search for: prognost

I am trying to develop a prognostic model using logistic regression. I built a full , approximate models with the use of penalization - design package. Also, I tried Chi-square criteria, step-down techniques. Used BS for model validation. The main purpose is to develop a predictive model for future patient population. One...

Dear all, I am using R 2.9.2 on Windows XP. I am undertaking a simulation study to consider methods of external validation in the context of missing covariates in the validation data set. I would like to use Royston's measure of prognostic separation as a method of external validation. Although there is no R code for this, the author informs me that it should be easy: 1. Calculate the linear predictor xb from the proportional hazards model or other model of interest. 2. Calculate the ranks r1,...,rn of xb. In case of ties, do not...

Hi, In the boot package, the original statistic is simply the statistic function evaluated on the original data (called t0). However, in Harrell et al 1996 "Multivariable prognostic models..." Stats Med vol 15, pp. 361--387, it is different (p. 372): The statistic function evaluated on the original data is called "D_app" (apparent statistic), whereas "D_orig" (original statistic) is derived by first fitting the model to a bootstrap sample, then freez...

...maybe but how often do >you actually see exponential KM curves in real life? Exponential curves are rare. But proportional hazards does not imply exponential. > A trial design could in fact try to get all the control sample to "event" at the same time if enough was known about prognostic factors and natural trajectory You are a dreamer. We know very little about even the diseases we know best. The life insurers are in no danger yet from accurate predictions by the medical community. Terry T

Hi, I would like to use a random Forest model to get an idea about which variables from a dataset may have some prognostic significance in a smallish study. The default for the number of trees seems to be 500. I tried changing the default to ntree=2000 or ntree=200 and the results appear identical. Have changed mtry from mtry=5 to mtry=6 successfully. Have seen same problem on both a Windows machine and our linux sys...

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)...

Hi, I was reading a paper published in JCO "Prediction of risk of distant recurrence using 21-gene recurrence score in node-negative and node-positive postmenopausal patients with breast cancer treated with anastrozole or tamoxifen: a TransATAC study" (ICO 2010 28: 1829). The author uses a method to estimate the 9-year risk of distant recurrence as a function of continuous recurrence

Hi R experts, I am trying to do a prognostic model validation study, using cancer survival data. There are 2 data sets - 1500 cases used to develop a nomogram, and another of 800 cases used as an independent validation cohort. I have validated the nomogram in the original data (easy with the Design tools), and then want to show that it als...

Dear list   I have 5 markers that can be used to detect an infection in combination. Could you please advise me how to use functions in ROCR/ other package to produce the ROC curve for a combination of markers?   I have used the following to get ROC statistics for each marker. pred <- prediction(y$marker1, y$infectn) perf <-performance(pred,"tpr","fpr")

> How's forever work for you? ;-> Absolutely FINE thank you! When your WizWonder package is housebroken, let me try it if I'm interested. Until then, a (stubbornly) broken distro will persuade me to try something else. That's why I left Windows, I guess, if you prognosticate correctly, it will be why I leave RedHat/CentOS. btw this has nothing to do with Firewalls at all. I bought a firewall (router) and use it. If I had to upgrade firewall firmware versions, and the new versions broke running applications, I'd consider the new firewall firmware BROKEN....

...nformaticians, or R programmers to support molecular diagnostics, with open positions in Cambridge MA, USA (priority) and in Basel Switzerland (possible). We do a range of data analyses across product lifecycle (research, tech dev, clin dev, market access) to support the development of prognostic and predictive diagnostics. And of course, our main computational platform is R (using Emacs / ESS / org-mode for workflow, SNOW and add-ons for computation, etc), on a mixture of Microsoft and Linux workstations and clusters. Knowledge of "classic" experimental desi...

Dear all, I am comparing logistic regression models to evaluate if one predictor explains additional variance that is not yet explained by another predictor. As far as I understand Baron and Li describe how to do this, but my question is now: how do I report this in an article? Can anyone recommend a particular article that shows a concrete example of how the results from te following simple

...extracted for each factor level in a stratified Cox proportional hazard regression model? I have a cancer data set where the variable ?differentiation? is a factor with three levels: poor, intermediate and good. I would like to extract the hazard ratio for each grade level and relate it to another prognostic factor. I?ll appreciate very much if somebody helps me sort out this. Sincerely, Dora

...bly time-varying effects. My data are in counting process format as described in Therneau&Grambsh's `Modeling Survival Data', page 68. I'm trying to follow Harrell's `Regression Modeling Strategies' advices for the choice of my model. This study aims to the development of a prognostic model, so it'is primary predictive. I have to do stepwise model selection and provide a measure of predictive accuracy. I'm using rms's cph and validate function with bw=TRUE option. </framwork> <questions> 1. Is validate good at resampling from a counting process format...

I posted a while back about getting very slow writes. People suggested modifying (increasing) SO_SNDBUF and SO_RCVBUF and this actually helps enormously. However, there is obviously something still not right. Writes are still about 1/2 the speed of reads. This only seems to affect Win95 clients (NT machines are fine). Doing a write of a 20mb file to the server generates the following message:

...) or cph(Design). I have time varying effects (diagnosed with schoenfeld residuals Chi2 test and graph) so I first want to split time into 2 separate intervals : t<6months and t>=6months, to estimate one hazard ratio (hr) for each interval. I am analysing Overall survival according to 3 prognostic factors (age,deep,ldh). my dataframe (dtemp) looks like this: > dtemp[1:3,] id time status age_diag deep ldh 1 1 1.544148 1 65.42368 present elevated 2 2 17.051335 1 46.92676 present elevated 4 4 84.829569 0 65.86448 present normal my first mod...

...9-96. Low-dose hydrocortisone reduces norepinephrine duration in severe burn patients: a randomized clinical trial. Venet F, Plassais J, Textoris J, Cazalis MA, Pachot A, Bertin-Maghit M, Magnin C, Rimmel? T, Monneret G, Tissot S. Crit Care. 2015 Jan 26;19:21. A strategy to build and validate a prognostic biomarker model based on RT-qPCR gene expression and clinical covariates. Tournoud M, Larue A, Cazalis MA, Venet F, Pachot A, Monneret G, Lepape A, Veyrieras JB. BMC Bioinformatics. 2015 Mar 28;16:106. [[alternative HTML version deleted]]

Hi there, I need some help to figure out what is the proper model in survival analysis for my data. Subjects were randomized to 3 treatments in trial 1, some of them experience the event during the trial; After period of time those subjects were randomized to 3 treatments again in trial 2, but different from what they got in 1st trial, some of them experience the event during the 2nd trial (I

I have to study censured datas concernig the occurence of infection at the point of insertion of catheter in patients with renal disease. Catheter may be removed for ather reasons than infection, in this case, the observation is censored. Each has exactly 2 observations. The question are the pronostic factors of infection (the other variables are; age, sex, type of renal disease...). Could you

Dear all, not really a R question but: If I want to check for the classification accuracy of a LDA with previous PCA for dimensionality reduction by means of the LOOCV method: Is it ok to do the PCA on the WHOLE dataset ONCE and then run the LDA with the CV option set to TRUE (runs LOOCV) -- OR-- do I need - to compute for each 'test-bag' (the n-1 observations) a PCA