Re: [R] nlme varFixed

Dear Franz Only attachments of specific types are allowed on the R lists and yours did not come through. It might be necessary to show your code as well. Have you thought of trying the mailing list dedicated to mixed models? https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models Michael O

[R] nlme varFixed

Dear R-project team, I have a problem with the function varFixed() of the nlme-package. I used it with the squid-data of Zuur et. al 2009 (chapter 4), to fix increasing residuals (heterogenetiy) (see graph in the email) I get the message ' Variance function structure of class varFixed with n

Re: [R] NLME regression with weights, syntax in r

1. No data, so may be impossible to help. Can you provide a minimal REPREX? 2. But probably better posted on r-sig-mixed-models anyway if you don't get a useful answer here. Cheers, Bert On Sun, Oct 30, 2022 at 3:20 AM LEPREVOST Florian (SNCF / DIR TECHNOLOGIES INNOVATION ET PROJETS GROUPE / IR

[R] NLME regression with weights, syntax in r

Hi all, I found this (very) old post which had a similar problem but went without an answer (https://stat.ethz.ch/pipermail/r-help/2004-October/058325.html) I am trying to fit a power curve to model some observations in an nlme. However, I know some observations to be less reliable than others

Re: [R] nlme gls issue

: R-help@r-project.org Subject: Re: [R] nlme gls issue On Fri, 16 Sep 2022 13:48:55 + Kayla Bazzana wrote: > Hi there, > > I'm having issues running a gls within the nlme package that neither > I nor any of my colleagues can figure out. The gls itself seems to > run fine (i.e.

Re: [R] nlme gls issue

On Fri, 16 Sep 2022 13:48:55 + Kayla Bazzana wrote: > Hi there, > > I'm having issues running a gls within the nlme package that neither > I nor any of my colleagues can figure out. The gls itself seems to > run fine (i.e. doesn't give an error message and produces a seemingly > normal sum

Re: [R] nlme::lme sigma parameter standard deviation or variance?

Modifying the first example in help('lme', pac='nlme'): library(nlme) fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age fm1$sigma fm1.2 <- lme(2*distance ~ age, data = Orthodont) # random is ~ age fm1.2$sigma Conclusion: Standard deviation, as indicate

Re: [R] nlme::lme sigma parameter standard deviation or variance?

You can run a test. Multiply all your data by a scalar, say 2. If this changes the result lme_mod$sigma by a factor of 2, then it is a std deviation. If it changes the result by a factor of 4, then it is a variance. HTH, Eric On Sat, Dec 18, 2021 at 11:26 AM Courtney Van Den elzen wrote: > > Hi

[R] nlme::lme sigma parameter standard deviation or variance?

Hi R-help, I am a researcher fitting linear mixed models using the package nlme. I am wondering whether the sigma value that is outputted as part of the model object is standard deviation or variance? for example, I might fit a model lme_mod <- nlme::lme(response ~ predictor1 + predictor2, random

[R] nlme::gls potential bug

Hi there, I have been using the nlme::gls package created in R to fit a pretty simple model (linear with AR error) y(t) = beta*x(t) + e(t)              where e(t) ~ rho*e(t-1) + Z(t)        and Z(t)~ N(0,sig^2) I call the R routine glsObj <- nlme::gls(y ~ x -1, data=data, correlation = nlm

[R] nlme package, fixing variance.covariance matrix of residuals

Dear R team, I would like to do a multivariate meta-analysis in R using the nlme package. In meta-analysis I fix the residuals to known sampling errors. As I do a multivariate analysis, I have a variance-covariance matrix of sampling errors. Unfortunately, via varFixed I can only fix a vector o

Re: [R] {nlme} Question about modeling Level two heteroscedasticity in HLM

Hi Bert, Thank you so much for your kind guidance! I will post my question there. Best, Yen 引述 Bert Gunter : A better place for this post would be on R's mixed models list: r-sig-mixed-models . Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming alon

