search for: cen

Dear, I wanna to compare AUC generated by two distribution models using the same sample. I tried improveProb function's example code below. set.seed(1) library(survival) x1 <- rnorm(400) x2 <- x1 + rnorm(400) d.time <- rexp(400) + (x1 - min(x1)) cens <- runif(400,.5,2) death <- d.time <= cens d.time <- pmin(d.time, cens) rcorrp.cens(x1, x2, Surv(d.time, death)) #rcorrp.cens(x1, x2, y) ## no censoring set.seed(1) x1 <- runif(1000) x2 <- runif(1000) y <- sample(0:1, 1000, TRUE) rcorrp.cens(x1, x2, y) improveProb(x1, x2, y)...

Hello, When i run the code below from Weibull distribution with 30% censoring by using optim i get an error form R, which states that Error in optim(start, fn = z, data = q, hessian = T) :? ? objective function in optim evaluates to length 25 not 1 can somebody?help me remove this error. Is my censoring approach correct. n=25;rr=1000 p=1.5;b=1.2 for (i in 1:rr){ q&...

I have two alternative Cox models with C-statistics 0.72 and 0.78. My question is if 0.78 is significantly greater than 0.72. I'm using rcorrp.cens. I cannot find the U statistics in the output of the function. This is the output of the help example: > x1 <- rnorm(400) > x2 <- x1 + rnorm(400) > d.time <- rexp(400) + (x1 - min(x1)) > cens <- runif(400,.5,2) > death <- d.time <= cens > d.time <- pmin(d...

Hi, I'm trying to calculate 95% confidence interval of C statistic of logistic regression model using rcorr.cens in rms package. I wrote a brief function for this purpose as the followings; CstatisticCI <- function(x) # x is object of rcorr.cens. { se <- x["S.D."]/sqrt(x["n"]) Low95 <- x["C Index"] - 1.96*se Upper95 <- x["C Index"] + 1.96*s...

Dear all, I am planning to use nlme library for analysis of experiments in semiconductor industry. Currently I am using "lm" but plan to move to "lme" to handle within wafer / wafer-to-wafer and lot-to-lot variation correctly. So far everything is working well, but I have a fundamentel question: NLME offers "maximum likelihood" and "restricted maximum

...m having difficulties with plot.locfit.3d, at least I think that is the problem. I have a large dataframe (about 4 MM cases) and was hoping to see a non-parametric estimate of the hazard plotted against two variables: > fit <- locfit(~surv.yr+ ur_protein + ur_creatinine, data=TRdta, cens = 1-death, family = "hazard", xlim=c(0,10)) # it took somewhere between 1 and 2 hours to complete, but it did complete and reported no errors or warnings. > plot(fit, pv=c("ur_protein", "ur_creatinine")) Error in if (from == to) rep.int(from, length.out) else...

Dear list, i am a student of psychology and have to do a multilevelanalysis on some data. About that i have one general and one specific question. This is what i have copied from the help-file on lme: data(bdf) fm <- lme(langPOST ~ IQ.ver.cen + avg.IQ.ver.cen, data = bdf, random = ~ IQ.ver.cen | schoolNR) summary(fm) after summary(fm) i get the following error: Error in verbose || attr(x, "verbose") : invalid `y' type in `x || y' I assume that i have not installed the package nlme correcty, but re...

...e drop in concordance index due to omitting one covariate is significant. I think (but I'm not sure) here are two ways to do that: 1) predict two cox model (the full model and model without the covariate of interest) and estimate the concordance index (i.e. area under the ROC curve) with rcorr.cens for both models, then compute the difference 2) predict the two cox models and estimate directly the difference between the two c-indices using rcorrp.cens. But it seems that the rcorrp.cens gives me the drop of Dxy index. Do you have any hint? Thanks Stefano [[alternative HTML version delete...

Dear R-devel, I'm working on Prof. Loader's new version of locfit to try to get it pass R CMD check. I'm almost there, but I have a problem with some Rd files that I hope some one can help me resolve. Here's an example: In the package there's a function called locfit.censor(). This function can be used in a few different ways: locfit.censor(x, y, cens, ...) locfit.censor(formula, ...) locfit(formula, ..., lfproc=locfit.censor) What I did in locfit.censor.Rd is have something like: \synopsis{ locfit.censor(x, y, cens, ..., iter=3, km=FALSE) } \usage{ locfit(for...

...bottlenecks. Any help in speeding it up would be appreciated. `dat` is a dataframe of samples from a regular grid. The first two columns are the spatial coordinates of the samples, the remaining 20 columns are the abundances of species in each cell. I need to calculate the species richness in adjacent cells for each cell in the sample. For example, if I have nine cells in my dataframe (X = 1:3, Y = 1:3): a b c d e f g h i I need to calculate the neighbour-richness for each cell; for a, this is the richness of cells b, d and e combined. The neighbour richness of cell e would be the comb...

