similar to: question on prediction in coxph

Displaying 20 results from an estimated 9000 matches similar to: "question on prediction in coxph"

2008 Apr 29
2
Help on extract paramters from fitted models
Hi, I have a question about how to extract paramters from a fitted model. I can extract coefficients and std, but from some other statistics, I dont know how to extract. Can anyone help? Here it is an example: > coxout<-coxph(Surv(t,t.censor)~x) > coxout Call: coxph(formula = Surv(t, t.censor) ~ x) coef exp(coef) se(coef) z p x 0.349 1.42 0.257 1.36 0.17 Likelihood
2004 Oct 15
1
categorical varibles in coxph
Hello, I wonder when I do coxph in R: coxph( Surv(start, stop, event) ~ x, data=test) If x is a categorical varible (1,2,3,4,5), should I creat four dummy varibles for it? if yes, how can I get the overall p value on x other than for each dummy variable? Thanks Lisa Wang Princess Margaret Hospital Phone 416 946 4501
2009 Aug 19
2
Problem with predict.coxph
We occasionally utilize the coxph function in the survival library to fit multinomial logit models. (The breslow method produces the same likelihood function as the multinomial logit). We then utilize the predict function to create summary results for various combinations of covariates. For example:
2013 Nov 14
1
issues with calling predict.coxph.penal (survival) inside a function
Thanks for the reproducable example. I can confirm that it fails on my machine using survival 2-37.5, the next soon-to-be-released version, The issue is with NextMethod, and my assumption that the called routine inherited everything from the parent, including the environment chain. A simple test this AM showed me that the assumption is false. It might have been true for Splus. Working this
2008 Apr 29
1
AIC extract and comparison
Hi, I need to fit models and use AIC method to campare the best fitted model manually. When i extract AIC by using extractAIC, it gave me the df and AIC values. Now the problem is, how can I compare the AIC values from two models? is there anyway to extract AIC with no df so that I can compare directly? Thank you! > extractAIC(coxout) [1] 1.000 1723.038 [[alternative HTML version
2013 Feb 24
1
Use of the newdata parameter in the predict.coxph function
Hello, I've executed the following predict.coxph function to enable prediction for new variable values (error is included). *predict(cox_out,newdata=data.frame(Meter3.Value=100.001, Meter4.Value=200.001,Meter5.Value=300.001,Meter10.Value= 400.001,type="expected")) Error in model.frame.default(data = data.frame(Meter3.Value = 100.001, : variable lengths differ (found for
2008 May 09
1
predicting from coxph with pspline
Hello. I get a bit confused by the output from the predict function when used on an object from coxph in combination with p-spline, e.g. fit <- coxph(Surv(time1, time2, status)~pspline(x), Data) predict(fit, newdata=data.frame(x=1:2)) It seems like the output is somewhat independent of the x-values to predict at. For example x=1:2 gives the same result as x=21:22. Does the result span the
2012 Jun 29
1
predicting expected number of events using a coxph model
I fit a coxph model: coxphfit <- coxph(Surv(sampledLifetime, !sampledCensoredQ) ~ curpbc6 + prevpbc6, sampledTimeSeries) Now I'm trying to predict the expected number of events using a new dataset. The documentation suggests that coxPred <- predict(coxphfit, newdata = testTimeSeries, type="expected") will do what I want, but I get the error Error in
2006 Dec 29
2
Survfit with a coxph object
I am fitting a coxph model on a large dataset (approx 100,000 patients), and then trying to estimate the survival curves for several new patients based on the coxph object using survfit. When I run coxph I get the coxph object back fairly quickly however when I try to run survfit it does not come back. I am wondering if their is a more efficient way to get predicted survival curves from a coxph
2010 Nov 19
4
calculating martingale residual on new data using "predict.coxph"
Hi list, I was trying to use "predict.coxph" to calculate martingale residuals on a test data, however, as pointed out before http://tolstoy.newcastle.edu.au/R/e4/help/08/06/13508.html predict(mycox1, newdata, type="expected") is not implemented yet. Dieter suggested to use 'cph' and 'predict.Design', but from my reading so far, I'm not sure they can
2009 Feb 23
1
predicting cumulative hazard for coxph using predict
Hi I am estimating the following coxph function with stratification and frailty?where each person had multiple events. m<-coxph(Surv(dtime1,status1)~gender+cage+uplf+strata(enum)+frailty(id),xmodel) ? > head(xmodel) id enum dtime status gender cage uplf 1 1008666 1 2259.1412037 1 MA 0.000 0 2 1008666 2 36.7495023 1 MA 2259.141 0 3 1008666
2011 May 06
2
coxph and survfit issue - strata
Dear users, In a study with recurrent events: My objective is to get estimates of survival (obtained through a Cox model) by rank of recurrence and by treatment group. With the following code (corresponding to a model with a global effect of the treatment=rx), I get no error and manage to obtain what I want : data<-(bladder)
2011 Oct 01
4
Is the output of survfit.coxph survival or baseline survival?
