search for: reclassification

...Cox model? > I believe I saw someone mentioning the possibility, but I can't find the > syntax in the R help. > > Thanks, > Peter Godsk ----- Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/NRI-reclassification-table-improveProb-Cox-tp4653768p4653770.html Sent from the R help mailing list archive at Nabble.com.

Dear all, I am interested 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 poss...

Dear Sirs. I am working with the R packages Hmisc and PredictABEL to make NRI estimates from my Cox models with and without a specific biomarker. According to Pencina et al (Statistics in Medicine 2010, DOI: 0.1002/sim.4085 ), a continuous/non-categorical NRI (NRI>0) is to be used when there are no obvious reason to categorize risk, such as the risk of future cardiovascular events in patients

Hi all, Is the reclassify function useful for really reclassifing ? I couldnt find any samples or documents about this function. I want to pick a packet that''s over a specific rate, and reclassify that to arbitrary class that I specify. I''ve tested with the ingress filter, but it didnt work. (the script below in the ingress, and a simple qdisc, class structure at the egress)

Hi, I am trying to calculate net reclassification improvement (NRI) and Inegrated Discrimination Improvement (IDI) for a survival dataset to compare 2 risk models. It seems that the improveProb() in Hmisc package does this only for binary outcome, while rcorrp.cens() does take survival object, but doesn't output NRI or IDI. Can anyone suggest...

...ave generated several ROC curves and would like to compare the AUCs. The data are cross sectional and the outcomes are binary. I am testing which of several models provide the best discrimination. Would it be most appropriate to report AUC with 95% CI's? I have been looking in to the "net reclassification improvement" (see below for reference) but thus far I can only find a version in Hmisc package which requires survival data. Any idea what the best approach is for cross-sectional data? Thanks Pencina MJ, D'Agostino RB Sr, D'Agostino RB Jr, Vasan RS. Evaluating the added predictive a...

Dear all I have used the lda and predict functions to classify a set of objects of unknown origin. I would like to use a jackknife reclassification to assess the degree to which the outcomes deviate from that expected by chance. However, I can't find any function that allows me to do this. Any suggestions of how to generate the jackknife reclassification to assess classification accuracy? (BTW, commands I used to generate predictions appen...

Dear All, I am using a specific approach for my master thesis. In essence, a supervised reclassification is used as an intermediate step to find chemical parameters which are able to reclassify defined groups. These variables will be used in a next step where location and scale estimators of the groups are important. Traditionally linear discriminant analysis is used for reclassification which uses gr...

Dear all I am trying to compare the performances of several methods using the AUC0.1 and not the whole AUC. (meaning I wanted to compare to AUC's whose x axis only goes to 0.1 not 1) I came to know about the Mcneil Hanley test from Bernardo Rangel Tura and I referred to the original paper for the calculation of "r" which is an argument of the function cROC. I can only find the

...diction") library(MASS)#get lda for (i in c(1:4)) { for (k in c(1:4)) { if(i==k)break()#using the same variable will not work in lda dis<-lda(g~var[,i]+var[,k],CV=TRUE,fold=6)#linear discriminant function ct<-table(g,dis$class) pre<-sum(diag(prop.table(ct)))# Prediction of cv-reclassification #store the results *a<-i+4*(k-1)* store[a,1]<-paste(label[i],label[k]) store[a,2]<-round(pre,4) } } store/ I have got two for-loops getting "disturbed" by an if-break-case (disturbed means, that I don?t need the information for these cases). By using /*a<-i+4*(k-1)*/ fo...

Hello Thanks to Frank Harrell for the great Design package. I noted from Pencina's Article (Statistics in Medicine Vol 27, pp157-172) that the result obtained for the Net Reclassification Index depends upon categorical cut-offs for risk (eg in the paper <6%, 6-20% and >20%). I wondered how the improveprob function arrives at its cut-offs, and whether there was any function to change the default cut-offs used. Thanks for any help you can offer. Yours sincerely David McAllist...

Dear list, I am trying to work out how the improveProb() function works and how to interpret the results, and I have a few questions. I would be grateful if anyone could shed some light on these. in the Net Reclassification Improvement section of the output, is the 2P column the two-sided p-value for the differences in classification? So if a limit is set at 0.05, then lower values indicate significant differences in the classification of both models? is the index value the actual percentage of improvement? Could thi...

Hi! I replace some elements of a matrix a > a [,1] [,2] [,3] [1,] 1 2 3 [2,] 4 5 6 [3,] 7 8 9 [4,] 10 11 12 according to a reclassification matrix such > pares [,1] [,2] [1,] 1 2 [2,] 5 6 [3,] 8 7 to get > b [,1] [,2] [,3] [1,] 1 2 3 [2,] 4 5 6 [3,] 7 8 9 [4,] 10 11 12 As both a and pares can be very large, I'd like to know the fastest way for this operation in...

Hi, I would like to compare differences in AUC from 2 different models, glm and gam for predicting presence / absence. I know that in theory the model with a higher AUC is better, but what I am interested in is if statistically the increase in AUC from the glm model to the gam model is significant. I also read quite extensive discussions on the list about ROC and AUC but I still didn't find

I'm trying to do a rewrite of the dspam_plugin for dovecot 1.1b1. There are some API changes that warranted an update of the plugin. Also, I wanted the dspam_plugin to be able to handle pristine mails for dspam retraining, as opposed to the signature based retraining. Question: How can I retrieve the full unix path for a specific mail? The original code uses mail_get_first_header() to

Dear R-Help, I have a clustering problem with hclust that I hope someone can help me with. Consider the classic hclust example: hc <- hclust(dist(USArrests), "ave") plot(hc) I would like to cut the tree up in such a way so as to avoid small clusters, so that we get a minimum number of items in each cluster, and therefore avoid singletons. e.g. in this example, you can see

Hello, What exactly is the use of the "reclassify" option in the policing options of tc filters? According to LARTC: " reclassify Most often comes down to reclassification to Best Effort. This is the default action. " I don''t quite get the meaning of that. It could mean to let other filters handle it, but that is exactly the "continue" option. Could someone explain how this option is used? Thanks

Hi, on my small Xen-virtualised server with 48 MiB RAM I use Postfix and Dovecot, because the Debian administrators dislike qmail [1], which is in my opinion despite some maintainability and code quality issues a quite well designed software, because it mostly follows the UNIX principles. Postfix is not able to sort my E-Mail into different Maildir folders and after I looked at procmail's