Re: [R] {nlme} Question about modeling Level two heteroscedasticity in HLM

Hi Jeff, Thank you for your response! I appreciate the guide. I will post my question there! Best, Yen 引述 Jeff Newmiller : If you don't get a response it is because you did not read the Posting Guide which indicates that the R-sig-ME mailing list is where this question would have been

Re: [R] {nlme} Question about modeling Level two heteroscedasticity in HLM

A better place for this post would be on R's mixed models list: r-sig-mixed-models . Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Aug 16

Re: [R] {nlme} Question about modeling Level two heteroscedasticity in HLM

If you don't get a response it is because you did not read the Posting Guide which indicates that the R-sig-ME mailing list is where this question would have been on-topic. -- Sent from my phone. Please excuse my brevity. On August 16, 2017 6:17:03 AM PDT, b88207...@ntu.edu.tw wrote: >Hello de

[R] {nlme} Question about modeling Level two heteroscedasticity in HLM

Hello dear uesRs, I am working on modeling both level one and level two heteroscedasticity in HLM. In my model, both error variance and variance of random intercept / random slope are affected by some level two variables. I found that nlme is able to model heteroscedasticity. I learned ho

Re: [R] PROC MIXED RANDOM equivalence in R nlme

Hi David: Thanks for your response and suggestions. --Dennis On 8/11/17 2:03 PM, David Winsemius wrote: On Aug 11, 2017, at 7:56 AM, Dennis F. Kahlbaum wrote: Hi Robert: Thanks for your response, as well. I'm sorry. As you've discovered, I made some capitalization errors when posting my R

Re: [R] PROC MIXED RANDOM equivalence in R nlme

> On Aug 11, 2017, at 7:56 AM, Dennis F. Kahlbaum wrote: > > Hi Robert: > > Thanks for your response, as well. > > I'm sorry. As you've discovered, I made some capitalization errors when > posting my R code. The actual R code does use "lme", "data", and "random". > > The dataframe is indeed

Re: [R] PROC MIXED RANDOM equivalence in R nlme

Hi Robert: Thanks for your response, as well. I'm sorry. As you've discovered, I made some capitalization errors when posting my R code. The actual R code does use "lme", "data", and "random". The dataframe is indeed named "emiss" and each item in the formula is a column in the dataframe. I

Re: [R] PROC MIXED RANDOM equivalence in R nlme

y Onkelinx wrote: > Dear Dennis, > > Your question assumes that people know both SAS PROC MIXED and R nlme. > Only a limited number of people do. Add the mathematical formulation > of the model. That will increase the number of people that can help > you. Adding the number o

Re: [R] PROC MIXED RANDOM equivalence in R nlme

On 8/10/2017 8:34 AM, Dennis F. Kahlbaum wrote: -- snip -- I don't have real help, but I'll remind you that R is case sensitive, and it looks like that will be at least one problem in the solution your are working on below: lme not LME data not DATA random = RANDOM -

Re: [R] PROC MIXED RANDOM equivalence in R nlme

Dear Dennis, Your question assumes that people know both SAS PROC MIXED and R nlme. Only a limited number of people do. Add the mathematical formulation of the model. That will increase the number of people that can help you. Adding the number of levels in each categorical variable and the number

[R] PROC MIXED RANDOM equivalence in R nlme

I am trying to reproduce some old SAS PROC MIXED code using R and nlme. The data consists of emission readings from vehicles and fuel properties. All variables are real numbers except "study" and "vehicle", which are character. Unfortunately, since the data are confidential, I'm unable to provi

Re: [R] nlme & VarIdent

I suggest that you post instead on the r-sig-mixed-models list which specializes in just this sort of query, and where you are therefore likely to receive a quicker more authoritative response. Cheers, Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and

[R] nlme & VarIdent

Hello, All the help I've read (including Pinheiro and Bates book, 'Mixed Effects Models in S and S-PLUS') regarding how to fit a linear mixed-effects model where variances change with a factor's levels indicates this is done through the 'weights' argument to 'lme', using something like 'weight

