search for: gls

Displaying 20 results from an estimated 378 matches for "gls".

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2012 Apr 19
2
Gls function in rms package
Dear R-help, I don't understand why Gls gives me an error when trying to fit a model with AR(2) errors, while gls (from nlme) does not. For example: library(nlme) library(rms) set.seed(1) d <- data.frame(x = rnorm(50), y = rnorm(50)) gls(y ~ x, data=d, correlation = corARMA(p=2)) #This works Gls(y ~ x, data=d, correlation = corARMA...
2006 Mar 07
1
lme and gls : accessing values from correlation structure and variance functions
Dear R-users I am relatively new to R, i hope my many novice questions are welcome. I have problems accessing some objects (specifically the random effects, correlation structure and variance function) from an object of class gls and lme. I used the following models: yah <- gls (outcome~ -1 + as.factor(Trial):as.factor(endpoint)+ as.factor(Trial):as.factor(endpoint):trt, data=datt[datt$Trial<4,], correlation = corSymm(form=~1|as.factor(Trial)/as.factor(subject)), weights=varIdent(form=~1|endpoint))...
2008 May 09
1
Which gls models to use?
Hi, I need to correct for ar(1) behavior of my residuals of my model. I noticed that there are multiple gls models in R. I am wondering if anyone has experience in choosing between gls models. For example, how should one decide whether to use lm.gls in MASS, or gls in nlme for correcting ar(1)? Does anyone have a preference? Any advice is appreciated! Thanks, -- Tom [[alternative HTML version delete...
2006 Aug 09
1
Joint confidence intervals for GLS models?
Dear All, I would like to be able to estimate confidence intervals for a linear combination of coefficients for a GLS model. I am familiar with John Foxton's helpful paper on Time Series Regression and Generalised Least Squares (GLS) and have learnt a bit about the gls function. I have downloaded the gmodels package so I can use the estimable function. The estimable function is very useful because it allow...
2003 Oct 31
0
strange logLik results in gls (nlme)
I am trying to analyse a data with gls/lm using the following set of models prcn.0.lm <- lm( log10(Y)~(cond-1)+(cond-1):t ,prcn) prcn.1.gls <- gls( log10(Y)~(cond-1)+(cond-1):t ,prcn,cor=corAR1()) prcn.0.gls <- gls( log10(Y)~(cond-1)+(cond-1):t ,prcn) prcn.1m.gls <- gls( log10(Y)~(cond-1)+(cond-1):t ,prcn,cor=corAR1(),metho...
2012 May 02
3
Consulta gráfica
  Hola,   Por favor, ¿podríais indicarme qué recursos (librerías o ideas) pueden resultar de utilidad para crear un gráfico del estilo del de la figura 3.8 del siguiente link?   http://www.tsc.uvigo.es/BIO/Bioing/ChrLDoc3.html#3.5   Actualmente estoy utilizando funciones muy básicas y la verdad es que no me encuentro muy satisfecha con el resultado.   Muchas gracias.   Eva [[alternative HTML
2004 Sep 03
0
ML vs. REML with gls()
Hello listmembers, I've been thinking of using gls in the nlme package to test for serial correlation in my data set. I've simulated a sample data set and have found a large discrepancy in the results I get when using the default method REML vs. ML. The data set involves a response that is measured twice a day (once for each level of a tre...
2003 Sep 25
1
Error from gls call (package nlme)
Hi I have a huge array with series of data. For each cell in the array I fit a linear model, either using lm() or gls() with lm() there is no problem, but with gls() I get an error: Error in glsEstimate(glsSt, control = glsEstControl) : computed gls fit is singular, rank 2 as soon as there are data like this: > y1 <- c(0,0,0,0) > x1 <- c(0,1,1.3,0) > gls(y1~x1) Error in glsEstimate(...
2009 Sep 22
1
odd (erroneous?) results from gls
..., and that I ought to post it to one of the developer lists. I posted to r-sig-mixed-models, but didn't get any response. So, with good intentions, I decided to try posting once more, but to this more general list. The goal is (1) FYI, to make you aware of this issue, in case it is an error in gls (2) For my information, in case I have made an error, in the hope that one of you folks might be able to correct me. Thanks in advance for your time. The issue is in 2 parts. (A) I've used gls to fit a model with two fixed effects and a corExp object. By my count, this fitting process estimat...
