search for: gnm

...y package logmult, in order to follow the new CRAN policies. But I just noticed it broke jackknife/bootstrap using several workers via package parallel. The reason is that I'm running model replicates on the workers, and the formula includes non-standard terms like Mult() which are provided by gnm. If gnm is not attached to the global namespace, these functions are not found. What would be the best solution to fix this? I tried changing the environment of the formula to be gnm's namespace, but so far I failed. Here's a reproducer using only gnm: > dat <- structure(c(326, 688...

...with option --no-install but it got stuck on checking for missing documentation entries. I can't see a way of getting round this. Perhaps I have misunderstood the NEWS? I can't find this behaviour documented elsewhere. R CMD check output given at the end, Thanks, Heather ## original D:\gnm>RCMD CHECK gnm RCMD CHECK gnm * checking for working latex ... OK * using log directory 'd:/gnm/gnm.Rcheck' * using Version 2.3.1 (2006-06-01) * checking for file 'gnm/DESCRIPTION' ... OK * this is package 'gnm' version '0.8-5' * checking package dependencies ......

Hi Milan, I expect I may be able to do something about the way the terms are evaluated, to ensure the evaluation is done in the gnm namespace (while still ensuring the variables can be found!). In the meantime, I think the following will work: Mult <- gnm::Mult f <- Freq ~ Eye + Hair + Mult(Eye, Hair) gnm::gnm(f, family=poisson, data=dat) Hope that helps, Heather On Wed, Apr 29, 2015, at 05:57 PM, Milan Bouchet-Vala...

In checking my vcdExtra package, the following NOTE newly appeared (R-Forge, using R version 3.0.1 Patched (2013-08-20 r63635)) Package in Depends field not imported from: ?gnm? These packages needs to imported from for the case when this namespace is loaded but not attached. In the DESCRIPTION file, I have Depends: R (>= 2.10), vcd, gnm (>= 1.0.3) In NAMESPACE: # we are a vcd extension import(vcd) I've read 1.1.1 of R-Exts, but it is not clear to me...

Hi all I want to construct a generalised nonlinear model (binomial family) using gnm, of the form: Response = a + b variable1 + c variable2 + d variable3 - d b variable4 - d c variable5, with the parameters b, c, and d appearing more than once. Hence, I think I need to use a custom nonlin function with gnm. One of my predictor variables is categorical, so I have created a dummy...

...Beta1) and shift the inflection point around with a few other parameters (Beta2). I have a ton of data, but I often have trouble getting the routine to fit. (I've been using nlin in SAS, which seems sloppier in terms of accepted convergence.) Now, from what I can tell, I can use nls, gnls, or gnm to fit something like this, but I can't tell which would be better, or if there's something else I should be trying. To do this right, though, I have to do a lot more reading, but I'd like to know where to start. (I have more of a physics/computer background, so I immediately jump to...

Hi everyone! In a package I'm developing, I have created a custom function to get jackknife standard errors for the parameters of a gnm model (which is essentially the same as a glm model for this issue). I'd like to add support for bootstrap using package boot, but I couldn't find how to proceed. The problem is, my data is a table object. Thus, I don't have one individual per line: when the object is converted to a da...

...linear vs. sigmoidal fit of the relationship between my dependent variable (y) and one explaining parameter (x2), both including the confounding effects of a third variable (x1): quasi-pois-lin <- glm(y ~ x1 + x2, family = quasipoisson(link="identity"), data=fit) quasi-pois-sig <- gnm(y ~ x1 + Mult(1, Inv(Const(1) + Exp(Mult(1 + offset(-x2), Inv(1))))), family = quasipoisson(link="identity"), data=fit) I can perform the linear model but not the sigmoidal one and I get an error message: Error in if (all(diagInfo < 1e-20) || all(abs(score) < tolerance * sqrt(tole...

Hi, I am quite new to R and would like to do nonlinear regressions with Poisson distributed data. I would like to estimate paramters of an equation of this type: FR = [c*NO * exp(a+b*NO)] / [(c+NO)*(1+exp(a+b*NO))] a,b and c are parameters, NO are input values I found both the gnm and gnlr3 function which should be able to do this regression but I can't manage to make it work. How can I write my equation to fit into these functions? If I understand it correct I have to split my equation in a "mu", a "shape" and a "family" part for the gnl...

