search for: royston

Dear R-list readers: Royston described the effect of sample size on the p-value obtained from the Shapiro-Francia test (Estimating departure from normality. Stat Med 1991;10:1283-93). He developed two indices from the Shapiro-Francia test (i) V' - an index of departure from normality and (ii) v' - a plot o...

...ort only the linear predictor of the Cox model. I have used Harrell's c index for censored data (rcorr.cens) as a measure of discrimination and have constructed smoothed calibration plots. I would like to include some measures of overall model performance, such as the censored Brier score and Royston/Sauerbrei's D statistic (Stat Med 2004). With this in mind, I have 3 questions: 1) Can the "sbrier" function of the "ipred" library be used to calculate the censored Brier score for a specific time point given known predictions for that timepoint? library(ipred) data &l...

Dear R I am trying to understand and use the flexible parametric survival model suggested by Royston and Parmar. However I am stuck trying to plot the adjusted survival curves for different covariates in the following code: library(flexsurv) library(graphics) spl <- flexsurvspline(Surv(futime, fustat) ~ rx+ecog.ps+resid.ds+age, data = ovarian, k=2, scale="odds") spl the code "p...

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 x...

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

...sleep[rep(1:nrow(sleep),10),] coef(summary(glm(extra ~ group, data=sleep10))) coef(summary(glm(extra ~ group, data=sleep10, weights=rep(0.1,nrow(sleep10))))) My reason for asking is so that I can fit a model to a stacked multiple imputation data set, as suggested by: Wood, A. M., White, I. R. and Royston, P. (2008), How should variable selection be performed with multiply imputed data?. Statist. Med., 27: 3227-3246. doi: 10.1002/sim.3177 Other suggestions would be most welcome. _______________________________________________ Steve Taylor Biostatistician Pacific Islands Families Study Faculty of...

...onths sooner (Oct 31 2006) according to <http://www.freebsd.org/security/index.html> If 5.4 is expected to be an extended-life branch, I would consider moving them up to 5.4 instead, to get a leap on current technology. Has that decision been made yet? -- Clifton -- Clifton Royston -- cliftonr@tikitechnologies.com Tiki Technologies Lead Programmer/Software Architect "I'm gonna tell my son to grow up pretty as the grass is green And whip-smart as the English Channel's wide..." -- 'Whip-Smart', Li...

Howyd all? Seems that I have been routed. Possibly by a physical B&E, but who knows? Probably some of you do.... anyways, some politically sensitive email was deleted from a user account and the line low -tr & inserted into my .xinitrc . Duncan (Dhu) Campbell

Hi, Does anyone know if the D'agostino test is available with R ? Alex

These are new boxes. http://www.supermicro.com/products/system/1U/5015/SYS-5015B-MT.cfm core 2 Q6600 CPU 8Gb 667 RAM Boxes were memtested from Fri-Mon okay. 6.3-RELEASE (amd64) installs fine. Build cycle okay. Running (no load) for a week or so. However, when I try to configure gmirror they hang on boot. After some fiddling it appears issuing #kldload geom_mirror hangs the boxes very hard.

Hi, I am using logistic regression to classify a binary psychometric data. using glm() and then predict.glm() i got the predicted odds ratio of the testing data. Next i am going to plot ROC curve for the analysis of my study. Now what i will do: 1. first select a cut-off (say 0.4) and classify the output of predict.glm() into {0,1} segment and then use it to draw ROC curve using ROCR package

...a port, but in a similar fashion of for example, > isn't sudo important enough to be included as an imported tool in the > base system? Usually I've installed it as a package off the install CD, before the system is even booted the first time. -- Clifton -- Clifton Royston -- cliftonr@tikitechnologies.com Tiki Technologies Lead Programmer/Software Architect "My own personal theory is that this is the very dawn of the world. We're hardly more than an eyeblink away from the fall of Troy, and scarcely an interglaciation removed from the Altamira c...

I am new to R, and I am trying to cut a continuous variable BMI into different categories and can't figure out how to use it. I would like to cut it into four groups: <20, 20-25, 25-30 and >= 30. I am having difficulty figuring the code for <20 and >=30? Please help. Thank you. -- View this message in context:

...test(test1) > $W: > [1] 0.9606107 > > $n: > [1] 76 > > $p: > [1] 0.06176898 > > +++++++++++++++++++++++++++++++++++++++++++ > "Shapiro.Wilk.test" <- function(x) > { > # > #This function is an S version of the procedure described by > # J. P. Royston (1982) in "An Extension of Shapiro and Wilk's W Test > # for Normality to Large Samples" from Applied Statistics, 31 no.2 > # pp. 115-124. > # > n <- length(x) > index <- 1:n > m <- qnorm((index - 0.375)/(n + 0.25)) > y &l...

Hi, could anyone give recommendations (or share experience) regarding using ZFS: - FreeBSD 7-Stable (amd64 with 8GB RAM) + special tuning necessary (apart from increasing kernel memory to 1 or more GB for ZFS) - Samba 3.2 + ACLs possible directly under ZFS? + recommended compile options? - NFS - email (imap) - jails (I have seen some problems exist with using snaphots within

Hi Adrian, Sunday, April 4, 2004, 10:22:33 PM, you wrote: AP> We have thought about using static MAC entries per port on managed AP> switches installed at the client endpoints, but that would require a AP> overwhelming budget. We are also thinking about L2TP and PPPoE, but I AP> am uncertain about compatibility. AP> What would you recommand ? Are there any other elegant

I successfully did my first FreeBSD upgrade yesterday after looking at the manual, and cross referencing with Googling and getting help from our network engineer here at CWU. Before the upgrade, running df showed: Filesystem 1K-blocks Used Avail Capacity Mounted on /dev/da0s1a 507630 77662 389358 17% / devfs 1 1 0 100% /dev /dev/da0s1e

Hello again :) With POLLING enabled I experience about 10%-25% performance drop when copying files over network. Tested with both SAMBA and NFS. Is it normal? FreeBSD 7.1-PRERELEASE #0: Sat Sep 6 01:52:12 CEST 2008 fxp0: <Intel 82801DB (ICH4) Pro/100 Ethernet> port 0xc800-0xc83f mem 0xe1021000-0xe1021fff irq 20 at device 8.0 on pci1 # ifconfig fxp0 fxp0:

We have 10 SuperMicro PDSMi+ 5015M-MTs that are panic'ing every few days. This started shortly after upgrade from 6.2-RELEASE to 6.3-RELEASE with freebsd-update. Other than switching to a debugging kernel, a little sysctl tuning, and patching with freebsd-update, they are stock. The debugging kernel was built from source that is also being patched with freebsd-update. These systems are

Howdy list, Sorry if this is a frequently discussed topic, or an off-topic question, but I couldn't find much info about my question by performing quick searches in the archives, and my question is pretty tightly related to security... Background: =========== I have a number of FreeBSD machines. Most are 4.x, but a few are 5.x (mainly the testing/devel machines). I also have a single Red