Re: [R] nlme

Wild guess: Santiago is putting a and b in his formula when they are the coefficients he wants to extract? If Mr S wants better answers he needs to read about reproducibility and avoid HTML format email. -- Sent from my phone. Please excuse my brevity. On October 24, 2016 2:58:42 PM CDT, Wil

Re: [R] nlme

> summary(nlme(Btronc~a+b*dbh**2*haut, data=cbind(dat,g="a"), fixed=a+b_1, > start=start, > > groups=~g, weights=varPower(form=~dbh))) Shouldn't 'fixed' be a formula? Perhaps a+b~1? Bill Dunlap TIBCO Software wdunlap tibco.com On Mon, Oct 24, 2016 at 9:03 AM, Santiago Bueno wrote: > Dear peo

Re: [R] nlme

Without access to the data, or commented, minimal, self-contained, reproducible code, it's pretty hard to speculate. I suggest that you reframe your question so that we can see what you can see. Andrew On 25 October 2016 at 03:03, Santiago Bueno wrote: > Dear people: > > > I am getting the foll

[R] nlme

Dear people: I am getting the following error when trying to run the piece of code below. Any insights?? Error in nlme.formula(Btronc ~ a + b * dbh^2 * haut, data = cbind(dat, : object 'a' not found library(nlme) start <- coef(lm(Btronc~I(dbh**2*haut),data=dat)) names(start) <- c("a",

Re: [R] nlme: fewer observations than random effects in all level 1 groups

Dear John, Please send questions on mixed models to r-sig-mixedmodels. Your model is too complex for the data. You're fitted time*CorT as random slopes. These random effects require 10 parameters. But you have only 4 data points per level of SS. Furthermore within each level of SS only one level

[R] nlme: fewer observations than random effects in all level 1 groups

I am getting a warning message when I run lme: Warning message: In lme.formula(fixed = value ~ CorT + time + CorT * time, data = GD) : fewer observations than random effects in all level 1 groups I don't know what the message means, nor if I need to be concerned about the message. I would be g

Re: [R] 'nlme' package not compiling

> On Apr 18, 2016, at 12:48 AM, Angelo Varlotta > wrote: > > Hi, > I'm trying to install from source code the 'nlme' package in > RStudio. When I try, I get the following error message: > > ld: warning: directory not found for option > '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2' >

[R] 'nlme' package not compiling

Hi, I'm trying to install from source code the 'nlme' package in RStudio. When I try, I get the following error message: ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2' ld: library not found for -lgfortran clang: error: linker command failed wit

Re: [R] nlme splines model.frame.default error

On 2015-06-02 Tue 14:20, Jacob Wegelin wrote: I want to use a specialized function to compute knots on the fly to pass to splines::bs within a call to nlme::lme. The specialized function will compute knots from the x-axis variable (the x argument in a call to splines::bs). The syntax works w

[R] nlme splines model.frame.default error

I want to use a specialized function to compute knots on the fly to pass to splines::bs within a call to nlme::lme. The specialized function will compute knots from the x-axis variable (the x argument in a call to splines::bs). The syntax works with lm. But when I try it with lme, the followin

Re: [R] nlme package: changing reference for varIdent parameter estimates in summary.gls

that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: R-help [mailto:r-help-boun...@r-project.org] Namens Kornak, John Verzonden: dinsdag 23 december 2014 22:29 Aan: r-help@R-project.org Onderwerp: [R] nlme package: changing refer

[R] nlme package: changing reference for varIdent parameter estimates in summary.gls

Dear R experts, I am running gls models with heterogeneous group variances using the glm function in the nlme package with varIdent weights. I am interested in controlling the baseline level for the group variance function standard deviation estimates by applying the relevel function to the gr

[R] nlme Indometh SSbiexp

Dear all, Probably a very stupid question. I am trying to reproduce the example of Pinheiro & Bates pp.278--287 on R 3.0.2 (Windows). I'd like to run : ### mod.nls <- nls(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data=Indometh) mod.lis <- nlsList(conc ~ SSbiexp(time, A1, lrc1, A2, lrc2), data=In

Re: [R] ..nlme: start values necessary even though using self-start function?..