...odel should be something like this: ^y_1 = a1 ^y_2 = a1 + k2**u ^y_3 = a1 + k2**u + k3**u ... ^y_m = a1 + k2**u + k3**u + ... + km**u or, generically ^yi = a1 + k * sum_j=2^i j**u and I need to fit a non-linear least-squares regression model to find the tripplet a1,k,u. I had a look to the gnm package, but I don't have the lesser idea how to formulate this problem to use this package. Can someone help me with that? cheers, Ronaldo

In previous versions of the gnm package, the terms component of "gnm" objects had a "classID" attribute. This caused problems when used with str as the following simple example illustrates: > x <- 1 > attr(x, "classID") <- "type1" > str(x) Class 'type1' Class ...

...N now reports errors in examples using MASS::loglm(), using R Under development (unstable) (2013-09-11 r63906) > Caesar.mod0 <- loglm(~Infection + (Risk*Antibiotics*Planned), data=Caesar) Error: could not find function "loglm" In DESCRIPTION I have Depends: R (>= 2.10), vcd, gnm (>= 1.0.3) Suggests: ca,gmodels,Fahrmeir,effects,VGAM,plyr,rgl,lmtest,MASS,nnet,ggplot2,Sleuth2,car and the vcd DESCRIPTION has Depends: R (>= 2.4.0), grid, stats Suggests: KernSmooth, mvtnorm, kernlab, HSAUR, coin Imports: utils, MASS, grDevices, colorspace so, in an R 3.0.0 console, lib...

...output I wasn't sure how much to paste and > didn't know about VERBOSE=1. I captured the verbose output in a > typescript file: > > http://www.smontanaro.net/typescript > > Lots of undefined symbols. Hi Skip, You currently need to configure with NM=/usr/sfw/bin/gnm, ie ./configure --enable-optimized NM=/usr/sfw/bin/gnm as GenLibDeps.pl doesn't parse Sun nm output in llvm 2.6 and later. Cheers, Nathan

...u. vcdExtra was originally designed to serve as a sandbox for introducing extensions of mosaic plots and other visualizations for categorical data, particularly those that apply to (poisson surrogate) loglinear models fitted using glm() and related, generalized nonlinear models fitted with gnm() in the gnm package. See package?vcdExtra for information and an overview. Heather Turner, Achim Zeileis and Duncan Murdoch contributed substantially to the latest release. In addition, it contains a tutorial vignette, "Working with categorical data with R and the vcd package", vignet...

This is a wrapper around gnm by Turner and Firth to make fitting log-multiplicative models as convenient as possible: it provides simple functions, good starting values, jackknife or bootstrap standard errors, and direct plotting of the results. In addition, it makes it possible to identify scores from RC(M) association model...

This is a wrapper around gnm by Turner and Firth to make fitting log-multiplicative models as convenient as possible: it provides simple functions, good starting values, jackknife or bootstrap standard errors, and direct plotting of the results. In addition, it makes it possible to identify scores from RC(M) association model...

Hello, Has anyone written R functions for applying self-controlled case series methods (http://statistics.open.ac.uk/sccs/). In fact only thing needed is to modify glm function to allow absorption of effect. Eg. in Poisson model individual effect is used as factor, but it is considered as nuisance term where parameter estimates are not needed. Could anyone point how absorbing individual

...mating the parameters (i,j and k) with the nls function, which sees the error distribution as normal, I would however like to do the same as nls with the assumption that the errors are poisson distributed. Is there a way to do this with R? Are there packages designed for this? I tried with the gnm package, but don't understand how to transform my equation to a generalised equation. Is there an option for nls to choose family = poisson? Lower in the mail the code with the model and visualisations I use to check my results. I also copied the test dataset from my txt file. I am using...

Hello everyone, I wanted to ask if there is an R-package to fit the following Poisson regression model log(\lambda_{ijk}) = \phi_{i} + \alpha_{j} + \beta_{k} i=1,\cdots,N (subjects) j=0,1 (two levels) k=0,1 (two levels) treating the \phi_{i} as nuinsance parameters. Thank you very much -- -Tony [[alternative HTML version deleted]]

> I don't know anything about Solaris, but your paste doesn't actually > contain any errors, just warnings (unless I'm reading "ld: warning: > relocation error:" wrong). It might help to run make without -j until > it fails, and then use `make VERBOSE=1` to print the exact commands > it's running. Sorry. There was so much output I wasn't sure how much