similar to: calibrate.cph plots

Dear all, when i do the calibration plot, i put the x label y label , there is some labels are i did not put it , like "resample optimism added ..." i want to get rid of the these label , is any body know how can i get rid of these label. these are the following command i used cal <- calibrate(f, u=12, method=c("boot"), B=100,m=70, data=a1)

Dear R users: In Prof. Harrell's library rms, calibrate.rms plot the Bias-corrected Probability and Apparent Probability. The latter one can be retrieved from class calibrate.default. But how to retrieve the former one. BW *Yao Zhu* *Department of Urology Fudan University Shanghai Cancer Center Shanghai, China* [[alternative HTML version deleted]]

 Dear R-users,   I  have two questions regarding validation and calibration of Survival regression models.   1.  I am trying to calibrate and validate a cox model using val.surv. here is my code:  f.1<-cph(Surv(time,event)~age, x=T, y=T, data=train)  test1<-test[,"age"]  val.surv(f.1, newdata=data.frame(test1), u=10)    but I get an error message:    Error in val.surv(f.1, newdata

Hi, I created a logistic regression model using the glmnet package. This model is of class "glmnet" or "lognet". I wanted to plot a calibration curve for this model using the calibrate() function from rms package, but the objects used are different, rms requires a fit from lrm(). Is there another function for getting the calibration plot for this glmnet object, or can anyone

Hi R-users, can anyone explain me how to play around with the options of the bootstrap calibration curve obtained using the calibrate() function in Design package? I am trying to colour the diagonal, i.e. the ideal curve, in red, and also hide the bias-corrected curve. Thanks, Dave _________________________________________________________________ Show them the way! Add maps and directions to

Hi, the calibrate.cph() function in rms package generate calibration curve for Cox model on the same dataset where the model was derived using bootstrapping or cross-validation. If I have the model built on dataset 1, and now I want to produce a calibration curve for this model on an independent dataset 2, how can I do that? Thanks John [[alternative HTML version deleted]]

Dear WizaRds, dear Thomas, First of all, I want to tell you how grateful I am for all your support. I wish I will be able to help others along one day the same way you do. Thank you so much. I am struggling with a multistage sampling design: library(survey) multi3 <- data.frame(cluster=c(1,1,1,1 ,2,2,2, 3,3), id=c(1,2,3,4, 1,2,3, 1,2), nl=c(4,4,4,4, 3,3,3, 2,2), Nl=c(100,100,100,100,

I have been attempting to use cph models to get better calibration of my models for which I had originally used logistic regression. I tried running with 40 repetitions and got an error. I then tried 500 repetitions (thinking that the NaNs in the output below might be caused by that choice) and then let my computer crunch for several hours and got only the same error message and

Thanks again, Great to see confirmations of more and more things working! > I wonder what's the fastest method to test the function (previously I setup the ups and unplug the utility from the ups for testing). > is "upsrw driver.flag.allow_killpower=1" then "upscmd driver.killpower" the correct testing procedure? At least by intent of this new feature -- yes.

Thanks again, Great to see confirmations of more and more things working! > I wonder what's the fastest method to test the function (previously I setup the ups and unplug the utility from the ups for testing). > is "upsrw driver.flag.allow_killpower=1" then "upscmd driver.killpower" the correct testing procedure? At least by intent of this new feature -- yes.

Jim Klimov <jimklimov+nut at gmail.com> > > I believe some fixes were applied to the branch since your report (most visibly, about battery time settings), are you in position to test how it behaves now? :) Hi: I got another ups for testing. so I test the new commit for both APC SRT3000XL and SMT2200RM2U. the results below: 1. I get the new attribute "ups.test.result" for

Jim Klimov <jimklimov+nut at gmail.com> > > I believe some fixes were applied to the branch since your report (most visibly, about battery time settings), are you in position to test how it behaves now? :) Hi: I got another ups for testing. so I test the new commit for both APC SRT3000XL and SMT2200RM2U. the results below: 1. I get the new attribute "ups.test.result" for

Hi, Sorry not to provide R-code in my previous mail. R code is below #install.packages("rms") require(rms) #install.packages("mstate") library(mstate) require(splines) library(ggplot2) library(survival) library(splines) #install.packages("survsim") require(survsim) set.seed(10) df<-crisk.sim(n=500, foltime=10, dist.ev=rep("lnorm",2),

I'm studying the calibration function in the survey package in preparation for raking some survey data. Results from the rake function below agree with other sources. When I run calibrate, I get a warning message and the M and F weights seem to be reversed. Even allowing for that, the deviation between calibrated and raked weights is much more than I expected. I see that in the calibrate

Hi all, I have a question on the package « survey” I have some difficulties to use the function ‘calibrate’. Although it works well with one single factor variable, I cannot use it for 2 and get the message “Erreur dans regcalibrate.survey.design2(design, formula, population, aggregate.stage = aggregate.stage, : Population and sample totals are not the same length.” Here is the format

Good afternoon! I need to evaluate the goodness-of-fit (aka calibration) for survival probability estimates from a Cox model. I tried to use 'calibrate' in the Design package but I'm not sure if it should/would produce what I need (ie a chi-sq type statistic with a table of expected vs observed probabilities). Any other functions I should be aware of? Also, has anybody come across

On Jun 26, 2017, at 7:03 AM, Andrea de Lutti <adelutti at gmail.com> wrote: > > Are there no warnings for battery test? not sure if you saw my reply on 2016-06-17: Do you mean a notification that a test is in progress, or something for the results? There is the REPLBATT message in upsmon when the battery test fails, but I don't think the generic Qx protocol supports the RB

On Jun 27, 2017, at 9:23 AM, Andrea de Lutti <adelutti at gmail.com> wrote: > > Sorry, I didn't received it... You should be subscribed to the list now. > I don't have any REPLBATT message Right, you would only get REPLBATT messages when the UPS reports that the battery *needs to be replaced* (and then at regular intervals per the upsmon.conf parameters). > , but

Hola a todos, Estoy iniciandome en R y la verdad es que aun estoy muy muy verde.... Estoy intentando clasificar unos datos con support vector machines, pero me da fallo al usar la funcion predict. El código que uso es el siguiente: calibrate<-read.table("calibration.txt", header=TRUE) calibrate$calibration<-as.factor(calibrate$calibration)

I have been working on fitting Cox model for prediction by using rms package. I want to measure model's calibartion and discrimination. Discrimination was measured by using validate() in rms, Dxy can be transferred to Harrell's c index. But in this way, I cannot get 95%CI of c index. How can I do this in R? And by the way, what value should be in c index to present the model's well?