This seems to be a bug in the package. Maybe the code was written for S, or maybe R has changed in the many years since the former maintainer decided to be unhelpful. I'll put this on the list for the next release. On 30/09/2014 09:13, Matthias Kuhn wrote: Dear list. I am stuck with an "su

[R] ..nlme: start values necessary even though using self-start function?..

Dear list. I am stuck with an "subscript out of bounds" error when I play with an nlme-example from the yellow Pinheiro/Bates book. It is about using nlme() using the formula interface for non-linear mixed models. The following code snippet is inspired by the book (in section 8.2), using the Oran

Re: [R] nlme function summary.lmList cannot be found with new versions

On 20/11/2013 21:42, Ben Bolker wrote: megan herting chla.usc.edu> writes: Hello, I installed the newest version of R (3.0.2) as well as the newest version of nlme (3.1-113) in order to use summary.lmList and other nlme functions. Once loading the new library, lmList and summary.lm can be fo

Re: [R] nlme function summary.lmList cannot be found with new versions

megan herting chla.usc.edu> writes: > > Hello, > > I installed the newest version of R (3.0.2) as well as the > newest version of > nlme (3.1-113) in order to use summary.lmList and other > nlme functions. Once > loading the new library, lmList and summary.lm can be found, > but a number of

[R] nlme function summary.lmList cannot be found with new versions

Hello, I installed the newest version of R (3.0.2) as well as the newest version of nlme (3.1-113) in order to use summary.lmList and other nlme functions. Once loading the new library, lmList and summary.lm can be found, but a number of additional functions cannot be found via command. Versions

Re: [R] nlme starting values are not the correct length

elp-bounces@r- >> project.org] On Behalf Of Lara Reichmann >> Sent: Wednesday, December 05, 2012 1:53 AM >> To: r-h...@lists.r-project.org >> Subject: [R] nlme starting values are not the correct length >> >> Dear R community, >> >> I am trying to fit

Re: [R] nlme starting values are not the correct length

Hi see inline > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Lara Reichmann > Sent: Wednesday, December 05, 2012 1:53 AM > To: r-h...@lists.r-project.org > Subject: [R] nlme starting values are not

[R] nlme starting values are not the correct length

Dear R community, I am trying to fit an nlme model where I want to estimate the fixed effects of two treatments on the parameters on the following equation Photo~(a*(1-exp(-c*PARi/a)))-b I was able to fit a simple model without covariates following the method described in Mixed-Effects Methods

Re: [R] nlme: spatial autocorrelation on a sphere

t it doesn't work for gls() [I was feeling a little bit lazy making up my example data, so I used gls() instead of [n]lme()]. I know that other 'pseudo-spatial' corStructs such as corBrownian etc. (in the ape package) *do* work, so I'm not sure exactly why corRSpher doesn't

Re: [R] nlme: spatial autocorrelation on a sphere

27;pseudo-spatial' corStructs such as corBrownian etc. > (in the ape package) *do* work, so I'm not sure exactly why > corRSpher doesn't -- a quick look suggests that the problem *might* > be that it inherits from 'corSpatial', and there's some hard-coded > s

Re: [R] nlme: spatial autocorrelation on a sphere

ssful. Dan From: Spencer Graves [spencer.gra...@prodsyse.com] Sent: 02 October 2012 04:29 To: Dan Bebber Cc: David Winsemius; r-help@r-project.org Subject: Re: [R] nlme: spatial autocorrelation on a sphere Hi, Dan: On 10/1/2012 8:07 PM, Dan Bebber wrote: > Please be ass

Re: [R] nlme: spatial autocorrelation on a sphere

Modeling for Data Fusion and Spatial Heteroskedasticity with R Package ramps. Journal of Statistical Software 25(10) From: David Winsemius [dwinsem...@comcast.net] Sent: 01 October 2012 17:32 To: Spencer Graves Cc: Dan Bebber; r-help@r-project.org Subject: Re:

