similar to: help with structuring random factors using lmer()

Can you provide the summary(m2) results? > -----Original Message----- > From: Simon Pickett [mailto:S.Pickett at exeter.ac.uk] > Sent: Wednesday, August 16, 2006 7:14 AM > To: Doran, Harold > Cc: r-help at stat.math.ethz.ch > Subject: [SPAM] - RE: [R] REML with random slopes and random > intercepts giving strange results - Bayesian Filter detected spam > > Hi again,

Hi R experts, I am interested on the effects of two dietry compunds on the growth of chicks. Rather than extracting linear growth functions for each chick and using these in an analysis I thought using ReML might provide a neater and better way of doing this. (I have read the pdf vignette("MlmSoftRev") and "Fitting linear mixed models in R" by Douglas Bates but I am not

Hi all, I have been bumbling around with r for years now and still havent come up with a solution for plotting reliable graphs of relationships from a linear regression. Here is an example illustrating my problem 1.I do a linear regression as follows summary(lm(n.day13~n.day1+ffemale.yell+fmale.yell+fmale.chroma,data=surv)) which gives some nice sig. results Coefficients:

Hi R experts, I have been using ReML as follows... model<-lmer(late.growth~mtf+year+treat+hatch.day+hatch.day:year+hatch.day:treat+ mtf:treat+ treat:year+ year:treat:mtf+(1|fybrood), data = A) then I wanted to plot the results of the three way interaction using lines() as follows... tmp<-as.vector(fixef(model)) graph1<-plot(mtf,fitted(f2), xlab=list("Brood Size"),

Hi, I would like to (if possible) set the default width and height for graphs at the start of each session and have each new graphic device overwrite the previous one. I only know how to do this using windows(width=,height=...) which opens up a new plotting device every time, so I end up with lots of graphs all over the place until I get the one I want! Thanks in advance, Simon Simon Pickett

Hi everyone, I have been using REML to derive intercepts and coeficients for each individual in a growth study. So the code is m2 <- lmer(change.wt ~ newwt+(newwt|id), data = grow) Calling coef(model.lmer) gives a matrix with this information which is what I want. However, as a test I looked at each individual on its own and used a simple linear regression to obtain the same information, then

Hi, I have been dabbling with str() to extract values from outputs such as lmer etc and have found it very helpful sometimes. but only seem to manage to extract the values when the output is one simple table, any more complicated and I'm stumped :-( take this example of the extracted coeficients from a lmer analysis... using str(coef(lmer(resp3~b$age+b$size+b$pcfat+(1|sex), data=b)))

Hi all, I have been using princomp() recently, its very useful indeed, but I have a question about how to specify the rows of data you want it to choose. I have a set of variables relating to bird characteristics and I have been using princomp to produce PC scores from these. However since I have multiple duplicate entries per individual (each bird had a varying number of chicks), I only want

Hi, I am an R newbie and one thing I am having trouble with binding variables that I have created within one data frame into a new data frame when using na.omit(). To illustrate this problem I will give the example I am working on and the approah I have been using:- data.frame1<-filepath.... attach(data.frame1) #create a new variable using a function new.variable<-rep(1,length(weight3))

Hello everyone, I have successfully made an error bar graph using the points() command with the arrows() command to maually add on the standard errors. However, one slightly annoying feature of using this method is that the points dont line up exactly with the arrows (if you look carefully the points are never perfectly in the centre of the arrow), even when you move the arrows around in an

Hi, Thanks for your response, it nearly worked! But it only wrote one coloumn of data and not the three columns I need. Using fixef(m1) doesnt give the same results as coef(m1) when you are using more than one random effect. I need the coefficients for each individual so I use coef(m1) to get this which results in an object of class lmer.coef, 3 columns by 700 rows. as.data.frame() wont work on

I have been using lmer in lme4() to analyse the effect of dropping a term from the model as below anova.name<-anova(m1,m2) Where m1 is an original model and m2 has one term removed. I can then create my own type III tables for each variable in the model. However with many variables this becomes exceedingly time consuming! anova.lme in nlme() and Anova() in car dont seem to work for lme

Hi all, This is partly a statistical question as well as a question about R, but I am stumped! I have count data from various sites across years. (Not all of the sites in the study appear in all years). Each site has its own habitat score "habitat" that remains constant across all years. I want to know if counts declined faster on sites with high "habitat" scores. I can

hi all, I often have a data frame like this example data.frame(sq=c(1,1,1,2,2,3,3,3,3),area=c(1,2,3,1,2,3,1,2,3),habitat=c("garden","garden","pond","field","garden","river","garden","field","field")) for each "sq" I have multiple "habitat"s each with an associated "area". I

Hi all, I've used R for basic programming and data management for a few years now. One of the things that I think could be improved is the data editor. Its a great feature and I use it alot by calling edit(data.frame); very useful to see if what you tried to do actually worked. However, one of the annoying things about it is that when you scroll down the window it doesnt show you all the

Hi all, This could be naivety/stupidity on my part rather than a problem with model output, but here goes.... I have fitted a fairly simple model m1<-glm(count~siteall+yrs+yrs:district,family=quasipoisson,weights=weight,data=m[x[[i]],]) I want to know if yrs (a continuous variable) has a significant unique effect in the model, so I fit a simplified model with the main effect ommitted...

Hi all, I would like to 1. Read in an arcmap image into R (I can export pretty much any type of image jpeg, bitmap etc from arcmap) 2. Use R to create a nice colour legend in the plot First of all, Is this possible? So far I'm stuck on point 1. I have tried read.pnm() from pixmap and read.jpeg() from rgl. the pnm example provided works fine x <-

Hi all, I have been trying to use zeroinfl() with the pscl package with R version 2.1.1. and with the newest versions of the contrib packages compatible with R 2.1.1. I have read the examples, the vignette and all the posts relating to zeroinfl() but I am still confused as to how to structure the model. Here is a small example; the error message is the same for big data sets

Hi, I'm testing Dovecot to migrate from my old Courier IMAP/POP server. It work fine but I have some problems to start the sieve server "pysieved" from Neale Pickett in PAM auth, I got the message: Traceback (most recent call last): File "/usr/share/pysieved/pysieved.py", line 97, in <module> main() File "/usr/share/pysieved/pysieved.py", line

Hi all, I recently discovered how great win.metafile is for getting high resolution graphics into word. Having problems with specifying families though... #pdf works fine pdf("test.pdf",width=14,height=9) par(family="Helvetica") plot(1:10) text(4,4,"trial") dev.off() windows 2 #metafile doesnt like helvetica family