations.

penalty

the spline term penalty specified by user.

theta.list

the history of ctrl.pts of length m (the length of algorithm iterations), including ctrl.pts for each algorithm iteration.

VarianceMatrix

the variance matrix of the estimated coefficients of the basis matrix, which is the inverse of the negative Hessian matrix.

References

Boyd, S., and Vandenberghe, L. (2004) Convex optimization. Cambridge University Press.

Gray, R. J. (1992) Flexible methods for analyzing survival data using splines, with applications to breast cancer prognosis. Journal of the American Statistical Association, 87(420): 942-951.

Gray, R. J. (1994) Spline-based tests in survival analysis. Biometrics, 50(3): 640-652.

Perperoglou, A., le Cessie, S., and van Houwelingen, H. C. (2006) A fast routine for fitting Cox models with time varying effects of the covariates. Computer Methods and Programs in Biomedicine, 81(2): 154-161.

Wood, S. N. (2017) P-splines with derivative based penalties and tensor product smoothing of unevenly distributed data. Statistics and Computing, 27(4): 985-989.

Examples

data(ExampleData)
z <- ExampleData$z
time  <- ExampleData$time
event <- ExampleData$event

lambda  = c(0,1)
fit   <- coxtp(event = event, z = z, time = time, lambda=lambda)

fit a Cox non-proportional hazards model

Description

Fit a Cox non-proportional hazards model via maximum likelihood.

Usage

coxtv(
  event,
  z,
  time,
  strata = NULL,
  nsplines = 8,
  knots = NULL,
  degree = 3,
  ties = "Breslow",
  stop = "ratch",
  tol = 1e-06,
  iter.max = 20,
  method = "ProxN",
  gamma = 1e+08,
  btr = "dynamic",
  tau = 0.5,
  parallel = FALSE,
  threads = 2L,
  fixedstep = FALSE
)

Arguments

event

failure event response variable of length nobs, where nobs denotes the number of observations. It should be a vector containing 0 or 1.

z

input covariate matrix, with nobs rows and nvars columns; each row is an observation.

time

observed event times, which should be a vector with non-negative values.

strata

a vector of indicators for stratification. Default = NULL (i.e. no stratification group in the data), an unstratified model is implemented.

nsplines

number of basis functions in the splines to span the time-varying effects. The default value is 8. We use the R function splines::bs to generate the B-splines.

knots

degree

degree of the piecewise polynomial for generating the B-spline basis functions—default is 3 for cubic splines. degree = 2 results in the quadratic B-spline basis functions.

ties

stop

tol

tolerance used for stopping the algorithm. See details in stop below. The default value is 1e-6.

iter.max

maximum iteration number if the stopping criterion specified by stop is not satisfied. The default value is 20.

method

a character string specifying whether to use Newton method or proximal Newton method. If "Newton" then Hessian is used, while the default method "ProxN" implements the proximal Newton which can be faster and more stable when there exists ill-conditioned second-order information of the log-partial likelihood. See details in Wu et al. (2022).

gamma

parameter for proximal Newton method "ProxN". The default value is 1e8.

btr

tau

a positive scalar used to control the step size inside the backtracking line-search. The default value is 0.5.

parallel

if TRUE, then the parallel computation is enabled. The number of threads in use is determined by threads.

threads

an integer indicating the number of threads to be used for parallel computation. The default value is 2. If parallel is false, then the value of threads has no effect.

fixedstep

if TRUE, the algorithm will be forced to run iter.max steps regardless of the stopping criterion specified.

Details

The model is fit by Newton method (proximal Newton method).

Value

An object with S3 class coxtv.

call

the call that produced this object.

beta

bases

ctrl.pts

estimated coefficient of the basis matrix of dimension nvars by nsplines. Each row represents a covariate's coefficient on the nsplines-dimensional basis functions.

