similar to: sbrier (Brier score) and coxph

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

Hi, Today we've seen the following problem with the R-2.12 that we use for our Windows builds: > installed.packages() Error: subscript out of bounds After some investigation we discovered that the cause of this failure was that 1 of the 890 packages currently installed on the machine (Windows Server 2003 R2) had its DESCRIPTION file empty:

On Mon, 2007-05-14 at 23:41 +0200, vax9000 at gmail.com wrote: > Full_Name: vax, 9000 > Version: 2.4.0, 2.2.1 > OS: 2.4.0: Mac OS X; 2.2.1: Linux > Submission from: (NULL) (192.35.79.70) > > > To reproduce this bug, first go to the website "http://llmpp.nih.gov/DLBCL/" and > download the 14.8M data set "Web Figure 1 Data file". The direct link is >

Hello, I am using the val.prob function in the Design package. I understand how the Brier quadratic error score is calculated, but I do not know how the Brier score computed on the calibrated rather than raw predicted probabilities (B cal) is calculated. My question is: how are the calibrated probabilities calculated? Any explanation of this, or references to explanations of this, would be

Dear all, I would like to obtain the Brier score prediction error at different times t for an extended Cox model. Previously I have used the 'pec' function (pec{pec}) to obtain prediction error curves for standard Cox PH models but now I have data in the counting process format (I have a covariate with a time-varying effect) and it seems that the pec function does not support the counting

Hi, I have probability estimates from two predictive models. I have these estimates and also a binary outcome for a validation data set not used in calibrating either model. I would like to calculate the Brier score for both models on this binary outcome and test the hypothesis that the Brier scores are equal from the two models. I have not been able to find an R function to do this, can

Hi, I am attempting to evaluate the prediction error of a coxph model that was built after feature selection with glmnet. In the preprocessing stage I used na.omit (dataset) to remove NAs. I reconstructed all my factor variables into binary variables with dummies (using model.matrix) I then used glmnet lasso to fit a cox model and select the best performing features. Then I fit a coxph model

Hi, I have a Type * which may come from an IntegerType as shown below: Type.getIntegerBitWidth() tells me numBits. But how to extract the IntegerType.getSignBit? If pType isIntegerType, I need to know if it is signed or unsigned... How to achieve this? Thx Alex llvm::Type * getRandomValid_IntegerType(llvm::LLVMContext &C) { using namespace llvm; //--- determine num of bits

Hi all, can I access the numeric limits of the llvm types, e.g. HalfTy, FloatTy, DoubleTy, etc. in a fashion like the std numeric_limits tool? std::numeric_limits<half>::min() std::numeric_limits<half>::max() In c++API, I want to initialize values and need to know the correct range for the llvm types.... Thx Alex

Hi Dear R-users I have a database with 18000 observations and 20 variables. I am running cox regression on five variables and trying to use survfit to plot the survival based on a specific variable without success. Lets say I have the following coxph: >library(survival) >fit <- coxph(Surv(futime, fustat) ~ age + rx, data = ovarian) >fit what I am trying to do is plot a survival

On Aug 31, 2010, at 9:03 AM, Talin wrote: > 4) What is the meaning of the "inlinedAt" argument for DebugLoc::get()? Does it mean the location where the inlined code was defined, or the location where it was expanded? the location where it was expanded - Devang

Hi all! To clarify, it must have been removed from the copy-pasta, but “net ads join -U” did produce a password prompt as expected. The dig command produced the following: root at host:~$ dig -t SRV _ldap._tcp.domain.local ; <<>> DiG 9.9.5-9+deb8u6-Debian <<>> -t SRV _ldap._tcp.domain.local ;; global options: +cmd ;; Got answer: ;; ->>HEADER<<- opcode:

Hello, I would like to get the likelihood ratio and score tests for specific variables in a multivariate coxph model. The default is Wald, so the tests for each separate variable is based on Wald's test. I have the other tests for the full model but I don't know how to get them for each variable. Any idea? David Biau. [[alternative HTML version deleted]]

Looks like the GSO is involved? I got this while running Dom0 only (no guests), with a BOINC/Rosetta@home application running on all 4 cores. changeset: 10649:8e55c5c11475 Build: x86_32p (pae). ------------[ cut here ]------------ kernel BUG at net/core/dev.c:1133! invalid opcode: 0000 [#1] SMP CPU: 0 EIP: 0061:[<c04dceb0>] Not tainted VLI EFLAGS: 00210297 (2.6.16.13-xen

It seems to me that summary for ridge coxph() prints summary but returns NULL. It is not a big issue because one can calculate statistics directly from a coxph.object. However, for some reason the score test is not calculated for ridge coxph(), i.e score nor rscore components are not included in the coxph object when ridge is specified. Please find the code below. I use 2.9.2 R with 2.35-4 version

Hi all! I had originally been using a DHCP-assigned address. I have now switched to a static IP, but that didn't solve the problem (same error message). I'm attaching my resolv.conf, nsswitch.conf and krb5.conf files. I have not manually altered either of them, although krb5.conf appears to have been updated by some tool somewhere along the way because my domain is listed as the

My question is, how to compute hazard function(H(t)) after building the coxph model. I even aware of the terminology that differs from hazard function(H(t)) and the hazard rate(h(t)). Here onward I wish to calculate both. Here what I have done in two different methods; ##########################################################################################

Hi folks, With this series, the bulk of the work of pvops64 is done. Here, I integrate most of the paravirt.c and paravirt.h files, making them applicable to both architectures. CONFIG_PARAVIRT is _not_ present yet. Basically, this code is missing page table integration (patches currently being worked on by Jeremy). Enjoy

Hi folks, With this series, the bulk of the work of pvops64 is done. Here, I integrate most of the paravirt.c and paravirt.h files, making them applicable to both architectures. CONFIG_PARAVIRT is _not_ present yet. Basically, this code is missing page table integration (patches currently being worked on by Jeremy). Enjoy

Here are some issues that I am unclear about. What would be great is if the answers could be incorporated into the comments and documentation for DIFactory and DebugInfo.h: 1) What types of DIScope are valid arguments for DebugLoc::get()? The method takes an MDNode* argument, so looking at the function signature is no help. For example, DIFile is a subtype of DIScope, however looking at