Well,

I assume you are using the rms package. Calibration through bootstrap can
be conducted through the val.surv function. Penalizing degrees
of freedom can be conducted with the pentrace function. Other way of
calibration can also be conducted.

I suggest you take a look at the book below. There are several examples of
R codes.  Specially chapter 23.

 1.
Steyerberg EW. Clinical Prediction Models: A Practical Approach to
Development, Validation, and Updating. 1o ed. Springer; 2008.

Dr. Pedro Emmanuel A. A. do Brasil
http://blog.ipec.fiocruz.br/lapclin-chagas/
Curriculum Lattes:  http://lattes.cnpq.br/6597654894290806
ResearchGate.net: https://www.researchgate.net/profile/Pedro_Brasil2/
Instituto Nacional de Infectologia/Instituto de Pesquisa Clínica Evandro
Chagas
Fundação Oswaldo Cruz
Rio de Janeiro - Brasil
Av. Brasil 4365,
CEP 21040-360,
Tel 55 21 3865-9648
e-mail: pedro.brasil@ipec.fiocruz.br
e-mail: emmanuel.brasil@gmail.com

---Apoio aos softwares livres
www.zotero.org - gerenciamento de referências bibliográficas.
www.broffice.org ou www.libreoffice.org - textos, planilhas ou
apresentações.
www.epidata.dk - entrada de dados.
www.r-project.org - análise de dados.
www.ubuntu.com - sistema operacional


2013/9/4 <r-sig-epi-request@r-project.org>

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> Date: Wed, 4 Sep 2013 21:10:04 +0800 (CST)
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> Subject: [R-sig-Epi] help
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> hi, dear friend , i am dealing with a survival data for cancer. a variable
> progression doesn't satisfy PH assumption, i have tried the paramatric
> survival models, but they did not fit very well. at last ,i tried the
> extension of Cox model with time-dependent variable, finding that the model
> fit well with the smallest AIC, and the average or weight  HR is 1.6. when
> progression occured in the first follow-up year, the HR was biggest ,and HR
> gone down in the second year, like the picture showed. after having reading
> over the examples in R help documents, i am not sure if i can plot
>  nomogram for 5 year survival prediction. and cph may did not work well
> when applied to  the Cox model with time-dependent variable,  i can use
> coxph, set  " tt=function(x,t,...) {x *log(t)}"  as a alternative. but most
> important, how can i complete the nomogram ,validate and calibrate.ie.setup
> may help,but not show in detail.
>        can you help me to plot a nomogram?  thanks for  reading.
>
>                                                                Dong
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