Hessian

the Hessian matrix of the log-partial likelihood, of which the dimension is nsplines * nvars by nsplines * nvars.

internal.knots

the internal knot locations (breakpoints) that define the B-splines.

nobs

number of observations.

theta.list

the history of ctrl.pts of length m (the length of algorithm iterations), including ctrl.pts for each algorithm iteration.

VarianceMatrix

the variance matrix of the estimated coefficients of the basis matrix, which is the inverse of the negative Hessian matrix.

References

Boyd, S., and Vandenberghe, L. (2004) Convex optimization. Cambridge University Press.

Gray, R. J. (1992) Flexible methods for analyzing survival data using splines, with applications to breast cancer prognosis. Journal of the American Statistical Association, 87(420): 942-951.

Gray, R. J. (1994) Spline-based tests in survival analysis. Biometrics, 50(3): 640-652.

Luo, L., He, K., Wu, W., and Taylor, J. M. (2023) Using information criteria to select smoothing parameters when analyzing survival data with time-varying coefficient hazard models.

Examples

data(ExampleData)
z <- ExampleData$z
time <- ExampleData$time
event <- ExampleData$event
fit <- coxtv(event = event, z = z, time = time)

fit a cross-validated Cox non-proportional hazards model with P-spline or Smoothing-spline where penalization tuning parameter is provided by cross-validation

Description

Fit a Cox non-proportional hazards model via penalized maximum likelihood. The penalization tuning parameter is provided by cross-validation.

Usage

cv.coxtp(
  event,
  z,
  time,
  strata = NULL,
  lambda = c(0.1, 1, 10),
  nfolds = 5,
  foldid = NULL,
  knots = NULL,
  penalty = "Smooth-spline",
  nsplines = 8,
  ties = "Breslow",
  tol = 1e-06,
  iter.max = 20L,
  method = "ProxN",
  gamma = 1e+08,
  btr = "dynamic",
  tau = 0.5,
  stop = "ratch",
  parallel = FALSE,
  threads = 1L,
  degree = 3L,
  fixedstep = FALSE
)

Arguments

event

failure event response variable of length nobs, where nobs denotes the number of observations. It should be a vector containing 0 or 1.

z

input covariate matrix, with nobs rows and nvars columns; each row is an observation.

time

observed event times, which should be a vector with non-negative values.

strata

a vector of indicators for stratification. Default = NULL (i.e. no stratification group in the data), an unstratified model is implemented.

lambda

a user specified sequence as the penalization coefficients in front of the spline term specified by penalty. This is the tuning parameter for penalization. The function IC can be used to select the best tuning parameter based on the information criteria. Users can specify larger values when the absolute values of the estimated time-varying effects are too large. When lambda is 0, Newton method without penalization is fitted.

nfolds

number of folds for cross-validation, the default value is 5. The smallest value allowable is nfolds=3.

foldid

an optional vector of values between 1 and nfolds identifying what fold each observation is in. If supplied, nfolds can be missing.

knots

penalty

If P-spline or Smooth-spline, then lambda is initialized as a sequence (0.1, 1, 10). Users can modify lambda. See details in lambda.

nsplines

number of basis functions in the splines to span the time-varying effects. The default value is 8. We use the R function splines::bs to generate the B-splines.

ties

tol

tolerance used for stopping the algorithm. See details in stop below. The default value is 1e-6.

iter.max

maximum iteration number if the stopping criterion specified by stop is not satisfied. The default value is 20.

method

gamma

parameter for proximal Newton method "ProxN". The default value is 1e8.

btr

tau

a positive scalar used to control the step size inside the backtracking line-search. The default value is 0.5.

stop

parallel

if TRUE, then the parallel computation is enabled. The number of threads in use is determined by threads.

threads

an integer indicating the number of threads to be used for parallel computation. The default value is 2. If parallel is false, then the value of threads has no effect.

degree

degree of the piecewise polynomial for generating the B-spline basis functions—default is 3 for cubic splines. degree = 2 results in the quadratic B-spline basis functions.

If penalty is P-spline or NULL, degree's default value is 3.

