similar to: convenient way to calculate specificity, sensitivity and accuracy from raw data

Dear R-colleagues, I am quite a newbie to R fighting my stupidity to solve a probably quite simple problem of generating artificial data with defined features. I am conducting a study of inter-observer-agreement in child-bronchoscopy. One of the most important measures is Kappa according to Fleiss, which is very comfortable available in R through the irr-package. Unfortunately medical doctors

Dear R-colleagues, another question from a newbie: I am creating a lot of simple pivot-charts from my raw data using the reshape-package. In these charts we have medical doctors judging videos in the columns and the videos they judge in the rows. Simple example of chart/data.frame "input" with two categories 1/0: video 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 1 1 0 0

Hi All, I am using fleiss kappa for inter rater agreement. Are there any know issues with Fleiss kappa calculation in R? Even when I supply mock data with total agreement among the raters I do not get a kappa value of 1. instead I am getting negative values. I am using the irr package version 0.70 Any help is much appreciated. Thanks and Regards M [[alternative HTML version deleted]]

I'm looking for a function in R that extends kappa to multiple raters when there is more than one response per subject. For example, say a group of doctors have to assign diseases to patients. Each patient will be assigned one to many diseases, and the number of doctors assigning diseases to any one patient will be two to many. Here's an extremely simple example of the type of data I

I am running my code in a loop and it does not work but when I run it outside the loop I get the values I want. n <- 1000; # Sample size fitglm <- function(sigma,tau){ x <- rnorm(n,0,sigma) intercept <- 0 beta <- 0 ystar <- intercept+beta*x z <- rbinom(n,1,plogis(ystar)) xerr <- x + rnorm(n,0,tau) model<-glm(z ~ xerr, family=binomial(logit))

The irr package seems to install correctly: > install.packages("irr") trying URL 'http://cran.us.r-project.org/src/contrib/irr_0.61.tar.gz' Content type 'application/x-tar' length 13848 bytes opened URL ================================================== downloaded 13Kb * Installing *source* package 'irr' ... ** R ** data ** help >>>

Hi, I have two sets of sensitivity, specificity, positive predictive value, and negative predictive value, and accuracy from two tests on the same subjects. Is there an R package that does such paired comparisons? Thanks, Gang Chen

Dear R colleagues, consider my data.frame named "df" with 3 columns - being level, prevalence and sensitivity - and 7 rows of data (see dump below). df <- structure(list(level = structure(1:7, .Label = c("0", "1", "10", "100", "1010", "11", "110"), class = "factor"), prevalence = structure(c(4L, 2L, 3L,

Hello, I have 50 raters and 180 cases which are rated as malignant, probably malignant, probably benign, and benign. I want to compare all the raters but I want a weighted kappa to penalize differences between malignant and benign more than differences between malignant and probably malignant. I only found the weighted option in the 2-rater functions (kappa2, wkappa, cohen.kappa). The

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Hi, I have a scenario where a doctor can have one or more specialties. For each doctor, one and only one of her specialties can be designated as primary. So I have tables called doctors, specialties, and doctors_specialties, the last of which has a boolean is_primary column. The doctor model class specifies that: has_and_belongs_to_many :specialties I want to enforce, at the lowest possible

Hi, I am a graduate student applying published R scripts to compare the classification accuracy of 2 predictive models, one built using discriminant function analysis and one using random forests (webpage link for these scripts is provided below). The purpose of these models is to predict the biotic integrity of streams. Specifically, I am trying to compare the classification accuracy (i.e.,

Hi, Is there a way when doing logistic regression for the output to spit out accuracy, sensitivity, and specificity? I would like to know these basic measures for my model. Thanks! [[alternative HTML version deleted]]

First of all, let me apologize, as this is probably an absurdly basic question. I did search before asking, but perhaps my ineptitude didn't allow me to apply what I read to what I'm doing. Totally new to R, and haven't done any code in any language in a long time. Basically I've got categories. They're department codes for doctors (say, 9999 for radiology or 5555 for

Hello there, newbie speaking Let''s say I have: class Office has_many :holidays #(just a list of dates when the office is closed) has_many :doctors #doctors who work in the office end class Doctor belongs_to :office has_many :holidays #(additional dates when this doctor is not available) end class Holiday (has a office_id, doctor_id and a date field) end From the app standpoint I

Dear all, My question might be more of a statistics question than a question on R, although it's on how to apply the 'quantreg' package. Please accept my apologies if you believe I am strongly misusing this list. To be very brief, the problem is that I have data on only a random draw, not all of doctors' patients. I am interested in the, say, median number of patients of

Hi, My questions concerns the ROCR package and I hope somebody here on the list can help - or point me to some better place. When evaluating a model's performane, like this: pred1 <- predict(model, ..., type="response") pred2 <- prediction(pred1, binary_classifier_vector) perf <- performance(pred, "sens", "spec") (Where "prediction" and

Dear Guru's, Is there a package (R of course) with programs for diagnostics - roc, sens , spec, kappa etc? Best wishes Fredrik L

hey all, got a rails app i''m finishing up. i have a little ajax on one of my pages where the person can choose a doctor from a drop down list and if the doctor isn''t there they can click a link which blinds down a little form to add a doctor. after they submit that mini-form the page updates the div which houses the drop-down so the doctor shows up. works very nicely IN FIREFOX.

Dear R Users, Do you know of an existing function that allows the production of sensitivity and specificity forest plots? See the following for an example: