similar to: Odd behavior of plot function

Sorry, that's a cut and paste error. It should be either tempx or xtemp throughout. Terry T On 06/11/2015 12:59 PM, John Nolan wrote: > Is there a misprint in your example? The first line of code uses tempx, but the rest uses a different variable xtemp? > > John > > -----"R-devel" <r-devel-bounces at r-project.org> wrote: ----- > To: "r-devel at

I would like to produce a complimentary log-log survival plot with only the points appearing on the graph. I am using the code below, taken from the plot.survfit page of help for the the survival package (version 2.35-7). I am running in R 2.10.0 on Windows XP, and the list of packages following the error is loaded. Is there some specific 'type= ' syntax, or an additional parameter that

My code is as follows: #include <iostream> #include <cmath> using namespace std; #define MATHLIB_STANDALONE 1 extern "C" { #include "R_ext/Applic.h" } typedef struct TT{ double ** tempX; double * tempY; int tempN; } TT, *MM; double fn(int N, double * beta, void * ex){ double total = 0; int i = 0,j = 0; double * betaFn = new double[N]; MM tmp = (MM)ex;

First a statistical issue: The survfit routine will produce predicted survival curves for any requested combination of the covariates in the original model. This is not the same thing as an "adjusted" survival curve. Confusion on this is prevalent, however. True adjustment requires a population average over the confounding factors and is closely related to the standardized

A problem has been pointed out by a French user of the survival package and I'm looking for a pointer. > options(OutDec= ",") > fit <- survfit(Surv(1:6 /2) ~ 1) > fit$time [1] NA 1 NA 2 NA 3 A year or two ago some test cases that broke survfit were presented to me. The heart of the problem was numbers that were almost identical, where table(x) and unique(x) gave

On the local machine the command R11 CMD Rd2pdf survfit.Rd works fine. R12 CMD Rd2pdf survfit.Rd fails with the message below. Converting Rd files to LaTeX ... survfit.Rd Creating pdf output from LaTeX ... Error in texi2dvi("Rd2.tex", pdf = (out_ext == "pdf"), quiet = FALSE, : Running 'texi2dvi' on 'Rd2.tex' failed. Messages: sh: texi2dvi: command not

I cloned therneau/survival and the installation failed since there is no definition for exported function survfit(). A file seems to be missing - there is survfit0() and survfit0.R but, compared to CRAN, no survfit.R. Georgi Boshnakov ---------------------------------------------------------------------- Message: 1 Date: Thu, 05 Sep 2019 12:53:11 -0500 From: "Therneau, Terry M.,

-------- Original Message -------- Subject: Re: How to obtain nonparametric baseline hazard estimates in the gamma frailty model? Date: Mon, 04 Nov 2013 17:27:04 -0600 From: Terry Therneau <therneau.terry at mayo.edu> To: Y <yuhanusa at gmail.com> The cumulative hazard is just -log(sfit$surv). The hazard is essentially a density estimate, and that is much harder. You'll notice

I am getting some unexplained changes in the latest version of survival, and finally traced it down to this: model.response acts differently for Surv objects. Here is a closed form example using a made up class Durv = diagnose survival.?? I tracked it down by removing methods one by one from Surv; I had just added some new ones so they were my suspects. test <- data.frame(time=1:8,

The first thing you are missing is the documentation -- try ?survfit.object. fit <- survfit(Surv(time,status)~1,data) fit$std.err will contain the standard error of the cumulative hazard or -log(survival) The standard error of the survival curve is approximately S(t) * std(hazard), by the delta method. This is what is printed by the summary function, because it is what user's

For a fitted Cox model, one can either produce the predicted survival curve for a particular "hypothetical" subject (survfit), or the predicted curve for a particular cohort of subjects (survexp). See chapter 10 of Therneau and Grambsch for a long discussion of the differences between these, and the various pitfalls. By default, survfit produces the curve for a hypothetical

Yes, that is exactly the problem.? The code found in the "config" script is never run.? But why doesn't it get run? On 9/6/19 5:44 AM, Georgi Boshnakov wrote: > I cloned therneau/survival and the installation failed since there is no definition for exported function survfit(). > A file seems to be missing - there is survfit0() and survfit0.R but, compared to CRAN, no

Hi Terry, On 03/16/2016 08:03 AM, Therneau, Terry M., Ph.D. wrote: > Is the phrase "index <- match(x, sort(unique(x)))" reliable, in the > sense that it will never return NA? This is assuming that match() and unique() will never disagree on equality between 2 floating point values. I believe they share some code internally (same hashing routine?), so maybe it's reliable.

> Further I appreciate your new function survmean(). At the moment it > seems to be intended as internal, and not documented in the help. The computations done by print.survfit are now a part of the results returned by summary.survfit. See 'table' in the output list of ?summary.survfit. Both call an internal survmean() function to ensure that any future updates stay in

Hello, right now, i have a program to collect data into a table. right now, my table is table1 <- data.frame(trial = NA, x = NA, y = NA) for each time when i want to add data into my data, i have to copy data of table into an array for each column, and then i add new data into my array, then i copy my array into the table one column by one column. For example temptrial <- table1$trial;

On Sat, Jun 1, 2019 at 3:22 AM Therneau, Terry M., Ph.D. via R-devel <r-devel at r-project.org> wrote: > > In the next version of the survival package I intend to make a non-upwardly compatable > change to the survfit object. With over 600 dependent packages this is not something to > take lightly, and I am currently undecided about the best way to go about it. I'm looking

The combination of survfit, coxph, and factors is getting confused. It is not smart enough to match a new data frame that contains a numeric for sitenew to a fit that contained that variable as a factor. (Perhaps it should be smart enough to at least die gracefully -- but it's not). The simple solution is to not use factors. site1 <- 1*(coxsnps$sitenew==1) site2 <-

On 6/1/19 1:32 PM, Marc Schwartz wrote: > >> On Jun 1, 2019, at 12:59 PM, Peter Langfelder <peter.langfelder at gmail.com> wrote: >> >> On Sat, Jun 1, 2019 at 3:22 AM Therneau, Terry M., Ph.D. via R-devel >> <r-devel at r-project.org> wrote: >>> In the next version of the survival package I intend to make a non-upwardly compatable >>> change

> Dear All, > > I have built a survival cox-model, which includes a covariate * time interaction. (non-proportionality detected) > I am now wondering how could I most easily get survival predictions from my model. > > My model was specified: > coxph(formula = Surv(event_time_mod, event_indicator_mod) ~ Sex + > ageC + HHcat_alt + Main_Branch + Acute_seizure +

A bug in the survival routines was reported to me today. The root cause is a difference between table, unique, and sort. > temp <- rep(c(1, sqrt(2)^2, 2), 1:3) > unique(temp) [1] 1 2 2 > table(temp) temp 1 2 1 5 I'm using 2.10 on Linux, the user reported from 2.9 on Windows. 1. Minor issue: I think the root rounding occurs in factor. I didn't see any discussion of