If penalty is Smooth-spline, degree's default value is 2.

fixedstep

if TRUE, the algorithm will be forced to run iter.max steps regardless of the stopping criterion specified.

Details

The function runs coxtp length of lambda by nfolds times; each is to compute the fit with each of the folds omitted.

Value

An object of class "cv.coxtp" is returned, which is a list with the ingredients of the cross-validation fit.

model.cv

a "coxtp" object with tuning parameter chosen based on cross-validation.

lambda

the values of lambda used in the fits.

cve

the mean cross-validated error - a vector having the same length as lambda. For the k-th testing fold (k = 1, ..., nfolds), we take the remaining folds as the training folds. Based on the model trained on the training folds, we calculate the log-partial likelihood on all the folds loglik0 and training folds loglik1. The cve is equal to -2*(loglik0 - loglik1). See details in Verweij (1993). This approach avoids the construction of a partial likelihood on the test set so that the risk set is always sufficiently large.

lambda.min

the value of lambda that gives minimum cve.

References

Boyd, S., and Vandenberghe, L. (2004) Convex optimization. Cambridge University Press.

Gray, R. J. (1992) Flexible methods for analyzing survival data using splines, with applications to breast cancer prognosis. Journal of the American Statistical Association, 87(420): 942-951.

Gray, R. J. (1994) Spline-based tests in survival analysis. Biometrics, 50(3): 640-652.

Verweij, P. J., and Van Houwelingen, H. C. (1993) Cross‐validation in survival analysis. Statistics in Medicine, 12(24): 2305-2314.

Wood, S. N. (2017) P-splines with derivative based penalties and tensor product smoothing of unevenly distributed data. Statistics and Computing, 27(4): 985-989.

Examples

data(ExampleData)
z <- ExampleData$z
time  <- ExampleData$time
event <- ExampleData$event
lambda  = c(0.1, 1)
fit  <- cv.coxtp(event = event, z = z, time = time, lambda=lambda, nfolds = 5)

helper function to get time-varying coefficients

Description

The function gives the time-varying coefficients based on a fitted coxtv or coxtp subject. Users can specify the time points to calculate the time-varying coefficients.

Usage

get.tvcoef(fit, time)

Arguments

fit

model from coxtv or coxtp.

time

time points to calculate the time-varying coefficients. If NULL, the observed event times for fitting the model will be used.

Value

A matrix of the time-varying coefficients. The dimension is the length of time by nvars, where nvars is the number of covariates in the fitted mode. Each row represents the time-varying coefficients at the corresponding time.

Examples

z     <- ExampleData$z
time  <- ExampleData$time
event <- ExampleData$event
fit   <- coxtv(event = event, z = z, time = time, degree = 2)
coef  <- get.tvcoef(fit)

plotting the baseline hazard

Description

Plotting the baseline hazard from a fitted baseline object.

Usage

## S3 method for class 'baseline'
plot(x, xlab, ylab, xlim, ylim, title, ...)

Arguments

x

fitted object from baseline function.

xlab

the title for the x axis.

ylab

the title for the y axis.

xlim

the limits of the x axis.

ylim

the limits of the y axis.

title

the title for the plot.

...

other graphical parameters to plot

Value

A plot is produced, and nothing is returned.

Examples

data(ExampleData)
z <- ExampleData$z
time  <- ExampleData$time
event <- ExampleData$event

fit   <- coxtv(event = event, z = z, time = time)
base.est <- baseline(fit)
plot(base.est)

plotting results from a fitted `coxtp` object

Description

This function creates a plot of the time-varying coefficients from a fitted coxtp model.

Usage

## S3 method for class 'coxtp'
plot(
  x,
  parm,
  CI = TRUE,
  level = 0.95,
  exponentiate = FALSE,
  xlab,
  ylab,
  xlim,
  ylim,
  allinone = FALSE,
  title,
  linetype,
  color,
  fill,
  time,
  ...
)

Arguments

x

model obtained from coxtp.

parm

covariate names fitted in the model to be plotted. If NULL, all covariates are plotted.