Dear all, I am confused with the output of survfit.coxph. Someone said that the survival given by summary(survfit.coxph) is the baseline survival S_0, but some said that is the survival S=S_0^exp{beta*x}. Which one is correct? By the way, if I use "newdata=" in the survfit, does that mean the survival is estimated by the value of covariates in the new data frame? Thank you very much!
2013 Jul 06
1
problem with BootCV for coxph in pec after feature selection with glmnet (lasso)
Hi, I am attempting to evaluate the prediction error of a coxph model that was built after feature selection with glmnet. In the preprocessing stage I used na.omit (dataset) to remove NAs. I reconstructed all my factor variables into binary variables with dummies (using model.matrix) I then used glmnet lasso to fit a cox model and select the best performing features. Then I fit a coxph model
2007 Nov 13
2
plotting coxph results using survfit() function
i want to make survival plots for a coxph object using survfit function. mod.phm is an object of coxph class which calculated results using columns X and Y from the DataFrame. Both X and Y are categorical. I want survival plots which shows a single line for each of the categories of X i.e. '4' and 'C'. I am getting the following error: > attach(DataFrame) >
2010 Nov 11
2
predict.coxph and predict.survreg
Dear all, I'm struggling with predicting "expected time until death" for a coxph and survreg model. I have two datasets. Dataset 1 includes a certain number of people for which I know a vector of covariates (age, gender, etc.) and their event times (i.e., I know whether they have died and when if death occurred prior to the end of the observation period). Dataset 2 includes another
2010 Jun 23
1
Probabilities from survfit.coxph:
Hello: In the example below (or for a censored data) using survfit.coxph, can anyone point me to a link or a pdf as to how the probabilities appearing in bold under "summary(pred$surv)" are calculated? Do these represent acumulative probability distribution in time (not including censored time)? Thanks very much, parmee *fit <- coxph(Surv(futime, fustat) ~ age, data = ovarian)*
2012 Nov 27
4
Fitting and plotting a coxph with survfit, package(surv)
Hi Dear R-users I have a database with 18000 observations and 20 variables. I am running cox regression on five variables and trying to use survfit to plot the survival based on a specific variable without success. Lets say I have the following coxph: >library(survival) >fit <- coxph(Surv(futime, fustat) ~ age + rx, data = ovarian) >fit what I am trying to do is plot a survival
2011 Feb 03
3
coxph fails to survfit
I have a model with quant vars only and the error message does not make sense: (mod1 <- coxph(Surv(time=strt,time2=stp,event=(resp==1))~ +incpost+I(amt/1e5)+rate+strata(termfac), subset=dt<"2010-08-30", data=inc,method="efron")) Call: coxph(formula = Surv(time = strt, time2 = stp, event = (resp == 1)) ~ +incpost + I(amt/1e+05) + rate + strata(termfac),
2006 Dec 21
1
: newbie estimating survival curve w/ survfit for coxph
I am wondering how to estimate the survival curve for a particular case(s) given a coxph model using this example code: #fit a cox proportional hazards model and plot the #predicted survival curve fit <- coxph( Surv(futime,fustat)~resid.ds+strata(rx)+ecog.ps+age,data=ovarian[1:23,]) z <- survfit(fit,newdata=ovarian[24:26,],individual=F) zs <- z$surv zt <-