similar to: Suggesting changes to HELP files?

Dear list members, I'm interested in showing that within-group statistical dependence is negligible, so I can use ordinary linear models without including random effects. However, I can find no mention of testing a model with vs. without random effects in either Venable & Ripley (2002) or Pinheiro and Bates (2000). Our in-house statisticians are not familiar with this, either,

Hi, I'm trying to fit a model using variance components in R, but if very new on it, so I'm asking for your help. I have imported the SPSS database onto R, but I don't know how to convert the commands... the SPSS commands I'm trying to convert are: VARCOMP RATING BY CHAIN SECTOR RESP ASPECT ITEM /RANDOM = CHAIN SECTOR RESP ASPECT ITEM /METHOD = MINQUE (1) /DESIGN

Hi all, I am not a very proficient R-user yet, so I hope I am not wasting people?s time. I want to run a linear mixed model with 3 random factors (A, B, C) where A and B are partially crossed and C is nested within B. I understand that this is not easily possible using lme but it might be using lmer. I encountered two problems when trying: Firstly, I can enter two random factors in lmer but

Trying to Stangle / Sweave a file $ cat vignette.Rnw %\VignetteEngine{knitr} \documentclass{article} \begin{document} \end{document} results in a misleading error message: ~/tmp$ R CMD Stangle vignette.Rnw Error: Vignette engine package not specified Execution halted when what is missing is the full specification knitr::knitr; 'vignette engine package and function not specified' ?

Hi, Recently I saw a couple of cases in which the package vignettes were somewhat complicated so that Stangle() (or knitr::purl() or other tangling functions) can fail to produce the exact R code that is executed by the weaving function Sweave() (or knitr::knit(), ...). For example, this is a valid document that can pass the weaving process but cannot generate a valid R script to be source()d:

I have obtained from transfer functions, the state space matrices for the following state space model. x* = Ax + Bu y = Cx + Du I have A, B, C, and D, now I would like to take the exogenous inputs and simulate the data using the state space model. I know there is a simulate function in the package dse1, but I am unsure as to what type of TSmodel to create to put into it. Could anyone give me

As a user, I am always annoyed beyond measure that Sweave vignettes precede the code by a command line prompt. It makes running examples by simple copying of the commands from the vignette to the console a pain. I know the idea is that it is clear what is the command, and what is the output, but I'd rather precede the output with some kind of marking. Is there any other solution possible /

> -------- Original Message -------- > Subject: Re: [R] How to extract R codes that embedded in a HTML file > using Stangle? > Date: Thu, 17 May 2007 17:01:30 +0000 > From: Tao Shi <shitao at hotmail.com> > To: ligges at statistik.uni-dortmund.de, lecoutre at stat.ucl.ac.be > CC: r-help at stat.math.ethz.ch > : <jmcconnell at

Does anyone know of an existing R package or code to run a mixed Hurdle model? I found glmmADMB, but that seems to be ZIP. Any recommendations? Thanks, Jeff [[alternative HTML version deleted]]

Dear listers, I am trying to assess variance components for a nested, mixed-effects model. I think I got an answer that make sense from R, but I have a warning message and I wanted to check that what I am looking at is actually what I need: my data are organized as transects within stations, stations within habitats, habitats within lagoons. lagoons: random, habitats: fixed the question is:

[I originally emailed this to Friedrich Leisch but got no response and I just wanted to make sure it made it in before release.] While working with Stangle(), I noticed a problem when using 'split = TRUE'. Particularly, when there are two chunks where one chunk's name is a prefix of another chunk's name, then the two chunks will be written to a single file rather than two

> See the 'Writing R Extensions' manual, specifically > Creating R Packages -> Writing package vignettes thank you, i saw this entry. However, this entry is rather about how to include documents (in particular Sweave-based) into a package. But I have meant smth else. Let me explain in example. Today I use emacs as environment for my R-sessions. I am quite happy to use

Hello everyone. I want to write some likelihood functions to use with optim. For example AR-structures, I have written a couple of functions that appear to get the job done. But, since I am new to R, I wanted to ask if there are any references in this topic. Thanks in advance, ******************************************* Antonio Paredes USDA- Center for Veterinary Biologics Biometrics Unit

Hello, I'm trying to find out if something has been written in R regarding data assimilation and inverse modeling. These searches do not return anything that look like Kalman filter variations (EK, SEEK, ROEK, etc.) help.search("assimilation") help.search("inverse model") Regards, ************************************************** AVIS DE NON-RESPONSABILITE: Ce

I need capabilities, for my data analysis, like the Pinheiro & Bates S-Plus/R package nlme() but with binomial family and logit link. I need multiple crossed, possibly interacting fixed effects (age cohort of twin when entered study, sex of twin, sampling method used to acquire twin pair, and twin zygosity), a couple of random effects other than the cluster variable, and the ability to

I have got pairs of time series, where one usually is shorter (n typically about 5400) than the other (n typically about 52000). I would like to calculate the ccf for these series, but I haven't found a smart way to let the shorter "slide" along the longer one in steps. Manually splitting the longer series into shorter ones of the same length as the shorter is possible, but tedious.

I added a bibliographic reference to one of my .Rnw documents, to wit: \begin{thebibliography}{9} \bibitem{Jose} Jos{\'{e}} C. Pinheiro and Douglas M. Bates, \emph{Mixed-Effects Models in S and S-PLUS}, Springer, 2000. \end{thebibliography} just before the \end{document}. When I run Sweave on the result these lines disappear without a trace. Is this intentional? Subquestion: is

I am trying to understand the proper way to encode the nesting structure for data in the context of nlme, in the specific case of individuals nested within species for which each individual is unique. I have searched through Pinheiro & Bates and also past postings, but without success. Take the Wafer data set which has 2 levels: Wafer (8 values) and Site nested within Wafer (10 values for

Now that R 3.0.0+ supports non-Sweave vignettes, R-exts \S 1.4.2 seems to imply that it is possible to include both Sweave and knitr vignettes in a single package. I'm wondering if anyone has tried this and/or if there are some hidden gotchas putting this into practice, and concerned about creating problems with CRAN checks if I try this. Consider two vignettes: pkg/vignettes/vign1.Rnw,

Hi all R gurus out there, Im a kind of newbie to kalman-filters after some research I have found that the dlm package is the easiest to start with. So be patient if some of my questions are too basic. I would like to set up a beta estimation between an asset and a market index using a kalman-filter. Much littarture says it gives superior estimates compared to OLS estimates. So I would like to