CI

if TRUE, confidence intervals are displayed. The default value is TRUE.

level

the level of confidence intervals. The default value is 0.95.

exponentiate

if TRUE, exponential scale of the fitted coefficients (hazard ratio) for each covariate is plotted. If FALSE, the fitted time-varying coefficients (log hazard ratio) are plotted.

xlab

the title for the x axis.

ylab

the title for the y axis.

xlim

the limits for the x axis.

ylim

the limits for the y axis.

allinone

if TRUE, the time-varying trajectories for different covariates are combined into a single plot. The default value is FALSE.

title

the title for the plot.

linetype

the line type for the plot.

color

the aesthetics parameter for the plot.

fill

the aesthetics parameter for the plot.

time

the time points for which the time-varying coefficients to be plotted. The default value is the unique observed event times in the dataset fitting the time-varying effects model.

...

other graphical parameters to plot

Value

A plot is produced, and nothing is returned.

Examples

data(ExampleData)
z <- ExampleData$z
time <- ExampleData$time
event <- ExampleData$event
fit <- coxtp(event = event, z = z, time = time)
plot(fit$lambda1)

plotting results from a fitted `coxtv` object

Description

This function creates a plot of the time-varying coefficients from a fitted coxtv model.

Usage

## S3 method for class 'coxtv'
plot(
  x,
  parm,
  CI = TRUE,
  level = 0.95,
  exponentiate = FALSE,
  xlab,
  ylab,
  xlim,
  ylim,
  allinone = FALSE,
  title,
  linetype,
  color,
  fill,
  time,
  ...
)

Arguments

x

model obtained from coxtv.

parm

covariate names fitted in the model to be plotted. If NULL, all covariates are plotted.

CI

if TRUE, confidence intervals are displayed. The default value is TRUE.

level

the level of confidence intervals. The default value is 0.95.

exponentiate

if TRUE, exponential scale of the fitted coefficients (hazard ratio) for each covariate is plotted. If FALSE, the fitted time-varying coefficients (log hazard ratio) are plotted.

xlab

the title for the x axis.

ylab

the title for the y axis.

xlim

the limits for the x axis.

ylim

the limits for the y axis.

allinone

if TRUE, the time-varying trajectories for different covariates are combined into a single plot. The default value is FALSE.

title

the title for the plot.

linetype

the line type for the plot.

color

the aesthetics parameter for the plot.

fill

the aesthetics parameter for the plot.

time

the time points for which the time-varying coefficients to be plotted. The default value is the unique observed event times in the dataset fitting the time-varying effects model.

...

other graphical parameters to plot

Value

A plot is produced, and nothing is returned.

Examples

data(ExampleData)
z <- ExampleData$z
time <- ExampleData$time
event <- ExampleData$event
fit <- coxtv(event = event, z = z, time = time)
plot(fit)

Study to Understand Prognoses Preferences Outcomes and Risks of Treatment

Description

The SUPPORT dataset tracks five response variables: hospital death, severe functional disability, hospital costs, and time until death and death itself. The patients are followed for up to 5.56 years. See Bhatnagar et al. (2020) for details.

Usage

data(support)

Format

A data frame with 9,104 observations and 34 variables after imputation and the removal of response variables like hospital charges, patient ratio of costs to charges and micro-costs following Bhatnagar et al. (2020). Ordinal variables, namely functional disability and income, were also removed. Finally, Surrogate activities of daily living were removed due to sparsity. There were 6 other model scores in the data-set and they were removed; only aps and sps were kept.