Re: [R] nlme: spatial autocorrelation on a sphere

___ From: David Winsemius [dwinsem...@comcast.net] Sent: 01 October 2012 17:32 To: Spencer Graves Cc: Dan Bebber; r-help@r-project.org Subject: Re: [R] nlme: spatial autocorrelation on a sphere On Oct 1, 2012, at 8:34 AM, Spencer Graves wrote: > On 10/1/2012 12:38 AM,

Re: [R] nlme: spatial autocorrelation on a sphere

On Oct 1, 2012, at 8:34 AM, Spencer Graves wrote: > On 10/1/2012 12:38 AM, David Winsemius wrote: >> > >> LMCTVTFY: http://cran.r-project.org/web/views/Spatial.html >> > > > What's LMCTVIFY? Please accept my apologies for attempting to be cute and I also apologize to Mr Bebber for rea

Re: [R] nlme: spatial autocorrelation on a sphere

class corStruct. -- David. > Dan > > From: David Winsemius [dwinsem...@comcast.net] > Sent: 01 October 2012 08:38 > To: Dan Bebber > Cc: r-help@r-project.org > Subject: Re: [R] nlme: spatial autocorrelation on a sphere > > On Sep 30, 2012, at 6:48 P

Re: [R] nlme: spatial autocorrelation on a sphere

ber 2012 08:38 To: Dan Bebber Cc: r-help@r-project.org Subject: Re: [R] nlme: spatial autocorrelation on a sphere On Sep 30, 2012, at 6:48 PM, Dan Bebber wrote: I have spatial data on a sphere (the Earth) for which I would like to run an gls model assuming that the errors are autcorrelated, i.e

Re: [R] nlme: spatial autocorrelation on a sphere

imagine it must be possible for nlme. Dan From: David Winsemius [dwinsem...@comcast.net] Sent: 01 October 2012 08:38 To: Dan Bebber Cc: r-help@r-project.org Subject: Re: [R] nlme: spatial autocorrelation on a sphere On Sep 30, 2012, at 6:48 PM, Dan Bebber

Re: [R] nlme: spatial autocorrelation on a sphere

On Sep 30, 2012, at 6:48 PM, Dan Bebber wrote: > I have spatial data on a sphere (the Earth) for which I would like to run an > gls model assuming that the errors are autcorrelated, i.e. including a > corSpatial correlation in the model specification. > > In this case the distance metric shoul

[R] nlme: spatial autocorrelation on a sphere

I have spatial data on a sphere (the Earth) for which I would like to run an gls model assuming that the errors are autcorrelated, i.e. including a corSpatial correlation in the model specification. In this case the distance metric should be calculated on the sphere, therefore metric = "euclid

Re: [R] nlme function examples for dose-respone

Hi, thx Bert, I forward the question. I forgot a detail. For each (location, plot, year) combination there are 6 (dose, response) pairs. $ plot: Factor w/ 4 levels "1","2","3","4": $ location : Factor w/ 5 levels "loc1","loc2",..: $ year: Factor w/ 3 levels "2009","2010",..: $ dose: num 27.3 32.

Re: [R] nlme function examples for dose-respone

1. Post on R-sig-mixed-models instead. Much more expertise and relevance there. 2. I would forget about mixed effects and treat the locations as fixed. With only 5, you don't have enough information to estimate the variance component with any precision anyway. 3. Feel free to ignore (2) and defe

[R] nlme function examples for dose-respone

Hi, I want to fit nonlinear dose-response curves, as "fun(X,a,b,c)", for each of our 5 trail locations. Our data basis is something like location plot year dose response For each location there are 4 plots as repetitions (over 3 years). So the interactions "location*year" and "location*plot" sho

Re: [R] Nlme not working on very similar initial values

Welcome to the wonderful world Of nonlinear model fitting in ill-conditioned problems. See also chaos theory. Bert Sent from my iPhone -- please excuse typos. On Apr 3, 2012, at 3:03 PM, Ramiro Barrantes wrote: > Hello, > > I am using CentOS Linux 6.0, R 2.14.1 and nlme 3.1-103 > > I am t