Dear R-help, This is an example in the {Hmisc} manual under rcorr.cens function: > set.seed(1) > x <- round(rnorm(200)) > y <- rnorm(200) > round(rcorr.cens(x, y, outx=F),4) C Index Dxy S.D. n missing uncensored Relevant Pairs Concordant Uncertain 0.4831 -0.0338 0....

...et ordinal scale; ranked) for each plant species and relev?. I found a lot of r-packages dealing with cluster analysis, but none of them is able to calculate a distance measure for ranked data. Podani recommends the use of Goodman and Kruskals' Gamma for the distance. I found the function rcorr.cens (outx=true) of the Hmisc package which should do it. What I don't understand is how to define the input vectors x, y with my vegetation dataset. The other thing how I can use the output of rcorr.cens for a distance measure in the cluster analysis (e.g. in vegan or amap). Any help would be grea...

Hi , I am trying to get some estimator based on lognormal distribution when we have left,interval, and right censored data. Since, there is now avalible pakage in R can help me in this, I had to write my own code using Newton Raphson method which requires first and second derivative of log likelihood but my problem after runing the code is the estimators were too high. with this email ,I provide simple exampl...

Good day R help list!!! I've been trying to do Bootstrap in R on Censored data. I encountered WARNING/ERROR messages which I could not find explanation. I've been searching on the literature for two days now and still can't find answers. I hope there's anyone out there who can help me with these two questions: 1. If the "Loglik converged before...

...ta.frame worked well for my other programs, how come I cannot make it run this time. Could you please tell me how I can fix it? *************************************************************************************************** >all<-data.frame(z1,z2,z3) >fit.model.all<- coxph(Surv(t,cen) ~z1+z2+z3,data=all) > reg.model.all<-step(fit.model.all) Start: AIC= 689.1 Surv(t, cen) ~ z1 + z2 + z3 Error in as.data.frame.default(data) : cannot coerce class "function" into a data.frame **************************************************************************************...

...sted to evaluate reclassification using net reclassification improvement and Integrated Discrimination Index IDI after survival analysis (Cox proportional hazards using stcox). I search a R package or a R code that specifically addresses the categorical NRI for time-to-event data in the presence of censored observation and, if possible, at different follow-up time points. I know that the ?PredictABEL? Package contains functions for NRI and IDI calculation but it is unclear for me if it allows censored observation. Package ?survIDINRI? calculates only continuous NRI and the function of Package ?Hm...

Thank you for Prof.Ripley's suggestion. I fixed the program by adding a lower scope, and the program ran, but I still got warning messages, and don't know what is going on, would this affect my results? ... Step: AIC= 12337.74 Surv(tlfup, cen) ~ MI[[j]]$trt + MI[[j]]$agem40 + MI[[j]]$agem40sq + mhtypeed1 + mhtypeed2 Df AIC <none> 12338 - MI[[j]]$agem40sq 1 12338 - MI[[j]]$agem40 1 12339 - mhtypeed2 1 12353 - mhtypeed1 1 12365 There were 50 or more warnings (use warnin...

...w that the nomogram is significantly different to an existing model based on 60 month survival data generated by it (eg by McNemar's test). Hence, somewhat shortened: #using R 2.01 on Windows library(Hmisc) library(Design) data1 #dataframe with predictor variables A and B, cens and time columns (months) ddist1 <- datadist(data1) options(datadist='ddist1') s1 <- Surv(data1$time, data1$cens) cph.nomo <- cph(s1 ~ A+B, surv=T, x=T, y=T, time.inc=60) survcph <- Survival(cph.nomo, x=T, y=T, time.inc=60, surv=T) surv5 <- function(...

Dear R-helpers, I recently switched from SAS to R, in order to model the occurrence of rare events through logistic regression. Is there a package available in R to calculate the Goodman-Kruskal Gamma? After searching a bit I found a function "rcorr.cens" which should do the job, but it is not clear to me how to...

...or continuous covariate. I want to truncate the suvival curve and only display the part with covariate value between 0 and 7. The following is the code I wrote: sm.options(list(xlab="log_BSI_min3_to_base", xlim=c(0,7), ylab="Median Progression Prob")) sm.survival(min3.base.prog.cen[,3],min3.base.prog.cen[,2],min3.base.prog.cen[,1],h=sd(min3.base.prog.cen[,3]),status.code=1 ) But the xlim option does not work. Can anyone help me with this problem? Thanks a lot. Rachel -- View this message in context: http://www.nabble.com/Question-about-sm.options---sm.survival-tf4279605.ht...