age: stores a double representing age.
death: death at any time up to NDI (National Death Index) date: 12/31/1994.
sex: 0=female, 1=male.
slos: days from study entry to discharge.
d.time: days of follow-up.
dzgroup: each level of dzgroup: ARF/MOSF w/Sepsis, COPD, CHF, Cirrhosis, Coma, Colon Cancer, Lung Cancer, MOSF with malignancy.
dzclass: ARF/MOSF, COPD/CHF/Cirrhosis, Coma and cancer disease classes.
num.co: the number of comorbidities.
edu: years of education of patients.
scoma: the SUPPORT coma score based on Glasgow D3.
avtisst: average TISS, days 3-25.
race: indicates race: White, Black, Asian, Hispanic or other.
hday: day in Hospital at Study Admit.
diabetes: diabetes (Com27-28, Dx 73).
dementia: dementia (Comorbidity 6).
ca: cancer state.
meanbp: mean arterial blood pressure day 3.
wblc: white blood cell count on day 3.
hrt: heart rate day 3.
resp: respiration rate day 3.
temp: temperature, in Celsius, on day 3.
pafi: PaO2/(0.01*FiO2) day 3.
alb: serum albumin day 3.
bili: bilirubin day 3.
crea: serum creatinine day 3.
sod: serum sodium day 3.
ph: serum pH (in arteries) day 3.
glucose: serum glucose day 3.
bun: bun day 3.
urine: urine output day 3.
adlp: adl patient day 3.
adlsc: imputed adl calibrated to surrogate, if a surrogate was used for a follow up.
sps: SUPPORT physiology score.
aps: apache III physiology score.

Details

Some of the original data was missing. Before imputation, there were a total of 9,104 individuals and 47 variables. Following Bhatnagar et al. (2020), a few variables were removed. Three response variables were removed: hospital charges, patient ratio of costs to charges and patient micro-costs. Hospital death was also removed as it was directly informative of the event of interest, namely death. Additionally, functional disability and income were removed as they are ordinal covariates. Finally, 8 covariates were removed related to the results of previous findings: SUPPORT day 3 physiology score (sps), APACHE III day 3 physiology score (aps), SUPPORT model 2-month survival estimate, SUPPORT model 6-month survival estimate, Physician's 2-month survival estimate for pt., Physician's 6-month survival estimate for pt., Patient had Do Not Resuscitate (DNR) order, and Day of DNR order (<0 if before study). Of these, sps and aps were added on after imputation, as they were missing only 1 observation. First the imputation is done manually using the normal values for physiological measures recommended by Knaus et al. (1995). Next, a single dataset was imputed using mice with default settings. After imputation, the covariate for surrogate activities of daily living was not imputed. This is due to collinearity between the other two covariates for activities of daily living. Therefore, surrogate activities of daily living were removed. See details in the R package (casebase) by Bhatnagar et al. (2020).

Source

Available at the following website: https://biostat.app.vumc.org/wiki/Main/SupportDesc.

References

Bhatnagar, S., Turgeon, M., Islam, J., Hanley, J. A., and Saarela, O. (2020) casebase: Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression. R package version 0.9.0, https://CRAN.R-project.org/package=casebase.

Knaus, W. A., Harrell, F. E., Lynn, J., Goldman, L., Phillips, R. S., Connors, A. F., et al. (1995) The SUPPORT prognostic model: Objective estimates of survival for seriously ill hospitalized adults. Annals of Internal Medicine, 122(3): 191-203.

Examples

data(support)
support <- support[support$ca %in% c("metastatic"),]
time <- support$d.time
death <- support$death
diabetes <-  model.matrix(~factor(support$diabetes))[,-1]
#sex: female as the reference group
sex <- model.matrix(~support$sex)[,-1]
#age: continuous variable
age <-support$age
age[support$age<=50] <- "<50"
age[support$age>50 & support$age<=60] <- "50-59"
age[support$age>60 & support$age<70] <- "60-69"
age[support$age>=70] <- "70+"
age <- factor(age, levels = c("60-69", "<50", "50-59", "70+"))
z_age <- model.matrix(~age)[,-1]
z <- data.frame(z_age, sex, diabetes)
colnames(z) <- c("age_50", "age_50_59", "age_70", "diabetes", "male")
data <- data.frame(time, death, z)
fit.coxtv <- coxtv(event = death, z = z, time = time)

testing the proportional hazards assumption from a `coxtv` or `coxtp` object

Description

Testing the proportional hazards assumption using a Wald test statistic.

