similar to: Problem with lmer and fixef

Dear R help list, I have done a lot of searching but have not been able to find an answer to my problem. I apologize in advance if this has been asked before. I am applying a mixed model to my data using lmer. I will use sample data to illustrate my question: >library(lme4) >library(arm) >data("HR", package = "SASmixed") > str(HR) 'data.frame': 120 obs.

I am having a problem extracting from "mer" objects.    I have constructed my problem using existing datasets.   Using the following commands:   require(lme4) fm1 <- lmer(Yield ~ 1 + (1 | Batch), Dyestuff) fixef(fm1) I get the following error message: "Error in UseMethod("fixef") : no applicable method for "fixef""   I know that "fixef" is in

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

Hi, I would like to extract the fitted values from a model using LMER but only for the fix portion of the model and not for the fix and random portion (e.g it is the procedure outpm or outp in SAS). I am aware of the procedure fitted() but I not sure it give the fitted values both for the fixed and random or only the fixed. I looked in the r help and the r list and I haven?t not found much

Dear R group, Tried to turn off the html in yahoo.  So far  not successful.  Apologies! I tried to get xyplot shrink fit for my mixed model.  But, the mixed model line is not seen in the graph. I would like to know if there is anything wrong with my code. Thanks, A.K. (fm1 <- lmer(Response3 ~1+ Wavelength*Start_Resp*time + (1|resid) + (1+time|Subject_BDat), family=binomial, data=Behavdat,

Hello! I am trying to model data on species abundance (count data) with a poisson error distribution. I have a fixed and a random variables and thus needs a mixed model. I strongly doubt that my model is overdispersed but I don't know how to get the overdispersion parameter in a mixed model. Maybe someone can help me on this point. Secondly, it seems that quasi models cannot be implemented

Hello! I would like to make a scatterplot of my data, but the problem is that several points have the same x and y values and are represented as only one point. I wonder if there is a way to represent the data points, but with point size representing the frequency of the depicted x-y value? Thank you! -- View this message in context:

I am attempting to build a package on r-forge and running into a weird error. I have been in correspondence with the R-forge admins and am turning to r-devel on the remote chance that someone might have a guess as to what is going wrong or a suggestion about further diagnostics/experiments I could try ... The package seems to build fine on my system(s) with R CMD build --compact-vignettes

Dear all, I'm trying to store/extract the mean& standard error of the fixed effects parameter and the variance of the random effects parameter from "lmer" procedure from mlmre4 package developed by bates n pinheiro. while storing fixed effects parameter is straight forward, the same is not true for storing the variance parameter of the random effects. kindly help me ~prabhu

Hello! It is not really linked to R, but can somebody explain me why we sometimes make a mantel test directly for to distance matrices and sometimes we first make a gradient analysis and then a mantel test between the axis? Thank you -- View this message in context: http://www.nabble.com/Mantel-test-tp25439984p25439984.html Sent from the R help mailing list archive at Nabble.com.

Hello, I plot the abundance of a species in relation to the date. To have the date as a continous variable I put it in the format "standard" in excel (f.ex. 39939 means 06.05.2009). R uses 39939 on the x axis, but I would like to have "06.05". I tried to use as.Date as suggested in some discussion but I don't manage to use it, the returned date is not correct. Do you have

Hello All, I would like to retrieve some of the results from the lmer(...) function in library lme4. If I run a model, say fm.1 <- lmer(y ~ 1 + (1 | x), data = dog) and try names(fm.1), I get NULL. Is there anyway to retrieve the information? Thanks

Dear all, I am running a mixed model using lmer. In order to obtain CI of individual coefficients I use mcmcsamp. However, I need advice which values that are most appropriate to present in result section of a paper. I have not used mixed models and lmer so much before so my question is probably very naive. However, to avoid to much problems with journal editors and referees addicted to

Hi, I have been having a tedious issue with lmer models with lots of factors and lots of levels. In order to get the basic information at the beginning of the print out I also have to generate these enormous tables as well. Is there a method command to leave off all of the effects and correlations? Or, do I have to go to string commands?

Dear all, I'm curious about how to interpret the results of the following code. The first model is directly from the help page of lmer; the second is the same model but using the Gamma family with log link. The fixed effects make sense, because y = 251.40510 + 10.46729 * Days is about the same as log(y) = 5.53613298 + 0.03502057 * Days but the random effects seem quite

Hello, I performed a Mantel test and plotted communitiy similarities. I would like to add a least square line. I thought about using abline taking as slope the r-statistic of the Mantel test and calculating the y-intercept analytically. Is this method correct? Is there any function for this calculation? Thank you -- View this message in context:

Hello, I would like to plot a large number of graphs (43) in a same window. I tried wit par(mfrow=c(8,5)), but when I give the code for the plots I receive a error message saying that the margins are to wide. Can someone help me? Is it possible to put so many graphs in a single window? Thank you -- View this message in context:

Hi, I wish to extract a subset of the information of given by summary(lmer.object) as a dataframe. In particular, I wish to extract just a table listing the Estimate, Std Error, and t-values rounded to 3 decimal places. I have learned how to extract the coefficients with "round(fixef(lmer.object),3)" and the standard errors with "round(sqrt(diag(vcov(a.lmer))),3)" but I do not

Hi All! I am desperately needing some help figuring out how to calculate LD50 with a GLMM (probit link) or, more importantly, the standard error of the LD50. I conducted a cold temperature experiment and am trying to assess after how long 50% of the insects had died (I had 3 different instars (non significant fixed effect) and several different blocks (I did 4 replicates at a time)=

Hello, R community, I have been using the lmer and mcmcsamp functions in R with some difficulty. I do not believe this is my code or data, however, because my attempts to use the sample code and 'sleepstudy' data provided with the lme4 packaged (and used on several R-Wiki pages) do not return the same results as those indicated in the help pages. For instance: > sessionInfo() R