Movatterモバイル変換

Type:

Package

Title:

Restricted Mean Time in Favor of Treatment

Version:

1.0

Author:

Lu Mao

Maintainer:

Lu Mao <lmao@biostat.wisc.edu>

URL:

https://sites.google.com/view/lmaowisc/

Description:

Contains inferential and graphical routines for comparing two treatment arms in terms of the restricted mean time in favor of treatment.

License:

GPL-2 |GPL-3 [expanded from: GPL (≥ 2)]

Encoding:

UTF-8

LazyData:

true

RoxygenNote:

7.1.1

Suggests:

knitr, rmarkdown

VignetteBuilder:

knitr

Depends:

R (≥ 2.10)

NeedsCompilation:

Packaged:

2021-05-21 12:41:32 UTC; lmao

Repository:

CRAN

Date/Publication:

2021-05-25 06:40:03 UTC

Bouquet plot

Description

Construct the bouquet plot based on the estimated stage-wise restricted mean win/losstimes.

Usage

bouquet(  x,  Kmax = NULL,  xlim = NULL,  ylim = NULL,  xlab = "Restricted mean win/loss time",  ylab = "Follow-up time",  group.label = TRUE,  cex.group = 1,  ...)

Arguments

x

An object returned byrmtfit.

Kmax

A positive integer; If specified, the stage-wise estimates overKmax,\ldots,K will be aggregated.

xlim

The x limits of the plot.

ylim

The y limits of the plot.

xlab

A label for the x axis, defaults to a description of x.

ylab

A label for the y axis, defaults to a description of x.

group.label

IfTRUE, group labels will appear on thetwo sides of the plot.

cex.group

Font size of the group labels ifgroup.label=TRUE.

...

Other arguments that can be passed to the underlyingplot method.

Value

No return value, called for side effects.

Examples

# load the colon cancer trial datalibrary(rmt)head(colon_lev)# fit the dataobj=rmtfit(ms(id,time,status)~rx,data=colon_lev)# bouquet plotbouquet(obj)

A dataset from a landmark colon cancer trial

Description

A landmark colon cancer trial on the efficacy of levamisole and fluorouracilwas reported by Moertel et al. (1990). The trial recruited 929 patients with stage C diseaseand randomly assigned them to levamisole treatment alone, levamisole combined with fluorouracil,and the control. The dataset here is restricted to the comparison between the combined treatmentand control groups, consisting of 304 and 314 patients, respectively.

Usage

colon_lev

Format

A data frame with 915 rows and 6 variables:

id: Unique patient ID.
time: Event time (years).
status: Event type; 1 = cancer relapse, 2 = death.
rx: "Lev+5FU" = combined treatment, "Control" = control.
age: Patient age (years) at randomization.
sex: 0 = female, 1 = male.

References

MOERTEL, C. G., FLEMING, T. R., MACDONALD, J. S., HALLER, D. G., LAURIE, J. A., GOODMAN, P. J.,UNGERLEIDER, J. S., EMERSON, W. A., TORMEY, D. C., GLICK, J. H. et al. (1990). Levamisole and fluorouracilfor adjuvant therapy of resected colon carcinoma. New Engl. J. Med. 322, 352–358.

A dataset from the HF-ACTION trial

Description

Over two thousand heart failure patients across the USA, Canada, and Franceparticipated in the Heart Failure: A Controlled Trial Investigating Outcomes of ExerciseTraining (HF-ACTION) between 2003–2007 (O'Connor et al., 2009).The primary objective of the trial was to evaluate the effect of adding exercisetraining to the usual patient care on the composite endpoint of all-cause hospitalizationand death.The dataset here contains a subgroup of 426 non-ischemic patientswith baseline cardio-pulmonary exercise test less than or equal to nine minutes.

Usage

hfaction

Format

A data frame with 1,448 rows and 5 variables:

patid: Unique patient ID.
time: Event time (years).
status: Event type; 1 = hospitalization, 2 = death.
trt_ab: 1 = exercise training, 0 = usual care.
age60: 1 = 60 years or older, 0 = otherwise.

