similar to: predictive accuracy

Hi R experts, I am trying to do a prognostic model validation study, using cancer survival data. There are 2 data sets - 1500 cases used to develop a nomogram, and another of 800 cases used as an independent validation cohort. I have validated the nomogram in the original data (easy with the Design tools), and then want to show that it also has good results with the independent data using 60

Hi all R users I did a logistic regression with my binary variable Y (0/1) and 2 explanatory variables. Now I try to draw my nomogram with predictive value. I visited the help of R but I have problem to understand well the example. When I use glm fonction, I have a problem, thus I use lrm. My code is: modele<-lrm(Y~L+P,data=donnee) fun<- function(x) plogis(x-modele$coef[1]+modele$coef[2])

Hi, I am trying to construct a logistic regression model from my data (104 patients and 25 events). I build a full model consisting of five predictors with the use of penalization by rms package (lrm, pentrace etc) because of events per variable issue. Then, I tried to approximate the full model by step-down technique predicting L from all of the componet variables using ordinary least squares

Alternate title: How can I persuade my students that R is for them? Alternate title: Can R replace SAS, SPSS or Stata for clinicians? I am teaching introductory statistics to twelve physicians and two veterinarians who have enrolled in a Mentored Clinical Research Training Program. My course is the first in a sequence of three. We (the instructors of this sequence) chose to teach R rather than

The rms package includes the nomogram function, which generates a list object that can be passed to plot for graphical production of nomograms. I would like to remove the "linear predictor" line in the graph, which means (I suspect) removing it from the nomogram output object. I've looked at the nomogram output object, but it is not clear to me if or how it might be edited to

System: R 2.3.1 on a Windows XP computer. I am validating several cancer prognostic models that have been published with a large independent dataset. Some of the models report a probability of survival at a specified timepoint, usually at 5 and 10 years. Others report only the linear predictor of the Cox model. I have used Harrell's c index for censored data (rcorr.cens) as a measure of

Dear R-Help, I am using 'rms' package to draw nomogram. I wonder how is the "Points" determined for each predictor in the model? Is it by the coefficient estimate (beta) relative to the highest effect in the model or? Thanks Lin -- View this message in context: http://r.789695.n4.nabble.com/points-tp4638552.html Sent from the R help mailing list archive at Nabble.com.

Dear R-users, I have used the nomogram function from the rms package for a logistic regresison model made with lrm(). Everything works perfectly (r version 2.15.1 on a mac). My question is this: if my final model is not the one created by lrm, but I internally validated the model and 'shrunk' the regression coefficients and computed a new intercept, how can I build a nomogram using that

Dear R-users, I am a novice R-user with some experience in using the RMS package for taking nomograms after various survival models. This time, I am trying to plot a nomogram after a Random Effects Cox, implemented by the "coxme" package. My questions are: 1. Is it possible to take a nomogram directly after the coxme survival function? 2. If not is there a way to take the linear

Hi, I would like to emphasize ("zoom") the zone of a nomogram where the probability are > 0.01 (nomogram built with nomogram, Design). As a consequence, I don't need to draw the part of the "Total points" axis with score < 60 equivalent in my case to a linear predictor < 4.5 - As far as I know, this is not possible with the arguments of the function. - Changing

Hi R users, I'd like to draw a nomogram using a competing-risks regression (crr function in R), rather than a cox regression. However, the nomogram function provided in the Design package is not good for this purpose. Do you have any suggestion. I really appreciate your help Many thanks F.Abdollah, MD San-Raffele hospital Milan, Italy -- View this message in context:

Dear all, I am using R 2.9.2 on Windows XP. I am undertaking a simulation study to consider methods of external validation in the context of missing covariates in the validation data set. I would like to use Royston's measure of prognostic separation as a method of external validation. Although there is no R code for this, the author informs me that it should be easy: 1. Calculate the

Dear Sir or Madam? I am a doctor of urology,and I am engaged in developing a nomogram of bladder cancer. May I ask for your help on below issue? I set up a dataset which include 317 cases. I got the Binary Logistic Regression model by SPSS.And then I try to reconstruct the model ?lrm(RECU~Complication+T.Num+T.Grade+Year+TS)? by R-Project,and try to internal validate the model through

Dear all, I am using the publically available GustoW dataset. The exact version I am using is available here: https://drive.google.com/open?id=0B4oZ2TQA0PAoUm85UzBFNjZ0Ulk I would like to produce a nomogram for 5 covariates - AGE, HYP, KILLIP, HRT and ANT. I have successfully fitted a logistic regression model using the "glm" function as shown below. library(rms) gusto <-

Hello, I am using Dr. Harrell's design package to make a nomogram. I was able to make a beautiful one without stratifying, however, I will need to stratify to meet PH assumptions. This is where I go wrong, but I'm not sure where. Non-Stratified Nomogram:

Dear all, I am comparing logistic regression models to evaluate if one predictor explains additional variance that is not yet explained by another predictor. As far as I understand Baron and Li describe how to do this, but my question is now: how do I report this in an article? Can anyone recommend a particular article that shows a concrete example of how the results from te following simple

Dear friends, Ecdf used to work nicely before. e.g. ecdf(df1v[,c(1:6)],group=df1v$trt,q=.5,col=1:2,label.curves=list(keys="l ines"), datadensity="rug") but now it does not work at all, even for a simpler code??? By the way, I used the same libraries. Thanks for your help. Ahmed [[alternative HTML version deleted]]

Dear friends, I need to fill in (duplicate the whole record) the missing days with the same record values as long as AE is the same value (i.e. "1"), once AE value changes, the process of duplication should proceed with the new AE value till it changes again. e.g. I need to fill in records: day 18-day 44, all the records are carried with the new AE value of "0". At the

> On Sep 14, 2017, at 12:30 AM, Bonnett, Laura <L.J.Bonnett at liverpool.ac.uk> wrote: > > Dear all, > > I am using the publically available GustoW dataset. The exact version I am using is available here: https://drive.google.com/open?id=0B4oZ2TQA0PAoUm85UzBFNjZ0Ulk > > I would like to produce a nomogram for 5 covariates - AGE, HYP, KILLIP, HRT and ANT. I have

Dear list, I'm facing the following problem : A cox model with my sex variable interacting with several continuous variables : cph(S~sex*(x1+x2+x3)) And I'd like to make a nomogram. I know it's a bit tricky and one mights argue that nomogram is not a good a choice... I could use the parameter interact=list(sex=("male","female"),x1=c(a,b,c))... but with rcs or pol