similar to: Are unpaired data suitable for Hmisc's improveProb ?

Dear, I wanna to compare AUC generated by two distribution models using the same sample. The AUC for model 1 consists of two columns, column A for 0/1 and column B for probability, eahc with the same row number of 3000. The AUC for model 2 consists of two columns, column A for 0/1 and column B for probability, eahc with the same row number of 10000 rows. I am wondering what value I should put

Dear, I wanna to compare AUC generated by two distribution models using the same sample. I tried improveProb function's example code below. set.seed(1) library(survival) x1 <- rnorm(400) x2 <- x1 + rnorm(400) d.time <- rexp(400) + (x1 - min(x1)) cens <- runif(400,.5,2) death <- d.time <= cens d.time <- pmin(d.time, cens) rcorrp.cens(x1, x2, Surv(d.time, death))

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

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

Hello, This is Elaine. I am using R 3.0 to download package vegan but failed. The warning message is package ‘vegan’ successfully unpacked and MD5 sums checked Warning: unable to move temporary installation ‘C:\Users\elaine\Documents\R\win-library\3.0\file16c82da53b1b\vegan’ to ‘C:\Users\elaine\Documents\R\win-library\3.0\vegan’ I cannot find the folder \file16c82da53b1b\ below

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

Greetings, I have 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

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

Dear, I am a newbie to R. Now I am learning to draw boxplot using graphics(). I want to highlight the median position with a round point and the value left (or on the top of)to the point. Please kindly share the command and thank you. Elaine [[alternative HTML version deleted]]

Hello, I want to know if two quadratic regressions are significantly different. I was advised to make the test using step 1 bootstrapping both quadratic regressions and get their slope coefficients. (Let's call the slope coefficient *â*^1 and *â*^2) step 2 use the slope difference *â*^1-*â*^2 and bootstrap the slope coefficent step 3 find out the sampling distribution above and

Hello, I have a matrix (class matrix) composed of GridCell (row and column). The matrix value is the beta diversity index value between two grids. Now I would like to get the average value of each GridCell. Please kindly advise how to make the calculation. Thank you. Elaine The matrix looks like (cited from Michael Friendly) I would like to get the average value of each color. Obs

Dear list I have a matrix composed of islandID as rows and speciesID as columns. IslandID: Island A, B, C….O (15 islands in total) SpeciesID: D0001, D0002, D0003….D0100 (100 species in total) The cell of the matrix describes presence (1) or absence (0) of the species in an island. Now I would like to search the species with absence (0) in all the islands (Island A to Island O.)

Dear List, This is Elaine, a postgraduate studying in bird distributions in East Asia. I want to calculate Simpson dissimilarity index, based on a presence/absence matrix of bird species in islands in East Asia. (matrix row: 36 islands/matrix column: species ID) (R package vegan to make NMDS and R package betapart) In most papers using vegan for NMDS and betapart for dissimilarity

As describe in the Hmisc package's improveProb function, that function is for binary Y. And it's best to use category-free methods. Frank Petergodsk wrote > Hi > > I'm new to R. > > Is it possible to use the improveProb function to generate categorybased > NRI using a Cox model? > I believe I saw someone mentioning the possibility, but I can't find the

Hello, I am making a boxplot of 13 boxes. I tried to color the box using 13 colors but failed. Only red and brown were displayed. Green, blue, and grey disappeared. Please kindly advise modification after checking the code below. Thank you in advance. Elaine R code # data input dataN <-read.csv("H:/a_mig_distance_B_NB/R_data/Mig_bird_586_20120925.csv",header=T, row.names=1)

Dear List, I want to compare the presence and absence of bird species based on the sites in a matrix. The matrix has 5 rows for Island A, B, C, D, and E. It has 100 columns for bird species D001-D100. In each cell of the matrix, the presence-absence of bird species will be recorded as 1 or 0. (For example, if species D001 is found on Island D, the matrix cell of species D001 and Island D

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")

Dear List, I ran a regression model using lm and produced a regression line using abline. The line ranges from -20 to 20 in x axis, and the section I only want is from -20 to 0. Please kindly advise any function in abline () to set the range of x axes. Thank you Elaine [[alternative HTML version deleted]]

Hello I have a table describing butterfly range traits. It is composed of three columns as below Species name range size (X) latitude of range midpoint (Y) There are 11 kinds of butterflies. Each has its range size, and the latitude of each range midpoint ranges from 9 to 19. I would like to have the average range size of every degree of latitude. For example, the average range

Dear List, I am using plot for homework. The x-axis covered from 0 to 80, with 4 intervals. However, the plot only showed 0, 40, 80. 20 and 60 disappeared. Please kindly advise how to show 0, 20, 40, 60, 80 for the axis interval. Thank you. Elaine [[alternative HTML version deleted]]