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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,

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 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

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

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

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])

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

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, 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

Hi R-help, ? I have fit a cox ph model to my data, but have beenreceiving an error when trying to fit a model to the nomogram. Here is the codeand corresponding error: ? ? >nomogramCF = nomogram(cph_age6_40avp4, +????????????????????lp.at= seq(-10,10,by =0.5),lp = TRUE, +?????????????????????? +??????????????????????funlabel="5year survival",

Dear R users, I am a new R user and something stops me when I try to write a academic article. I want to make a nomogram to predict the risk of prostate cancer (PCa) using several factors which have been selected from the Logistic regression run under the SPSS. Always, a calibration plot is needed to validate the prediction accuracy of the nomogram. However, I tried many times and read a lot of

dear professor: thank you for your help,witn your help i develop the nomogram successfully. after that i want to do the internal validation to the model.i ues the bootpred to do it,and then i encounter problem again,just like that.(´íÎóÓÚerror to :complete.cases(x, y, wt) : ²»ÊÇËùÓеIJÎÊý¶¼Ò»Ñù³¤(the length of the augment was different)) i hope you tell me where is the mistake,and maybe i have

dear professor: I have a problem about the nomogram.I have got the result through analysing the dataset "exp2.sav" through multinominal logistic regression by SPSS 17.0. and I want to deveop the nomogram through R-Projject,just like this : > n<-100 > set.seed(10) > T.Grade<-factor(0:3,labels=c("G0", "G1", "G2","G3")) >

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:

Hello, I am using Dr. Harrell's design 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: f1 <- cph(Surv(retime,dfs) ~ age+her2+t_stage+n_stage+er+grade+cytcyt+Cyt_PCDK2 , data=data11, surv=T,

I am a new user of R for Windows, enthusiast about the many functions of the Design and Hmisc libraries. I combined the results of a Cox regression model after multiple imputation (of missing values in some covariates). Now I got my vector of coefficients (and of standard errors). My question is: How could I use directly that vector to run programs such as 'nomogram', 'calibrate',

dear: I am a user of R project.And now ,I have a problem. I want to know what is the name of the datasets in the web page--"Draw a Nomogram Representing a Regression Fit" which come from the R-home(http://www.r-project.org/ Package rms version 3.0-0). And can you supply the dataset to me? wish for your help,thank you!

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 professor: I am a doctor of urinary,and I am developing a nomogram of bladder tumor.Now I have a problem about this. I have got the result like this through analysing the dataset "exp11.sav" through multinominal logistic regression by SPSS 17.0.(the Sig. is high,that is good ,it is just aexperimental data ) Parameter Estimates Ya B Std. Error Wald df Sig. Exp(B) 95%

Dear all: I have used the cph function in the rms package. log10 was used to transform the variables, as follows: fit<-cph(pfsurv~log10(x1)+log10(x2),x=T,y=T,surv=T) after I run the nomogram function. I found "variable limits and transformations are such that an infinite axis value has resulted." How to add variable limits in the nomogram function? Thanks a lot *Yao Zhu*