similar to: Design�s validate() output

Dear list, first accept my apologies for asking a non-R question. Can anyone point me to a good reference on logistic regression? web or book references would be great. I am interested in the use and interpretation of dummy variables and prediction models. I checked the contributed section in the CRAN homepage but could not find anything (Julian Faraway?s "practical Regression and ANOVA

Dear list, this must be an easy one: I have a data.frame of two columns, "ID" with four different levels (A to D) and numerical "size", and each of the 4 different IDs is repeated a different number of times. I would like to get the mean size for each ID as another data.frame. I have tried the following: >ID= as.character(unique(data[,1])) # I use unique() because

Dear list, first apologies for this is not strictly an R question but a theoretical one. I have read that use of k-means clustering assumes sphericity of data distribution. Can anyone explain me what this means? My statistical background is too poor. Is it another kind of distribution, like gaussian or binomial? What does it happen if the distribution is not spherical? Could you give me an

Dear list I would like to compare two measurements of disease severity (M1 and M2), one of the is continuous (M1 ranging from 1 to 10) and the other is ordinal (M2 takes Low, Medium, high and very high). Do you think is ok to use cor() function to test whether the two agree, i.e correlate? I am afraid that if I set M2 to 1,2,3 and 4, the function cor() will take them as continuous and

Dear list, I have a data.frame with nine categorical variables (0,1,2 and NAs) that I would like to get the number of events for each of them. I can extract this using summary() for each variable at a time with the as.factor()argument (otherwise it will get me the mean value): >summary(as.factor(mydf[,3])) 0 1 2 NA's 194 67 4 2 Trying to use apply() to get this for

Dear list, I have a categorical variable in a data.frame that I would like to plot using a histogram to show number of events. Values are 0, 1 and some NAs. I can?t make the hist() function to 1) include a column with the number of NAs 2) have the x axis to be categorical, I always get 0, 0.2, 0.4,... 1 divisions Can anyone help me? This is my code. "database" is my data.frame and

Dear list, I have a text file from a scanner that includes 20 lines of text (scanner settings) before it actually starts showing the readings in a tabular format (headings are ID, intensity, background and few others). I am a biologist with some experience using R and my question is if it is possible to read this file into an R workspace and store the actual readings in a dataframe,

when i try to validate my logistic regression model: fit<-glm(y~x,binomial,data=dataname,x=TRUE,y=TRUE) validate(fit,method="boot",B=150,...) i get the following error message: Error in UseMethod("validate") : no applicable method for "validate" any insight would be appreciated. many thanks! -- View this message in context:

Hi, I'm developing an experiment with logistic regression. I've come across the lrm function in the Design library. While I understand and can use the basic functionality, there are a ton of options that go beyond my knowledge. I've carefully read the help page for lrm, but don't understand many of the arguments and optional return values. (penalty, penalty.matrix,

Can anyone tell me what I might be doing incorrectly for an ordinal logistic regression for lrm? I cannot get R(2.9.1)to run either summary nor will it let me bootstrp to validate. ### Y is a 5 value measure with a range from 1-5, the independent variables are the same. N=75 but when we knock out the NAs it comes down to 51#### > lrm(formula = Y ~ permemp + rev + gconec + scorpstat, data =

Hi, I've come across a strange error when using the lrm.fit function and the subsequent predict function. The model is created very quickly and can be verified by printing it on the console. Everything looks good. (In fact, the performance measures are rather nice.) Then, I want to use the model to predict some values. I get the following error: "fit was not created by a Design

Buenas, foreros y foreras; No sé si esto es pregunta para hacer acá, lo preguntaría en stackoverfow, si no fuese que el inglés me intimida. Quiero usar el packete `bookdown` para escribir un libro, pero resulta que la salida tiene que ser PDF y no lo consigo. Siguiendo las instrucciones de acá: https://bookdown.org/yihui/bookdown/get-started.html llego a compilar sin ningún problema en formato

I am trying to obtain the AICc after performing logistic regression using the Design package. For simplicity, I'll talk about the AIC. I tried building a model with lrm, and then calculating the AIC as follows: likelihood.ratio <- unname(lrm(succeeded~var1+var2,data=scenario,x=T,y=T)$stats["Model L.R."]) #Model likelihood ratio??? model.params <- 2 #Num params in my model AIC

Gracias por haberte tomado la molestia de indagar. Entiendo que es eso lo que hago en el encabezado YAML, basandome en la explicación del comienzo del punto 3 de acá: https://bookdown.org/yihui/bookdown/output-formats.html Eso mismo, con el documento que propone el propio Yihui (punto 1.2 del mismo libro) no lo consigo compilar a PDF. Y se me hace extrañísimo, porque tampoco me da error ni nada

Según lo entiendo yo, a mí no me funciona. Lo intenté hacer, también, en la consola directamente. Preferiría poder hacerlo en el documento Rmd, pero de momento ni uno ni otro consigo. Si compila lo hace al libro GitBook y listo. Parece imposible. 2018-07-17 20:02 GMT+02:00 Javier Marcuzzi <javier.ruben.marcuzzi en gmail.com> : > Estimado Juan Abasolo > > Yo no lo utilize pero leí

Gracias, Javier, por la paciencia. Soy malo explicándome. Ese ejemplo que me das, que es el que da Yihui Xie, es el que no consigo compilar si no es a GitBook (que es HTML). El mismo Yihui propone en el libro al que nos referimos los dos y el ejemplo en cuestión (referido en el apartado Get Started) modificar el código YAML para compilar en PDF. Efectifvamente, lo que quiero es conseguir que

Gracias, Victor. Tampoco es eso. Si saco la linea site: bookdown::bookdown_site Me sigue compilando en HTML, pero sin hacerlo en todos los capítulos si no solamente el del index.Rmd que tengo abierto. No puedo explicar cuanto me sorprende! Supongo que tendré algún puntito de alguna i que falta y al ponerlo me parecerá tontería. Pero ahora todavía es MISTERIO. 2018-07-18 11:03 GMT+02:00 Víctor

Hi Group, I have a question about obtaining the bias-corrected c-index using validate from the Design library. As an example, consider the example from help page: library(Design) ?validate.lrm n <- 1000 age <- rnorm(n, 50, 10) blood.pressure <- rnorm(n, 120, 15) cholesterol <- rnorm(n, 200, 25) sex <- factor(sample(c('female','male'),

Hi folks, Using R Version 1.6.2 (2003-01-10) on SuSE Linux 7.2, I just installed Hmisc_1.5-3.tar.gz and Design_1.1-5.tar.gz These were taken from http://hesweb1.med.virginia.edu/biostat/s/library/r Checked the dependencies: Hmisc: grid, lattice, mva, acepack -- all already installed Design: Hmisc, survival -- survival already installed, so installed Hmisc first All seems to go

Dear R users I use Windows XP, R2.5.1 (I have read the posting guide, I have contacted the package maintainer first, it is not homework). In a research project on renal cell carcinoma we want to compute Harrell's c index, with optimism correction, for a multivariate Cox regression and also for some univariate Cox models. For some of these univariate models I have encountered an error