[R] Nlme not working on very similar initial values

Hello, I am using CentOS Linux 6.0, R 2.14.1 and nlme 3.1-103 I am trying to fit some models using nlme, and what was happening was that it would get to some datasets and just "stall", the memory usage would grow and grow and eventually crash. I looked carefully into one of the datasets and ra

[R] NLME error model with several responses

Hi! I am using the NLME package for R to modeling glucose-insuline response with Bergman's model, very similar to the example in the documentation for the NLME package. My question concerns the model for the residuals. I use a proportional model , Var(e_{ij})=(sigma_g*G(t))^2 for the glucose res

Re: [R] nlme error on dimensions in multiplication

Hello , can anyone reproduce the example - with or without errors? Thomas On 21.03.12 11:04, Thomas Wutzler wrote: > Hello R users, > > When trying to fit a nonlinear mixed model to a respiration time series, > I get the following error message: > > Error in recalc.varFunc(object[[i]], conLin)

[R] nlme error on dimensions in multiplication

Hello R users, When trying to fit a nonlinear mixed model to a respiration time series, I get the following error message: Error in recalc.varFunc(object[[i]], conLin) : dims [product 30] do not match the length of object [34] In addition: Warning message: In conLin$Xy * varWeights(object) :

[R] nlme Fixed Variance Function

Dear R users, I am trying to fit a gls model and weight my data points using a VarFixed structure. I have found many examples, but I do not understand the difference between the following models with varFixed specified in a different way: mod<-gls(y~x,weights=varFixed(~1/invsigma) mod<-gls(y~x,w

Re: [R] [nlme] How to calculate standard error of random effects in lme

Marcus Drescher tum.de> writes: > > Hi all, > > is there a way to calculate standard error of random effect > from the estimated model in lme? > Search in http://glmm.wikidot.com/faq , and post follow-up questions to the r-sig-mixed-models mailing list. Ben Bolker _

[R] [nlme] How to calculate standard error of random effects in lme

Hi all, is there a way to calculate standard error of random effect from the estimated model in lme? Best Marcus [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do

[R] nlme gls errors

Hi I keep getting an error like this: Error in `coef<-.corARMA`(`*tmp*`, value = c(18.3113452983211, -1.56626248550284, : Coefficient matrix not invertible or like this: Error in gls(archlogfl ~ co2, correlation = corARMA(p = 3)) : false convergence (8) with the gls function in nlme. The f

[R] nlme for exact binomial model

Hi I am conducting a meta-analysis on proportions and I'm interested in using the exact binomial likeliood for the within-study effects rather than the approximate approaches and I don't want to use the quasi-likelihood approach in R's glmmPQL. Does anyone know how I can do this using nlme? I c

[R] nlme: Computing REML likelihood value from ML likelihood value

Dear All, I have a question concerning the computation of the value of the Restricted Maximum Likelihood (REML) function evaluated at a given set of parameter estimates from the Maximum likelihood (ML) value. Following the book of Fitzmaurice, Laird and Ware (2004) "Applied Longitudinal Analysi

[R] nlme correlation structure

Dear all: i have the following problem I use gls, I have 10 repeated meassures. The 10 by 10 matrix has different variances in the diagonal (i know how to handle that) The correlation matrix is blocked: the first 3 repeated meassures have the same correlation, the next 4 have the same correlat

[R] nlme numeric data format

Dear R help folks I am trying to run nlme for the first time (currently without guidance of any textbooks), apologies if this is a bit simplistic. My model is 15 env predictors of diversity, grouped by 3 locations: mod1<-nlme(shan~Alt+EC+Phos+pH+DOC+NO3NO2+H2O+Amino+NH4+Birds+Plants+Seals+Human

Re: [R] nlme Output

data. ~ John Tukey Van: Edward Patzelt [mailto:patze...@umn.edu] Verzonden: dinsdag 7 september 2010 0:25 Aan: ONKELINX, Thierry CC: r-help@r-project.org Onderwerp: Re: [R] nlme Output The design is a repeat

