CsChange {CsChange}

Testing for Change in C-Statistic

Description

Calculate the confidence interval and p value for change in C-statistic. The adjusted C-statistic is calculated by using formula as "Somers' Dxy rank correlation"/2+0.5. The confidence interval was calculated by using the bootstrap method. The p value was calculated by using the Z testing method. Please refer to the article of Peter Ganz et al. (2016) <doi:10.1001/jama.2016.5951>.

Usage

CsChange(fit1,fit2,form1,form2,data,nb,signif,seed)

Arguments

fit1

an object from 'cph', 'coxph' or 'lrm' model

fit2

another object from 'cph', 'coxph' or 'lrm' model

form1

unnecessary, the formula used in fit1, i.e., 'y~x1'

form2

unnecessary, the formula used in fit2, i.e., 'y~x1+x2'

data

a data frame used in the fit1 or fit2

nb

the number of bootstrap replicate, with a default of 200

signif

the significant level of confidence interval, with a default of 0.05 and a two-sided test

seed

an integer used to set for random seed, with a default of 123

Value

change

in list 1, the change of C-statistic from fit1 to fit2

low, up

in list 1, the confidence interval of change

p

in list 1, the p value of testing for change

c

in list 2, the C-statistic of fit1 and fit2

low, up

in list 2, the confidence interval of change

Note

Please feel free to contact us, if you have any advice and find any bug!

Update description:

Version 0.1.1: Fix the error of "variables not found" for the 'coxph' model.

Version 0.1.2: Fix the error of data with missing value.

Version 0.1.3: a) Add the c statistic of fit1 and fit2 to the output. b) Fix the error of model with multiple variables. c) Fix the error of independent variable with functions, i.e., rcc(), ploy().

Version 0.1.4: a) Fix the error with the arguments of 'time=' and 'event=' in the coxph model. b) 'lrm' model was supported. c) Different dependent variables could be set.

Version 0.1.5: a) Apply 'boot.ci' function to compute the confidence interFix the error with the arguments of 'time=' and 'event=' in the coxph model. b) 'lrm' model was supported. c) Different dependent variables could be set.

Version 0.1.6: Fix minor bugs.

Version 0.1.7: Fix the error from the update that 'survival' is no longer attached by rms.

more functions will be included in 'CsChange' package!

Author(s)

Zhicheng Du<[e-mail]>, Yuantao Hao<[e-mail]>

References

Peter Ganz, Bettina Heidecker, Kristian Hveem, Christian Jonasson, Shintaro Kato, Mark R. Segal, David G. Sterling, Stephen A. Williams. Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients With Stable Coronary Heart Disease. JAMA. 2016; 315(23):2532-2541. doi:10.1001/jama.2016.5951

Examples

require("rms")
require("survival")
set.seed(123)
n=50
age=50+12*rnorm(n)
sex=factor(sample(c('Male','Female'), n,rep=TRUE, prob=c(.6, .4)))
cens=15*runif(n)
h=.02*exp(.04*(age-50)+.8*(sex=='Female'))
dt=-log(runif(n))/h
e=ifelse(dt <= cens,1,0)
dt=pmin(dt, cens)
units(dt)="Year"
data=data.frame(dt=dt,e=e,dt1=dt,dt2=dt,e1=e,e2=e,age,sex)
dd=datadist(age, sex)
options(datadist='dd')

#for 'cph' model
fit1=cph(Surv(dt,e)~age,data)
fit2=cph(Surv(dt,e)~age+sex,data)
CsChange(fit1,fit2,data=data,nb=20)

#for 'coxph' model
fit1=coxph(Surv(dt,e)~age,data)
fit2=coxph(Surv(dt,e)~age+sex,data)
CsChange(fit1,fit2,data=data,nb=20)

#for 'coxph' model
#fit1=coxph(Surv(dt1,e1)~age,data)
#fit2=coxph(Surv(dt2,e2)~age+sex,data)
#CsChange(fit1,fit2,data=data,nb=20)

#for 'coxph' model
#fit1=coxph(Surv(dt,e)~age+sex,data)
#fit2=coxph(Surv(dt,e)~rcs(age)+sex,data)
#CsChange(fit1,fit2,data=data,nb=20)#ignore the warnings messages