search for: haz

Hello R-users. I believe that the way basehaz (in the survival package) compute the baseline hazard function is false. I come to question this function when it gives me hazard probabilities greater than 1. Looking at the code I think I've localised the error : hazard probability is computed as : H <- -log(surv) but it seems to me...

Hello, If all I have access to is an empirically calculated hazard function, is it possible to compute an approximate value for the mean lifetime? I know that if the hazard function is essentially constant, the mean lifetime is 1/hazard rate. ?But if I'm confident that the empirical hazard function is not constant, I'm not sure how to go about calcula...

Hello: So i've fit a hazard function to a set of data using kmfit<-survfit(Surv(int, event)~factor(cohort)) this factor variable, "cohort" has four levels so naturally the strata variable has 4 values. I can use this data to estimate the hazard rate haz<-n.event/n.risk and calculate the cumulative hazar...

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...s/barshop_lab/Library/R/2.10/library' * installing *source* package 'Survomatic' ... ** libs ** arch - i386 gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -c haz.c -o haz.o gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Survomatic.so haz.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFounda...

...alysis with time-varying covariates. The data is already in a long format, but does not have a variable to signify the stopping point for the interval. The variable DaysEnrolled is the variable I would like to use to form this interval. This is what I have now: ID Age DaysEnrolled HAZ WAZ WHZ Food onARV HIVStatus LTFUp 1 71622 0.008 0 NA NA NA NA 0 HIV exposed, status indeterminate 0 2 71622 0.085 28 NA NA NA NA 0...

...uld specify initial values for coxph? I got a dataset from a student who uses Stata and try to replicate in R. I will share data to you in case you want to see for yourself. Let me know if you want text or Stata data file. In R, I try this: > cox2 <- coxph(Surv(yrs2,ratify)~ accession+ haz.wst+ haz.in +haz.out+ wefgov+ rle+ rqe + pol.free +tai.2001 + ny.gdp.pcap.pp.cd + eio, data=dat3, control=coxph.control(iter.max=1000),singular.ok=T) Warning message: Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights, So I wrote out the...

....pdf in my work. This package fits parametric frailty models to survival data. To ensure I was using it properly, I started by running some small simulations to generate some survival data (without any random effects), and analyse the data using the parfm package. I am using an exponential baseline hazard. When the baseline hazard rate drops to 0.001, I get the following error when trying to fit the model: Error in optimHess(par = ESTIMATE, fn = Mloglikelihood, obs = obsdata, : non-finite finite-difference value [1] In addition: Warning message: In log(pars) : NaNs produced Has anybody else...

Hello, I have a couple of questions with regards to fitting a coxph model to a data set in R: I have a very large dataset and wanted to get the baseline hazard using the basehaz() function in the package : 'survival'. If I use all the covariates then the output from basehaz(fit), where fit is a model fit using coxph(), gives 507 unique values for the time and the corresponding cumulative hazard function. However if I use a subset of the varaibl...

...o, per the posting guide, what is your sessionInfo()? Terry Therneau On 08/09/2012 04:11 AM, r-help-request at r-project.org wrote: > I have a couple of questions with regards to fitting a coxph model to a data > set in R: > > I have a very large dataset and wanted to get the baseline hazard using the > basehaz() function in the package : 'survival'. > If I use all the covariates then the output from basehaz(fit), where fit is > a model fit using coxph(), gives 507 unique values for the time and the > corresponding cumulative hazard function. However if I use a s...

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...Marta Garcia >> <marta000garcia@gmail.com> escribió: >> > Hola estimada comunidad, >> > >> > Tengo duda respecto de que es un objeto ggplot >> > >> > Es un gráfico? >> >> Igual me equivoco, pero que yo sepa, sí. >> >> Haz un 'print(p)', donde p es un objeto de tipo ggplot, a ver si ves >> el gráfico en pantalla. >> >> Un saludo. >> > > [[alternative HTML version deleted]]

Hi, I want to plot non parametric estimates of the empirical hazard function for right censored data. I've tried many functions from different packages (muhaz, Design, survival, eha, event), but none of them gave me what I wanted. Am I missing something? Here's what I want. The data below is the same used by Kiefer (J. Economic Literature, 1988), which...

Hello, Is it possible to create confidence intervals for hazard rates? ?I'm creating two muhaz objects:? haz1 <- muhaz(NumDaysCustomer[cRV=="true"],status[cRV=="true"]) haz2 <- muhaz(NumDaysCustomer[cRV=="false"],status[cRV=="false"]) and plotting them. ? There are many, many more observations in the...

Dear Gustaf, I wish you a happy new year! I am a PhD Staff at LSHTM and I have been trying to use WHO anthro macros in R with the file you posted on internet but when I double check the WHZ, HAZ, WAZ output with output from ENA or STATA, it differs slightly. Do you have any idea why that might be the case? Many thanks Severine

...d be greatly appreciated. Thank you. Z<-rbinom(20,1,0.5) #covariate time<-rgamma(20,shape=2,scale=0.5) #failure time del<-c(0,0,1,1,0,1,1,1,0,1,0,0,1,1,0,1,1,1,0,1) #event indicator ll<-function(p){ loglik1<-del*log(exp(Z*p[3])) #log of the first part of the likelihood function haz<-(time*exp(Z*p[3]))*p[1] ll2<-vector("numeric",length(1:20)) for (s in 1:20){ integrand<-function(x) x^(del[s]+1/p[2]-1)*exp(-x/p[2])*exp(-x*haz[s])/(gamma(1+1/p[2])*p[2]^(1/p[2])) ll2[s]<-log(integrate(integrand,0,Inf)$value) } loglik2<-as.vector(ll2) #second part of the...

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Hello, I am using Dr. Harrell's rms package to make a nomogram. I was able to make a beautiful one. However, I want to change 5-year survival probability to 5-year failure probability. I couldn?t get hazard rate from Hazard(f1) because I used cph for the model. Here is my code: library(rms) f1 <- cph(Surv(retime,dfs) ~ age+her2+t_stage+n_stage+er+grade+cytcyt+Cyt_PCDK2 , data=data11, surv=T, x=T, y=T, time.inc=5) surv<- Survival(f1) haz<- Hazard(f1) Here is the Error in UseMethod(&quo...

Tengo instalado el R2.9.0 y el TinnR 1.17.2.4 y cuando abro Tinn R no me detecta q el R este abierto por lo cual no me permite correr ningun programa, alguien sabe q puede estar pasando? Saludos -- José "... hoy el cambio cualitativo la liberacion, implica, cambios organicos, de instinto y biologicos, AL MISMO TIEMPO q cambios politicos y sociales" H. M. [[alternative HTML version

Buenas noches para cada uno. Me alegra saber que superamos los 200 usuarios y tengos expectativas con respecto a la I Conferencia de R-hispano en Murcia. No soy usuario de Linux por desconocimiento, algo que lamento. Debo instalar R en un equipo con Windows 7 a 64 bits. ¿Podrían indicarme por favor cómo instalarlo? ¿Se hace con el mismo archivo R-2.10.0-win32? ¿Debo cuidar o cambiar algo antes o