Re: [R] nlme Output

t; > -Oorspronkelijk bericht- > > Van: r-help-boun...@r-project.org > > [mailto:r-help-boun...@r-project.org] Namens Edward Patzelt > > Verzonden: maandag 6 september 2010 15:43 > > Aan: r-help@r-project.org > > Onderwerp: [R] nlme Output > > > &

Re: [R] nlme Output

Verzonden: maandag 6 september 2010 15:43 > Aan: r-help@r-project.org > Onderwerp: [R] nlme Output > > Everyone - > > What do the NaN's mean here? Is this analysis a problem? > > > Linear mixed-effects model fit by maximum likelihood > Data: tmp.dat >

[R] nlme Output

Everyone - What do the NaN's mean here? Is this analysis a problem? Linear mixed-effects model fit by maximum likelihood Data: tmp.dat AIC BIClogLik 1611.251 1638.363 -797.6253 Random effects: Formula: ~1 | group_id (Intercept) Residual StdDev: 0.0003077668 9.23671

Re: [R] nlme formula from model specification

> The combination of some data and an aching desire for an answer does not > ensure that a reasonable answer can be extracted from a given body of > data. > ~ John Tukey > > >> -Oorspronkelijk bericht- >> Van: r-help-boun...@r-project.org >> [mailto:r-help-boun...@r-p

Re: [R] nlme formula from model specification

...@r-project.org] Namens Mikkel Meyer Andersen > Verzonden: donderdag 2 september 2010 13:30 > Aan: r-help@r-project.org > Onderwerp: [R] nlme formula from model specification > > Dear R-community, > > I'm analysing some noise using the nlme-package. I'm wri

[R] nlme formula from model specification

Dear R-community, I'm analysing some noise using the nlme-package. I'm writing in order to get my usage of lme verified. In practise, a number of samples have been processed by a machine measuring the same signal at four different channels. I want to model the noise. I have taken the noise (the s

[R] nlme help

I would like to fit a nonlinear model with "nlme." The model is a nonlinear growth model with five time points: y = X*b + e, where design matrix X is defined as X= | 1 0 | | 1 1 | | 1 k | | 1 2k | | 1 3k | and parameter vector b = (b0, b1). And where "k" is a parameter

[R] NLME question...

I would like to fit a nonlinear model with "nlme." The model is a nonlinear growth model with five time points: y = X*b + e, where design matrix X is defined as X= | 1 0 | | 1 1 | | 1 k | | 1 2k | | 1 3k | and parameter vector b = (b0, b1). And where "k" is

[R] nlme question

I would like to fit a nonlinear model with "nlme." The model is a nonlinear growth model with five time points: y = X*b + e, where design matrix X is defined as X= | 1 0 | | 1 1 | | 1 k | | 1 2k | | 1 3k | and parameter vector b = (b0, b1). And where "k" is

Re: [R] nlme: constraints on fixed effects?

"Is there a way to set constraints on the fixed effects parameters?" Yes. (I suggest you read and follow the posting guide to get a better answer). Bert Gunter Genentech Nonclinical Statistics On Tue, Aug 3, 2010 at 11:11 AM, Marston, Sarah wrote: > Dear R Help, > > > > Is there a way to set c

[R] nlme: constraints on fixed effects?

Dear R Help, Is there a way to set constraints on the fixed effects parameters? Thank you. Sincerely, Sarah Marston [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listi

Re: [R] nlme w/no groups and spatially correlated residuals

Seth syr.edu> writes: > I would like to specify a spherical correlation structure for spatially > autocorrelated residuals in a model based upon the logistic function of a > response that is a proportion (0 to 1) (so usual binary logistic regression > is not an option). There is no need for a g-

[R] nlme w/no groups and spatially correlated residuals

Hi, I would like to specify a spherical correlation structure for spatially autocorrelated residuals in a model based upon the logistic function of a response that is a proportion (0 to 1) (so usual binary logistic regression is not an option). There is no need for a g-side random effect with gr

Re: [R] (nlme, lme, glmmML, or glmmPQL)mixed effect models with large spatial data sets

