search for: biochemist

Dear R helpers, running the following code of a glm model of the family poisson, gives predicted values < 0. Why? library(MASS) library(stats) library(mvtnorm) library(pscl) data(bioChemists) poisson_glm <- glm(art ~ fem + mar + kid5 + phd + ment, data = bioChemists, family = poisson) predicted.values = predict(poisson_glm) range(predicted.values) Thank you in advance for any hints. Best regards, P. Olsson [[alternative HTML version deleted]]

...lly like the numbers themselves. Thus, I'm looking at a recent JAMA article in which both numbers and dotplot of RR and 95% CI are presented and wondering about best way to do this in R. Essentially, the plot has 3 columns: variable names, RR and 95% CI, and dotplot of the same. Using the bioChemists data in the pscl package and errbar function in Hmisc package, the code below is in the right direction... but still pretty ugly. Wondering if folks would have alternative suggestions about how to go about this, or pointers on cleaning up the code below (eg, I know there are many functions fo...

...Or do I have to use bootstrap? What I tried until now is to use bootstrap to estimate these intervals. Any comments on the code are welcome. The data and the model are based on the examples in zeroinfl(). #aproximate prediction intervals with Poisson regression fm_pois <- glm(art ~ fem, data = bioChemists, family = poisson) newdata <- na.omit(unique(bioChemists[, "fem", drop = FALSE])) prediction <- predict(fm_pois, newdata = newdata, se.fit = TRUE) ci <- data.frame(exp(prediction$fit + matrix(prediction$se.fit, ncol = 1) %*% c(-1.96, 1.96))) newdata$fit <- exp(prediction$fit)...

Hi, I am a little confused at the output from predict() for a zeroinfl object. Here's my confusion: ## From zeroinfl package fm_zinb2 <- zeroinfl(art ~ . | ., data = bioChemists, dist = "negbin") ## The raw zero-inflated overdispersed data > table(bioChemists$art) 0 1 2 3 4 5 6 7 8 9 10 11 12 16 19 275 246 178 84 67 27 17 12 1 2 1 1 2 1 1 ## The default output from predict. It looks like it is doing a horrible j...

Hi, I am trying to replicate Lambert (1992)'s simulation with zero-inflated Poisson models. The citation is here: @article{lambert1992zero, Author = {Lambert, D.}, Journal = {Technometrics}, Pages = {1--14}, Publisher = {JSTOR}, Title = {Zero-inflated {P}oisson regression, with an application to defects in manufacturing}, Year = {1992}} Specifically I am trying to recreate Table 2. But my

...hat's possible, for any *particular, individual* subject. Others will undoubtedly know better than I. --Chris Ryan Sorkin, John wrote: > I am running a zero inflated regression using the zeroinfl function similar to the model below: > > fm_zinb2 <- zeroinfl(art ~ . | ., data = bioChemists, dist = "poisson") > summary(fm_zinb2) > > I have three questions: > > 1) How can I obtain a value for the parameter pie, which is the fraction of the population that is in the zero inflated model vs the fraction in the count model? > > 2) For any particular subj...

Hello ; I am doing a regression of count data (number of award and there are some covariates) I have estiamted the parameters of negative binomial distribuion (lambda is a function of covaraites, GLM model) by glm.nb function and training dataset. Now I want to predict the number of award (for example y=0, y=1, y=2,) or testing dataset. I dont know how to calculate this numbers? I would be very

...m course notes, available on the package's CRAN page, uses the following example on page 102: m5d.1 <- MCMCglmm(art ~ trait - 1 + at.level(trait, 1):fem + at.level(trait, 1):mar + at.level(trait, 1):kid5 + at.level(trait, 1):phd + at.level(trait, 1):ment, rcov = ~idh(trait):units, data = bioChemists, prior = prior.m5d.1, family = "zipoisson", verbose = FALSE) I have been unable to find an answer to the following questions and would appreciate any guidance: 1) Does at.level(trait, 1) index the poisson latent variable, or is that at.level(trait,2)? More generally, how does one fin...

Good Day All, I have a negative binomial model which I have developed using the MASS library. I now would like to develop some predictions from it. Running the predict.glm (stats library) using type="response" gives me a non-integer value which was rather puzzling. I would like to confirm that this is actually the mean predicted value of the probability mass function as opposed

Please help getting the R squared value in asymptotic regression model I use the code below model1<-nls(GN1~SSasymp (nrate,a,b,c), data = data.1 ) and R produced the modell coefficients without the R squared value? -- Ahmed M. Attia Research Assistant Dept. Of Soil&Crop Sciences Texas A&M University ahmed <ahmedatia@zu.edu.eg>.attia@ag.tamu.edu Cell phone:

I am running a zero inflated regression using the zeroinfl function similar to the model below: fm_zinb2 <- zeroinfl(art ~ . | ., data = bioChemists, dist = "poisson") summary(fm_zinb2) I have three questions: 1) How can I obtain a value for the parameter pie, which is the fraction of the population that is in the zero inflated model vs the fraction in the count model? 2) For any particular subject, how can I determine if the sub...

If this is off subject or has already been addressed, sorry. "Windows Genuine Advantage" looks like a move to make wine worthless. What I mean is that M$ development API pushes windows developers' applications to require you install IE 6.0 (soon 7.0) or later, making IE a key part of wine. If IE requires Genuine MicroSoft (Windows Genuine Advantage) to install, then most if not all

Hello, I am working with zero inflated models for a current project and I am getting wildly different results from R's zeroinfl(y ~ x, dist="negbin") command and Stata's zinb command. Does anyone know why this may be? I find it odd considering that zeroinfl(y ~ x, dist="poisson") gives identical to output to Stata's zip function. Thanks, --david [[alternative

I have installed R on my machine. Can anyone now suggest to me the best book/e-book from where I can learn the R language most efficiently? Thanks in advance -- Siddhant Gupta III Year Department of Biotechnology IIT Roorkee India [[alternative HTML version deleted]]

...subject. Others will undoubtedly know better than I. >> >> --Chris Ryan >> >> Sorkin, John wrote: >>> I am running a zero inflated regression using the zeroinfl function similar to >> the model below: >>> fm_zinb2 <- zeroinfl(art ~ . | ., data = bioChemists, dist = >>> "poisson") >>> summary(fm_zinb2) >>> >>> I have three questions: >>> >>> 1) How can I obtain a value for the parameter pie, which is the fraction of >> the population that is in the zero inflated model vs the fractio...

Dear R user, I am a biochemist/bioinformatician, at the moment working on protein clusterings by conformation similarity. I only started seriously working with R about a couple of months ago. I have been able so far to read my way through tutorials and set-up my hierarchical clusterings. My problem is that I cannot find a way t...