Code: extended model support for mtable

I finally got around to organizing and packaging my complete set of extended model support for mtable in Martin Elff’s memisc library. Here is a list of the models supported:

  • coxph, survreg – Cox proportional hazards models and parametric survival models from the survival library.
  • aftreg, phreg, weibreg – parametric AFT, proportional hazards, and Weibull¬†models available from the eha library.
  • mer – multilevel mixed effects models as provided by the lme4 package. The model objects produced in the beta lme4a package are not supported.

Here’s the file:¬†mtable-ext

It’s extremely easy to use, though I am sure there are some bugs and not all model features get reported. Here is an example of how to compare three Cox proportional hazard models as estimated with coxph (yes, I know, the Breslow and Exact models are the same; Exact was refusing to converge so I just stuck the Breslow model in to get the example done):

library(survival)
library(memisc)
source("mtable-ext.R")

> Efron <- coxph(Surv(start, end, switch) ~ Poll + Government + OldParty +
+                Experience + Right + Members, robust = TRUE, data = Sejm,
+                method = "efron")

> Breslow <- coxph(Surv(start, end, switch) ~ Poll + Government + OldParty +
+                  Experience + Right + Members, robust = TRUE, data = Sejm,
+                  method = "breslow")

> Exact <- coxph(Surv(start, end, switch) ~ Poll + Government + OldParty +
+                Experience + Right + Members, robust = TRUE, data = Sejm,
+                method = "exact")

mtable(Efron, Breslow, Exact)

[... some model call info ...]

=============================================
                  Efron    Breslow    Exact
---------------------------------------------
Poll            -2.120*** -1.931*** -1.931***
                (0.477)   (0.430)   (0.430)
Government      -1.603*   -1.461*   -1.461*
                (0.706)   (0.684)   (0.684)
OldParty        -0.186    -0.279    -0.279
                (0.243)   (0.209)   (0.209)
Experience      -0.195    -0.198    -0.198
                (0.167)   (0.156)   (0.156)
Right            1.427***  1.290***  1.290***
                (0.198)   (0.178)   (0.178)
Members         -0.002    -0.003    -0.003
                (0.007)   (0.007)   (0.007)
---------------------------------------------
Log-likelihood   -818.487  -832.625  -832.625
AIC              1648.973  1677.250  1677.250
BIC              1701.297  1729.574  1729.574
N               45280     45280     45280
=============================================

To convert the mtable object into a \(\text{\LaTeX{}}\) table, you just need to apply the toLatex function:

toLatex(mtable(Efron, Breslow, Exact))

Of course, many formatting options are available. See the documentation for details.

This entry was posted in Code, LaTeX, R. Bookmark the permalink.

One Response to Code: extended model support for mtable

  1. Aaron Erlich says:

    Hi,

    Thanks for this packages. It’s quite useful. I am wondering if there is any easy way to show that you want the exp(coef) rather then coefficient, which you might often want for cox models. I couldn’t see anything in the documentation of mtable that would let you do this.

Leave a Reply