Update on above. I sampled my data to create a 10,000 observation data set. I then tried lme with a correlation = corSpher and only one predictor, as a test. I set my memory.limit to the max allowable. It ran for a while then returned Error: cannot allocate vector of size 64.0 Mb. I can see

[R] (nlme, lme, glmmML, or glmmPQL)mixed effect models with large spatial data sets

Hi, I have a spatial data set with many observations (~50,000) and would like to keep as much data as possible. There is spatial dependence, so I am attempting a mixed model in R with a spherical variogram defining the correlation as a function of distance between points. I have tried nlme, lme

Re: [R] 'nlme' library - lme function results

Peter Ehlers wrote: > > > .. or get both from VarCorr(model): > > VarCorr(fm2) > #Subject = pdLogChol(1) > #Variance StdDev > #(Intercept) 3.266784 1.807425 > #Residual2.049456 1.431592 > > Krr.. I knew I had some sort of blackout. Dieter -- View this message in context

Re: [R] 'nlme' library - lme function results

Dieter Menne wrote: Michal Figurski wrote: I am running a simple mixed effects model using lme(). The call looks like this: fit <- lme(Analyte~Sample, data=Data, random=~1 | Run) I am particularly interested in the estimated random effects. When I print the 'fit' object, it looks somethin

Re: [R] 'nlme' library - lme function results

Michal Figurski wrote: > > I am running a simple mixed effects model using lme(). The call looks > like this: > fit <- lme(Analyte~Sample, data=Data, random=~1 | Run) > > I am particularly interested in the estimated random effects. When I > print the 'fit' object, it looks something like ex

[R] 'nlme' library - lme function results

Dear R-helpers I am running a simple mixed effects model using lme(). The call looks like this: fit <- lme(Analyte~Sample, data=Data, random=~1 | Run) I am particularly interested in the estimated random effects. When I print the 'fit' object, it looks something like example below: (...) Ra

[R] NLME

I am trying to use one of the variance function classes (e.g., varClasses -varConstPower or varPower) When I run the model under default conditions or specify varIdent explicitly I do not have any problems. If I try to use anything else I get error messages of the form "Error in na.fail.defaul

[R] nlme package - unbalanced data and Croissant (2008)

ll). I owe you a beer, payable at the useR! in two weeks if you like. Best, Giovanni # original message ### ------ Message: 61 Date: Tue, 23 Jun 2009 11:06:54 -0400 From: "Anthony A. Pezzola" Subject: [R] nlme package - unbalanced data and Croissant (2008) To:

[R] nlme package - unbalanced data and Croissant (2008)

Dear listserv members, In Croissant (2008) “Panel Data Econometrics in R: The plm Package” the authors seem to indicate that the nlme package for R cannot correctly handle unbalanced panel data: “Moreover, economic panel datasets often happen to be unbalanced (i.e., they have a different number

Re: [R] nlme weighted

Mollet, Fabian wur.nl> writes: > I'm fitting a non linear model (energy allocation model to individual > growth data) using your nlme routine. For each individual I have thus a > number of observations (age and size) to which I fit the nonlinear > function, with random effects for the individuals

[R] nlme weighted

Dear R-expert I'm fitting a non linear model (energy allocation model to individual growth data) using your nlme routine. For each individual I have thus a number of observations (age and size) to which I fit the nonlinear function, with random effects for the individuals on the estimated paramet

Re: [R] nlme: problem with fitting logistic function

I think you can do this very efficiently with AD Model Builder's random effects module. The software is now freely available at http://admb-project.org If you want, you can contact me directly to discuss the model. Dave -- David A. Fournier P.O. Box 2040, Sidney, B.C. V8l 3S3 Canada Pho

Re: [R] nlme: problem with fitting logistic function

Douglas Bates stat.wisc.edu> writes: > > 3) Use lmer in lme4. Your mileage may vary, I could not find a speedup > >   for my problems, but larger problem might give one. > > Did you mean nlmer in the lme4 package? If so, it may be worthwhile > trying the development branch but that is not somet

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