Usage

tvef.ph(fit, parm)

Arguments

fit

fitted coxtv or coxtp model.

parm

the names of parameters to be tested.

Value

tvef.ph produces a matrix. Each row corresponds to a covariate from the fitted object. The three columns give the test statistic, degrees of freedom and P-value.

Examples

data(ExampleData)
z <- ExampleData$z
time <- ExampleData$time
event <- ExampleData$event
fit <- coxtv(event = event, z = z, time = time)
tvef.ph(fit)

testing the significance of the covariates from a `coxtv` or `coxtp` object

Description

Testing the significance of the covariates from a coxtv or coxtp object using a Wald test statistic. The null hypothesis H_0: \beta(t) = 0 for any t, where t denotes the event time.

Usage

tvef.zero(fit, parm)

Arguments

fit

fitted coxtv or coxtp model.

parm

the names of parameters to be tested.

Value

tvef.zero produces a matrix. Each row corresponds to a covariate from the fitted object. The three columns give the test statistic, degrees of freedom and P-value.

Examples

data(ExampleData)
z <- ExampleData$z
time <- ExampleData$time
event <- ExampleData$event
fit <- coxtv(event = event, z = z, time = time)
tvef.ph(fit)

testing the significance of the covariates from a `coxtv` or `coxtp` object using a Wald test statistic

Description

Testing the significance of the covariates at each time point.

Usage

tvef.zero.time(fit, time, parm)

Arguments

fit

fitted coxtv or coxtp model.

time

the time points to test if the covariate is significant or not.

parm

the names of parameters to be tested.

Value

tvef.zero.time produces a list of length nvars. Each element of the list is a matrix with respect to a covariate. The matrix is of dimension len_unique_t by 4, where len_unique_t is the length of unique observed event time. Each row corresponds to the testing result at that time. The four columns give the estimations, standard error, test-statistic and P-value.

Examples

data(ExampleData)
z <- ExampleData$z
time  <- ExampleData$time
event <- ExampleData$event
fit   <- coxtv(event = event, z = z, time = time)
test  <- tvef.zero.time(fit)

example data with 2000 observations of 2 continuous variables

Description

Usage

Format

example data with 2000 observations of 2 binary variables

Description

Usage

Format

calculating information criteria from a coxtp object

Description

Usage

Arguments

Details

Value

References

Examples

example data for stratified model illustration

Description

Usage

Format

calculating baseline hazard and baseline cumulative hazard using the result from a coxtv or coxtp object

Description

Usage

Arguments

Value

Examples

get confidence intervals of time-varying coefficients from a fitted object

Description

Usage

Arguments

Value

Examples

fit a Cox non-proportional hazards model with P-spline or Smoothing-spline, with penalization tuning parameter chosen by information criteria or cross-validation

Description

Usage

Arguments

Details

Value

References

See Also

Examples

fit a Cox non-proportional hazards model

Description

Usage

Arguments

Details

Value

References

See Also

Examples

fit a cross-validated Cox non-proportional hazards model with P-spline or Smoothing-spline where penalization tuning parameter is provided by cross-validation

Description

Usage

Arguments

Details

Value

References

Examples

helper function to get time-varying coefficients

Description

Usage

Arguments

Value

Examples

plotting the baseline hazard

Description

Usage

Arguments

Value

Examples

plotting results from a fitted coxtp object

Description

Usage

Arguments

Value

Examples

plotting results from a fitted coxtv object

Description

Usage

Arguments

calculating information criteria from a `coxtp` object

calculating baseline hazard and baseline cumulative hazard using the result from a `coxtv` or `coxtp` object

plotting results from a fitted `coxtp` object

plotting results from a fitted `coxtv` object

testing the proportional hazards assumption from a `coxtv` or `coxtp` object

testing the significance of the covariates from a `coxtv` or `coxtp` object

testing the significance of the covariates from a `coxtv` or `coxtp` object using a Wald test statistic