References

O'CONNOR, C. M., WHELLAN, D. J., LEE, K. L., KETEYIAN, S. J.,COOPER, L. S., ELLIS, S. J., LEIFER, E. S.,KRAUS, W. E., KITZMAN, D. W., BLUMENTHAL, J. A. et al. (2009).Efficacy and safety of exercise training inpatients with chronic heart failure: Hf-action randomized controlled trial.J. Am. Med. Assoc. 301, 1439–1450.

Create a multistate event object

Description

Create a multistate event object

Usage

ms(id, time, status)

Arguments

id

A vector of id variable.

time

A vector of follow-up times.

status

A vector of event type,k if transitioning to statek,0 if censored andK+1 represents death.

Value

An object of classms used as an argument forrmtfit.

Plot the estimated treatment effect curve

Description

Plot the estimated overall or stage-wise restricted mean times in favor of treatment as afunction of follow-up time.

Usage

## S3 method for class 'rmtfit'plot(  x,  k = NULL,  conf = FALSE,  main = NULL,  xlim = NULL,  ylim = NULL,  xlab = "Follow-up time",  ylab = "Restricted mean time in favor",  conf.col = "black",  conf.lty = 3,  ...)

Arguments

x

An object returned byrmtfit.

k

If specified,\mu_k(\tau) is plotted; otherwise,\mu(\tau) is plotted.

conf

If TRUE, 95% confidence limits for the target curve are overlaid.

main

A main title for the plot

xlim

The x limits of the plot.

ylim

The y limits of the plot.

xlab

A label for the x axis, defaults to a description of x.

ylab

A label for the y axis, defaults to a description of y.

conf.col

Color for the confidence limits ifconf=TRUE.

conf.lty

Line type for the confidence limits ifconf=TRUE.

...

Other arguments that can be passed to the underlyingplot method.

Value

No return value, called for side effects.

Examples

# load the colon cancer trial datalibrary(rmt)head(colon_lev)# fit the dataobj=rmtfit(ms(id,time,status)~rx,data=colon_lev)# plot overal effect mu(tau)plot(obj)# set-up plot parametersoldpar <- par(mfrow = par("mfrow"))par(mfrow=c(1,2))# Plot of component-wise RMT in favor of treatment over timeplot(obj,k=2,conf=TRUE,col='red',conf.col='blue', xlab="Follow-up time (years)",    ylab="RMT in favor of treatment (years)",main="Survival")plot(obj,k=1,conf=TRUE,col='red',conf.col='blue', xlab="Follow-up time (years)",    ylab="RMT in favor of treatment (years)",main="Pre-relapse")par(oldpar)

Print a short summary of rmtfit objects

Description

Print the results for the restricted mean times in favor of treatment.

Usage

## S3 method for class 'rmtfit'print(x, ...)

Arguments

x

An object returned byrmtfit.

...

Further arguments passed to or from other methods

Value

No return value, called for side effects.

Print method for summary.rmtfit objects

Description

Produces a printed summary of the results for the restrictedmean times in favor of treatment

Usage

## S3 method for class 'summary.rmtfit'print(x, ...)

Arguments

x

An object returned bysummary.rmtfit.

...

Further arguments passed to or from other methods

Value

No return value, called for side effects.

Create a recurrent event object

Description

Create a recurrent event object

Usage

rec(id, time, status)

Arguments

id

A vector of id variable.

time

A vector of follow-up times.

status

A vector of event type, 1 = recurrent event, 2 = death, and 0 = censoring;

Value

An object of classrec used as an argument forrmtfit.

Estimate restricted mean times in favor of treatment

Description

Estimate and make inference on the overall and component-wiserestricted mean times in favor of treatment.

Usage

rmtfit(...)## Default S3 method:rmtfit(id, time, status, trt, type = "multistate", ...)## S3 method for class 'formula'rmtfit(formula, data, ...)

Arguments

...

