similar to: continuous time AR(1)

I am having trouble fitting correlation structures within nlme. I would like to fit corCAR1, corGaus and corExp correlation structures to my data. I either get the error "step halving reduced below minimum in pnls step" or alternatively R crashes. My dataset is similar to the CO2 example in the nlme package. The one major difference is that in my case the 'conc' steps are

Hi, I have been using the function lme() of the package nlme to model grouped data that is auto-correlated in time and in space (the data was collected on different days via a moving monitor). I am aware that I can use the correlation classes corCAR1 and corExp (among other options) to model the temporal and spatial components of the auto-correlation. However, as far as I can tell, I can only

  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

Hello all, I am trying to use lme to examine how a response variable (Chla) changes over time in different treatments (2 Temp & 2 Light levels). Within each treatment combination, there are two replicate tanks (each with unique TankID) with coral fragments in them. All tanks are subject to the same environment until Time=0, when treatments are imposed, and Chla is measured for each

Dear listers, I am trying to model the distribution of fox density over years in the Doubs department. Measurements have been taken on 470 plots in March each year and georeferenced. Average density is supposed to be different each year. In a first approach, I would like to use a general model of this type, taking spatial correlation into account:

Hi, I'm trying to introduce a (spatial) exponential correlation structure (with range=200 and nugget.effet of 0.3) in a lme model of this form: lme(ARBUS~YEAR, random=~1|IDSOUS). The structure of the data is "IDSOUS" "XMIN" "YMAX" "YEAR" "ARBUS" with 2 years of data and 5600 points for each year. I do:

I'd like to compare two models which were fitted using gls, however I'm having trouble interpreting the results of gls. If any of you could offer me some advice, I'd greatly appreciate it. Short explanation of models: These two models have the same fixed-effects structure (two independent, linear effects), and differ only in that the second model includes a corExp structure for

Dear R-help, Can anyone explain the meaning of the warning, Singular precision matrix in level -1, block 1 ? Or how to track down where it comes from? More precisely, using the nlme package, I'm issued with the warning itt2 <- lme(lrna~rx.nrti+lbrna, random=~1|patid, cor=corExp(form=~days|patid,nugget=T), weights=varPower( form=~lbrna),data=rna3) Warning messages: 1: Singular

Hi, I have tried and spend some times to find the answer myself but it couldn't find anything that could solve my issue, so I hope someone could help me with this, and I am sure this could benefit to other samba users also. OK, here is the story: I currently use samba (smbd -V: Version 4.2.4-6.3-3503-SUSE-SLE_12-x86_64) I have a server where samba is installed and another one where openldap is

Dear all, I?m analyzing this dataset containing biodiversity indices, measured over time (Week), and at various contaminant concentrations (Treatment). We have two replicates (Replicate) per treatment. I?m looking for the effects of time (Week) and contaminant concentration (Treatment) on diversity indices (e.g. richness). Initial analysis with GAM models showed temporal autocorrelation of

A couple weeks ago I posted a message on this topic to r-help, the response was that this seemed like odd behavior, 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

I know Tarkin is not the priority right now, but when it becomes it's good to know which company might feel nervous... ------------------------------------------ Compaq sued for alleged patent violations By Bloomberg News November 20, 2000, 5:30 a.m. PT WILMINGTON, Del.--Compaq Computer, the world's biggest personal computer maker, has been sued by a group for allegedly infringing

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 = "euclidean" in (for example) corSpher would be incorrect. I would be grateful for help on how to

Hi all, I wrote a piece of code that generates simulated variables. after variable generation I use them in several analyzes. However, when I use a for to repeat the procedure 1000 times I get an erro message in one of the "for" steps, precisely at this time: gls.temp<- gls(y2 ~ x2,correlation=corExp(form=~coord2[,1]+coord2[,2])) # coord 2 are spatial coordinates and the error

I am using R 2.7.0 on a linux platform. I am trying to reproduce a 2002 example using lme from the nlme library. I want to change the otimizer from the default (nlminb) to optim. Specifically, this is what I am trying to do: R> library(nlme) R> library(car) # for data only R> data(Blackmoor) # from car R> Blackmoor$log.exercise <- log(Blackmoor$exercise + 5/60, 2) R>

Dear all, Here is the question: For example, using the "petrol" data offered with R. pet3.lme<-lme(Y~SG+VP+V10+EP,random=~1|No,data=petrol) pet3.lme$sigma gives the residual StdDev. But I can't figure out how to extract the "(intercept) StdDev", although it is in the print out if I do "summary(pet3.lme)". In

Dear listers, As an exercise, I am trying to fit a logistic model with nlme. Blue tit pulli (youngs) were weighted occasionnally (for field reasons) along time in 17 nestboxes. Individuals where not idenfied but their age was known. This means that for a given age several measurements were done but individuals could not be identified from a time to the other. This makes repeated values for

Hello, I have been asked to perform a exponential correlation on a data set. Unfortunately, i did not find any simple example on how to do that with R. If the correlation is significant, one asked me to also find the thresold of the acceleration slope. Have any of you a little example or a good link to get me started? Best regards Blaise -- Mutt, c'est de la balle, quand ??a marche :-)

>>>>> "VW" == Viechtbauer Wolfgang (STAT) <Wolfgang.Viechtbauer at STAT.unimaas.nl> >>>>> on Fri, 26 Sep 2008 18:00:19 +0200 writes: VW> Hi all, I'm trying to fit a marginal (longitudinal) VW> model with an exponential serial correlation function to VW> the Orange tree data set. However, R crashes frequently VW>

Hello all, I'm new in R, and I have a data-frame like this (dput information below): Specie Fooditem Occurrence Volume 1 Schizodon vegetal 1 0.05 2 Schizodon sediment 1 0.60 3 Schizodon vegetal 1 0.15 4 Schizodon alga 1 0.05 5 Schizodon sediment 1 0.90 6 Schizodon