R help - Nov 2013 - Plot of coxph tt effects

Dear all, 

We are conducting a study in with a set of covariates and a time to event
outcome.
Covariates b1 and b3 violate proportionality. We applied a coxph with a “tt”
term to evaluate the nature of time dependence.

Call: 
coxph(formula = Surv(start - 1, stop, outcome) ~ tt(b1) + 
    b5 + tt(b3) + b4, data = data, tt = function(x,  t, ...) pspline(x + t/90)) 

We would like to plot the predicted effects. Following the logic of the tt
function, does it make sense to plot the residuals against the results from the
model with tt for the upsetting covariates?

As far as we know the there has not been updates of survfit for the tt 
function. So, we are unsure as to how to plot our curves.
  
I would appreciate if someone can give me an advise or a publication reference
that can help us in this matter.

Many thanks, 

Cesar  
	[[alternative HTML version deleted]]

On Nov 1, 2013, at 11:16 AM, cesar garcia perez de leon wrote:
> Dear all, 
> 
> We are conducting a study in with a set of covariates and a time to event
outcome.
> Covariates b1 and b3 violate proportionality.
Can you describe the basis for that statement?
> We applied a coxph with a ?tt? term to evaluate the nature of time
dependence.
> 
> Call: 
> coxph(formula = Surv(start - 1, stop, outcome) ~ tt(b1) + 
>    b5 + tt(b3) + b4, data = data, tt = function(x,  t, ...) pspline(x +
t/90))
> 
> We would like to plot the predicted effects. Following the logic of the tt
function, does it make sense to plot the residuals against the results from the
model with tt for the upsetting covariates?
> 
> As far as we know the there has not been updates of survfit for the tt 
function. So, we are unsure as to how to plot our curves.
> 
> I would appreciate if someone can give me an advise or a publication
reference that can help us in this matter.
Is there a reason not to use `cox.zph` and it's `print` and `plot` methods
for this purpose? I think it is already offering what you are trying to
re0invent.

-- 

David Winsemius
Alameda, CA, USA