Further arguments.

id

A vector of id variable.

time

A vector of follow-up times.

status

Fortype="multistate", k = entering into statek(K+1 represents death) and 0 = censoring;Fortype="recurrent", 1 = recurrent event, 2 = death,and 0 = censoring;

trt

A vector of binary variable for treatment group.

type

"multistate" = multistate data;"recurrent" =recurrent event data.

formula

A formula object. For multistate data, usems(id,time,status)~trt;for recurrent event data, userec(id,time,status)~trt.

data

A data frame, which contains the variables names in the formula.

Value

An object of classrmtfit. Seermtfit.object for details.

Methods (by class)

default: Default
formula: Formula

Examples

######################## Multistate outcome  ######################### load the colon cancer trial datalibrary(rmt)head(colon_lev)# fit the dataobj=rmtfit(ms(id,time,status)~rx,data=colon_lev)# print the event numbers by groupobj# summarize the inference results for tau=7.5 yearssummary(obj,tau=7.5)############################# Recurrent event outcome  ############################## load the HF-ACTION trial datalibrary(rmt)head(hfaction)# fit the dataobj=rmtfit(rec(patid,time,status)~trt_ab,data=hfaction)# print the event numbers by groupobj# summarize the inference results for tau=3.5 yearssummary(obj,tau=3.5,Kmax=4) # aggregating results for recurrent-event# frequency >=4.

Estimated restricted mean times in favor of treatment

Description

This class of objects is returned by thermtfit class of functions.Objects of this class have methods for the functionsprint,summary,plot, andbouquet.

Value

t

A vector of follow-up times\tau.

mu

A matrix withK+2 rows; Thekth row(k=1,\ldots, K)is\mu_k(\tau), the restricted mean time in favor of treatment on thekth state (or recurrent event); The(K+1)th row is thenet restricted mean survival time; The last row is the overal effect\mu(\tau).

var

A matrix withK+2 rows containing the variance estimatesformu.

mu10,mu01

Matrices withK+1 rows; Thekth row(k=1,\ldots, K)is the restricted mean win (mu10) and loss (mu01) times by the treatment on thekth state (or recurrent event); The(K+1)th row is thaton the survival time.

...

Summary of the analysis results

Description

Summarize the overall and stage-wise inferential results for the restrictedmean times in favor of treatment at a user-specified length of follow-up.

Usage

## S3 method for class 'rmtfit'summary(object, tau = NULL, Kmax = NULL, ...)

Arguments

object

An object returned byrmtfit.

tau

A positive real number for the follow-up time; Default is the maximumevent time in the data.

Kmax

A positive integer; If specified, the stage-wise estimates overKmax,\ldots,K will be aggregated.

...

Additional arguments affecting the summary produced.

Value

An object of classsummary.rmtfit with components

WL

A2\times(K+2)-dimensional matrix; Each row contains the estimates for thestage-wise and overall restricted mean win times for each group.

tab

A(K+2)\times 4-dimensional matrix summarizing the inferential resultsfor the stage-wise and overall restricted mean times in favor of treatment; Columns includeEstimate,Std.Err,Z value, andPr(>|z|).

...

Examples

#See examples for rmtfit().

Movatterモバイル変換

Bouquet plot

Description

Usage

Arguments

Value

See Also

Examples

A dataset from a landmark colon cancer trial

Description

Usage

Format

References

A dataset from the HF-ACTION trial

Description

Usage

Format

References

Create a multistate event object

Description

Usage

Arguments

Value

Plot the estimated treatment effect curve

Description

Usage

Arguments

Value

See Also

Examples

Print a short summary of rmtfit objects

Description

Usage

Arguments

Value

Print method for summary.rmtfit objects

Description

Usage

Arguments

Value

Create a recurrent event object

Description

Usage

Arguments

Value

Estimate restricted mean times in favor of treatment

Description

Usage

Arguments

Value

Methods (by class)

See Also

Examples

Estimated restricted mean times in favor of treatment

Description

Value

See Also

Summary of the analysis results

Description

Usage

Arguments

Value

See Also

Examples