similar to: how to print the plots

Dear R users, I am using lme and nlme to account for spatially correlated errors as random effects. My basic question is about being able to correct F, p, R2 and parameters of models that do not take into account the nature of such errors using gls, glm or nlm and replace them for new F, p, R2 and parameters using lme and nlme as random effects. I am studying distribution patterns of 50 tree

Dear r-helpers, Spencer Graves and Manual Morales proposed the following methods to simulate p-values in lme4: ************preliminary************ require(lme4) require(MASS) summary(glm(y ~ lbase*trt + lage + V4, family = poisson, data = epil), cor = FALSE) epil2 <- epil[epil$period == 1, ] epil2["period"] <- rep(0, 59); epil2["y"] <- epil2["base"]

Dear R-helpers, I have a time series analysis problem in R: I want to analyse the output of my simulation model which is proportional cover of shrubs in a savanna plot for each of 500 successive years. I have run the model (which includes stochasticity, especially in the initial conditions) 17 times generating 17 time series of shrub cover. I am interested in a possible periodicity of shrub

Dear R users, i'm using a custom function to fit ancova models to a dataset. The data are divided into 12 groups, with one dependent variable and one covariate. When plotting the data, i'd like to add separate regression lines for each group (so, 12 lines, each with their respective individual slopes). My 'model1' uses the group*covariate interaction term, and so the coefficients

Dear all, for a cross-validation I have to use predict.glmmPQL() , where the formula of the corresponding glmmPQL call is not given explicitly, but constructed using as.formula. However, this does not work as expected: x1<-rnorm(100); x2<-rbinom(100,3,0.5); y<-rpois(100,2) mydata<-data.frame(x1,x2,y) library(MASS) # works as expected model1<-glmmPQL(y~x1, ~1 | factor(x2),

Hi, I am using puppet as my configuration solution, it is a very good for system-level configuration management and compliance. But it is not good at batch jobs. For now, I have three options: puppi, MCollective and ControlTier. I don''t know much about them. Can anyone give me some advices that which of them is better at batch jobs. Thanks Yunfeng -- You received this message because

　　We meet a block issue in today''s nightly testing. Xen0 hang when we destroy a XenU guest. Block issue 1) xen0 hang when destroying a XenU guest http://bugzilla.xensource.com/bugzilla/show_bug.cgi?id=963 Thanks Yunfeng _______________________________________________ Xen-devel mailing list Xen-devel@lists.xensource.com http://lists.xensource.com/xen-devel

Hi: I think I found an error in plot.lm with the option which=5, of course I can be wrong , as usually happen, but I had work on it for a while and show it to some other people that work with R, and so far I don't see what I can be interpreting wrong. I also worked over the plot.lm's code and change some lines to get what I call "the right plot", if any body is

[cc'ing back to r-help] On Fri, Nov 18, 2011 at 4:39 PM, matteo dossena <matteo.dossena at gmail.com> wrote: > Thanks a lot, > > just to make sure i got it right, > > if (using the real dataset) from the LogLikelihood ratio test model1 isn't "better" than model, > means that temporal auto correlation isn't seriously affecting the model? yes. (or

Hi, I have a large matrix (SNPs) that I want to cycle over with logistic regression with interaction terms. I have made a loop but I am struggling to identify to the formula the name of the column in a way which is meaningful to the formula. It errors becasue it is not evaluated proporly. (below is a pilot with only 7 to 33 columns, my actual has 200,000 columns) My attempts: for (i in 7:33)

I was working on a project involving a linear model, and wanted to extract the standard error of a predictor. I am able to do so, but not in the way I would expect. I would have expected that if a created a model such as Model1 <- lm(y~x,z,d), the object Model1 would contain that information even though it does not print it out when I simply type Model1. I would also have (wrongly)

Hello, I have been using sink to create text file outputs. >sink("summ_model1and2.txt") > summary(model1) > summary(model2) > sink() Q1: Is there a way I could add a line of the text above the summary to act like a title? Also, I have been using the following to save plots from the lm function: > pdf("small.bin.ENN_MN_withQ.pdf") > par(mfrow = c(2, 2), oma

Hi everyone, I have recently experienced a strange behavior (strange from my knowledge) in rails. In my controllers ''new'' action, I am creating a few instance variables in the following manner : @controllerModel = ControllerModel.new @model1 = Model1.all @model2 = Model2.all in my ''new'' view, I am using the @controllerModel to create the form for new and I

The "tsdiag" function in the TSA package overrides the "tsdiag" function in the "stats" package. There are a few annoying bugs in the TSA's version of the function so I would like to use the "stats" function but still have access to other TSA functions. I have tried using stats::tsdiag( ) but as long as the TSA package is attached the function from

Hi, I am running R2.8.1 under Linux, and I am having trouble using the variance functions in nlme My basic model was something like: model0 <- lme( log(growth) ~ light * species.group , data=data, random=~light|species ) # with 20 odd species divided in 2 groups Following the methods in Pinheiro&Bates I tried to put a variance function in the model: model1 <- update(model0,

Greetings, Apologies for such a simple question, but I have been trying to figure this out for a few days now (I'm quite new to R), have read manuals, list posts, etc., and not finding precisely what I need. I am accustomed to working in Stata, but I am currently working through the multilevel package right now. In Stata, I would include the statement "if model1 == 1" at the end

Full_Name: Menelaos Stavrinides Version: 1.3. 1 OS: Windows 98 Submission from: (NULL) (193.129.76.90) When model simplification is used in glm (binomial errors) and anova is used two compare two competitive models one can use either an "F" or a "Chi" test. R always performs an F test (Although when test="Chi" the test is labeled as Chi, there isn't any

Dear R-gurus, I have an interpretation problem regarding lme models. I am currently working on dog locomotion, particularly on some variation factors. I try to figure out which limb out of 2 generated more dispersed data. I record a value called Peak, around 20 times for each limb with a record. I repeat the records during a single day, and on several days. I tried to build two models, one

Hello Fellow R Users,I have spent the last week trying to find a work around to this problem and I can't seem to solve it. I simply want to plot my GEE model result with 95% confidence bands. I am using the geepack package to run a basic GEE model involving nestling weights, to a Gaussian distribution, with "exchangeable" error structure. I am examining how nestling weight varies

Dear R users, I would like to extract df and Mean Sq values. I tried several things (e.g., str(model1), names(model1)) but I can't find a way to extract these values. I also tried to search using RSiteSearch. Any help will be appreciated. Thanks Taka, model1<-aov(dv~iv.1*iv.2*iv.3) summary(model1) Df Sum Sq Mean Sq iv.1 1 3.200 3.200