similar to: crash when using hazard.ratio.plot from rms package

Hello, I am constructing a nomogram using cph and nomogram commands in Dr. Harrell's Design/RMS package. The HR that I obtain for dichotomous and categorical variables are identical to those that I obtain using STATA stcox. However, the inter-quartile HR I obtain for continuous variables is obviously different, since STATA gives me HR for each unit (year, centimeter, etc) like coxph would

Dear all, I am using Windows and R 2.9.2 for my analyses. I have a large dataset and I am particularly interested in looking at time to an event for a continuous variable. I would like to produce a plot of log(relative risk) or relative risk (also known as hazard ratio) against the continuous variable. I have spent a long time looking for advice on how to do this but my search has proved

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,

Dear R-Helpers, I am a novice in survival analysis. I have the following code: for (i in 3:12) print(coxph(Surv(time, status)~a[,i], data=a)) I used it to fit the Cox Proportional Hazard models separately for every available parameter (columns 3:12) in my data set - with intention to compare the Hazard Ratios. However, some of my variables are in range 0.1 to 1.6, others in range 5000 to

http://r.789695.n4.nabble.com/file/n3058505/file.csv file.csv Hi, Rusers I have a problem in making a rcspline.plot with a Hmisc package. My data is in the upload attachment. My programme as follows: library(Hmisc) A<-read.csv("file.csv",header=TRUE) attach(A)

Hi, I'm using the rms package to do regression analysis using the lrm function. Retrieving odds ratios is possible using summary.rms. However, I could not find any information on how exactly the odds ratios for continuous variables are calculated. It doesn't appear to be the odds ratio at 1 unit increase, because the output of summary.rms did not match the coefficient's value. E.g.

Hi, I would like to compare the hazard functions of two samples using the Cox proportional hazards model. For sample 1 I have individual time-to- event data. For sample 2 I don't have individual data, but grouped data that allows to obtain a hazard function. I am wondering if there is an R function that allows to obtain a hazard ratio of the two hazard funtions (under the

Dear Forum, I have a question about interaction estimate in the Cox model: why the hazard ratio of the interaction is not produced in the summary of the model? (Instead, the estimate of the coefficient is given in the print of the model.) # Example: modINT <-cph( Surv(T_BASE, T_FIN,STATUS)~ NYHA + ASINI + RFP + FE_REC + XX_PR*XX_DISF) print(modINT) coef se(coef) z

Hello,   does anyone have an example on how to use restricted cubic splines function rcs within survfit.cph, if cph (Cox Proportional Hazard Regression) was done with restricted cubic splines (which I made to work)? Thank you. > [[alternative HTML version deleted]]

Hi, I am new to R. My question is: how to get the 'hazard ratio' using the 'coxph' function in 'survival' package? thanks, karena -- View this message in context: http://r.789695.n4.nabble.com/About-hazard-ratio-urgent-tp3595527p3595527.html Sent from the R help mailing list archive at Nabble.com.

Hi, I'm new to R and using it for Cox survival analysis. Thanks to this great forum I learned how to compute the HR with its confidence interval. My question would be: Is there any way to get the p-value for a hazard ratio in addition to the confidence interval? Thanks, Thierry -- Thierry Panje Visiting Student Researcher Department of Psychology Stanford

I'm looking for software that makes plots such as fig 4 (a)-(e), fig 5 anf fig 7 of Gray, Robert, "Flexible Methods for Analyzing Survival Data Using Splines, with Applications to Breast Cancer Prognosis," 1992, J Am Stat Assoc, pp 942-51. In other words, I'm looking for software that takes survival data and a continuous covariate as input and computes a curve giving log hazard

I am cleaning up the rms package to not export functions not to be called directly by users. rms uses generic functions defined in other packages. For example there is a latex method in the Hmisc package, and rms has a latex method for objects of class "anova.rms" so there are anova.rms and latex.anova.rms functions in rms. I use:

Dear All, For logistic regression models: is it possible to use validate (rms package) to compute bias-corrected AUC, but have variable selection with AIC use step (or stepAIC, from MASS), instead of fastbw? More details: I've been using the validate function (in the rms package, by Frank Harrell) to obtain, among other things, bootstrap bias-corrected estimates of the AUC, when variable

Greetings, I am new to R and have been comparing CPH survival analysis hazard ratios between R and SAS PhReg. The binary covariates' HRs are the same, however the continuous variables, for example age, have quite different HRs although in the same direction. SAS PhReg produces HRs which are the change in risk for every one increment change in the independent variable. How do I

Hi, I was reading a paper published in JCO "Prediction of risk of distant recurrence using 21-gene recurrence score in node-negative and node-positive postmenopausal patients with breast cancer treated with anastrozole or tamoxifen: a TransATAC study" (ICO 2010 28: 1829). The author uses a method to estimate the 9-year risk of distant recurrence as a function of continuous recurrence

Hi, I am new to time-dependent Cox model to estimate time dependent hazard ratios. Let me use aml dataset from survival package: > aml3<-survSplit(aml2,cut=c(5,10,20),end="time",start="start", event="status",episode="i") If I want to esimate hazard ratio for each of the time intervals 0-5, 5-10, 10-20 and >=20, would the following calculate

Hi I am trying to install "rms" package but while installing it shows following error package 'survival' 2.36-2 is loaded, but >= 2.36.3 is required by 'rms' what to do? i am using linux OS I have tried by updated r-base-core but it didnt work regards GRR [[alternative HTML version deleted]]

Dear R-users, I am using R 2.13.0 and rms 3.3-0 , but can not reproduce figure 7.8 of the handouts *Regression Modeling Strategies* ( http://biostat.mc.vanderbilt.edu/wiki/pub/Main/RmS/course2.pdf) by the following code. Could any one help me figure out how to solve this? setwd('C:/Rharrell') require(rms) load('data/counties.sav') older <- counties$age6574 + counties$age75

How can I extract the adjusted R^2 value from an ols object (using rms package)? library(rms) x <- rnorm(10) y <- x + rnorm(10) ols1 <- ols(y ~ x) Typing "ols1" displays adjusted R^2 among other things, but how can I assign it to a variable? I tried str(ols1) but couldn't see where to go from there. Thanks, Mark Seeto