2004 Apr 17
1
accessing log likelihood of poison model
Could someone tell me how to access the log likelihood of a poisson model? I've done the following.... <BEGIN R STUFF> freq.mod <- glm(formula = nfix ~ gls.gls + pol.gls + pol.rel + rac.gls + rac.pol + rac.rac + rac.rel + white + gls.gls.w + pol.gls.w + pol.rel.w + rac.gls.w + rac.pol.w + rac.rac.w + rac.rac.w + rac.rel.w, family = poisson, data = Complex2.freq, offset = lnoffset) summary(freq.mod) anova(freq.mod) <END R STUFF> And that's...
2010 Jul 08
0
Psudeo R^2 (or other effect size) in spatial gls regressions
Dear all, I have been using the function gls in the package nlme in R to fit some spatial regressions (as described in Dormann et al.). However, I have been struggling trying to find a way to calculate a measure of effect size from these models, so I wanted to know if any of you had an idea on how to do this. More precisely, I am producin...
2010 May 28
1
latex.rms and models fit with GLS
Hi, I have fit a model using the rms package with the Gls() function. Is there a way to get the model estimates, std errors, and p-values (i.e. what you get with print(fit)) into latex format? I have tried: f <- Gls(...) latex(f, file='') ... but I get the following error Error in replace.substring.wild(s, old, new, test = test, front = f...
2010 Jan 07
1
faster GLS code
Dear helpers, I wrote a code which estimates a multi-equation model with generalized least squares (GLS). I can use GLS because I know the covariance matrix of the residuals a priori. However, it is a bit slow and I wonder if anybody would be able to point out a way to make it faster (it is part of a bigger code and needs to run several times). Any suggestion would be greatly appreciated. Carlo *...
2009 Aug 20
1
definition of AIC and BIC in gls
Hello everybody, Please help with connecting the AIC and BIC numbers printed by summary.gls to the logLik number. 1. is the logLik number the true ML or density scaling constants have been omitted? 2. what is the formula for calculating the AIC and BIC from logLik (and how can I see it)? I tried printing summary.gls but it says object not found. Thank you very much. Stephen [[alt...
2006 Mar 16
2
DIfference between weights options in lm GLm and gls.
Dear R-List users, Can anyone explain exactly the difference between Weights options in lm glm and gls? I try the following codes, but the results are different. > lm1 Call: lm(formula = y ~ x) Coefficients: (Intercept) x 0.1183 7.3075 > lm2 Call: lm(formula = y ~ x, weights = W) Coefficients: (Intercept) x 0.04193 7.30660 > lm3 Call: lm(f...
2003 Oct 24
2
NLME: gls parameter evaluation inconsistency (PR#4757)
Full_Name: W.B.Kloke Version: 1.8.0 OS: FreeBSD-4.7 Submission from: (NULL) (195.253.22.63) I found a parameter evaluation inconsistency in NLME package. I tried to use gls() inside a function, and I wanted use gls() for different subsets of a data frame: prgls <- function(name){ gls( log10(Y)~(cond-1)+(cond-1):t ,pr,subset=subject==name)} Applying this function with a string as parameter like prgls("VM") yields an error Error in eval(expr, envir, enclo...
2002 Apr 14
0
gls
Dear all, I am confused. I have encountered some strange behaviour of gls > data(co2) > co2.y <- aggregate(co2,1,mean) > co2.y.data <- data.frame(co2=as.numeric(co2.y),year=seq(1959-1980,along=co2.y)) > co2.1.gls <- gls(co2~year+I(year^2), co2.y.data) > co2.2.gls <- update(CO2.1.gls, corr=corAR1()) > summary(CO2.2.gls) > plot(CO2.2.gls)...
2004 Dec 29
3
gls model and matrix operations
Dear List: I am estimating a gls model and am having to make some rather unconventional modifications to handle a particular problem I have identified. My aim is to fit a GLS with an AR1 structure, obtain the variance-covariance matrix (V), modify it as needed given my research problem, and then reestimate the GLS by brute force u...
2005 Nov 17
1
anova.gls from nlme on multiple arguments within a function fails
Dear All -- I am trying to use within a little table producing code an anova comparison of two gls fitted objects, contained in a list of such object, obtained using nlme function gls. The anova procedure fails to locate the second of the objects. The following code, borrowed from the help page of anova.gls, exemplifies: --------------- start example code --------------- library(nlme) ## stole...
2010 Mar 09
1
Computation of AIC for gls models
Dear Colleagues, We are using the phylog.gls.fit() function from the R package "PHYLOGR" (Diaz-Uriarte R, Garland T: PHYLOGR: Functions for phylogenetically based statistical analyses. 2007. Available at [http://cran.r-project.org/web/packages/PHYLOGR/index.html]) to correct for lack of independence between data points. (In our part...