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r - 从 clogit 模型中检索摘要时出错

问题描述

标签： rregressionlogistic-regressionsplinesurvival-analysis

解决方案

What's happening is that an object of class 'clogit' is being passed by inheritance to summary.cph which is apparently not designed for it. You can get the coefficients from the print.clogit function, which is what is being implicitly called when you ask for the models results:

 model
Call:
clogit(case ~ var1 + pspline(var2, df = 3) + strata(var3), data = generated_data)

               coef exp(coef) se(coef)      z     p
var1Low    -0.02063   0.97958  0.23019 -0.090 0.929
var1Medium -0.02171   0.97852  0.23831 -0.091 0.927
ps(var2)3  -0.05886   0.94284  0.40900 -0.144 0.886
ps(var2)4  -0.10752   0.89806  0.60868 -0.177 0.860
ps(var2)5  -0.16100   0.85129  0.65381 -0.246 0.805
ps(var2)6  -0.23156   0.79330  0.63652 -0.364 0.716
ps(var2)7  -0.26708   0.76561  0.61080 -0.437 0.662
ps(var2)8  -0.23270   0.79239  0.59903 -0.388 0.698
ps(var2)9  -0.23075   0.79394  0.59781 -0.386 0.700
ps(var2)10 -0.27852   0.75690  0.60117 -0.463 0.643
ps(var2)11 -0.26878   0.76431  0.64828 -0.415 0.678
ps(var2)12 -0.24330   0.78404  0.84486 -0.288 0.773

Likelihood ratio test=0.92  on 5.04 df, p=0.9702
n= 300, number of events= 200

As a bonus you get the LLR test value and a p-value. If you just want the matrix of the sort typically returned by a summary function, then make the obvious mods to the section of code in print.coxph:

{ coef <- model$coefficients
se <- sqrt(diag(model$var))
if (is.null(coef) | is.null(se)) 
    stop("Input is not valid")
if (is.null(model$naive.var)) {
    tmp <- cbind(coef, exp(coef), se, coef/se, pchisq((coef/se)^2, 
                                                      1, lower.tail = FALSE))
    dimnames(tmp) <- list(names(coef), c("coef", "exp(coef)", 
                                         "se(coef)", "z", "p"))} }

And then tmp will be the desired matrix:

 tmp
                  coef exp(coef)  se(coef)           z         p
var1Low    -0.02062820 0.9795831 0.2301878 -0.08961464 0.9285935
var1Medium -0.02171186 0.9785221 0.2383051 -0.09110952 0.9274056
ps(var2)3  -0.05886243 0.9428365 0.4089999 -0.14391797 0.8855652
ps(var2)4  -0.10752217 0.8980566 0.6086828 -0.17664728 0.8597855
ps(var2)5  -0.16099704 0.8512946 0.6538079 -0.24624519 0.8054924
ps(var2)6  -0.23155828 0.7932965 0.6365191 -0.36378845 0.7160160
ps(var2)7  -0.26708193 0.7656103 0.6108000 -0.43726573 0.6619186
ps(var2)8  -0.23269795 0.7923929 0.5990301 -0.38845785 0.6976772
ps(var2)9  -0.23074825 0.7939393 0.5978122 -0.38598783 0.6995057
ps(var2)10 -0.27852015 0.7569030 0.6011671 -0.46329903 0.6431500
ps(var2)11 -0.26877900 0.7643121 0.6482824 -0.41460174 0.6784335
ps(var2)12 -0.24329853 0.7840374 0.8448572 -0.28797593 0.7733652

I'm not sure a bug report is warranted but if you think otherwise, then Thomas Lumley is the clogit author. The help page for clogit does not describe a summary method and it appears that the print.clogit, with dispatching to print.coxph method was being used for the purposes typically assigned to summary.

In addition, the coefficients themselves could have been obtained with model$coef but that would not have returned the full matrix of coefficients pus ancillary statistical estimates,

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