similar to: Meaning of /, :, and %in% in lmer

Hello list, I'm trying to figure out how exactly the specification of nested random effects works in the lmer function of lme4. To give a concrete example, consider the rat-liver dataset from the R book (rats.txt from: http://www.bio.ic.ac.uk/research/mjcraw/therbook/data/ ). Crawley suggests to analyze this data in the following way: library(lme4) attach(rats) Treatment <-

Hello, I used the function cor to calculate the pearson correlation coefficient between variables. However, the resulting values do not correspond to the outcome of my excel-calculations, for which I used the formula Cor(x,y)=Cov(x,y)/(SD(x)*SD(y)) So my question is: How does the function "cor" compute the pearson correlation coefficient? Thank you in advance, Ake Nauta

Hello, We?re receiving reports of extremely slow rendering by users who are using the new geom_sf() feature in ggplot2. Importantly, this seems to be a graphics device issue, because the exact same plot takes vastly different amounts of time to render under different devices. We?re talking about 2 seconds vs. 100 seconds here, so not a small effect. In particular, the quartz device on OS X seems

Colleagues I am working in a Linux OS with R 2.6.2. I need to execute a telnet session to another Linux machine from R, perform some operations, then return to the original computer. When I am in an R session, this is easy to accomplish by typing: system("telnet -l username machinename") I am then asked for my password; once that is entered, I am connected to the remote

Hello -- I am curious if lmer can be used to fit a multilevel factor model such as a two-parameter item response model. The one parameter model is straightforward. A two-factor model requires a set of factor loadings multiplying a single random effect. For example, a logit model for the ith subject responding correctly to the jth item (j=1,..,J) is logit[p(ij)] = a1*item1(i) + ... + aJ *

Hello, certain manipulations of ggplot2 graphs, in particular aligning them, require the function grid:::unit.list(). See e.g. these posts on stackoverflow: http://stackoverflow.com/questions/34032621/element-replacement-in-grid-unit-vector http://stackoverflow.com/questions/32580946/setting-absolute-size-of-facets-in-ggplot2/32583612#32583612 http://stackoverflow.com/a/35823179/4975218 Since

Paul, Subassignment for units has been committed to r-devel. You should now be able to do things like ... x <- unit(1:3, "mm") x[2] <- unit(.5, "npc") (see grid/tests/units.R for more complex examples) Yes, I just tried the latest R devel and it works for me. However: This works for me for the three stackoverflow scenarios. I ran into an additional problem when

(Tried this query on r-help with no luck, maybe someone here can help?) I would like to call the 'RFinalizerEx' function that appears in Rinternals.h using ".Call". It worked for me in the past, but now I get an error message something like: 'call function name not in call table'. I'm using the 1.6.1 rpm from CRAN. Anyone know what's going on? Thanks. Tim --

Hi Subassignment for units has been committed to r-devel. You should now be able to do things like ... x <- unit(1:3, "mm") x[2] <- unit(.5, "npc") (see grid/tests/units.R for more complex examples) This works for me for the three stackoverflow scenarios. Any confirmation that it also works for you would be welcome. Paul On 07/03/16 07:34, Wilke, Claus O wrote: >

I have executed a Repeated Measures ANOVA with one DV (latency) and one within subject factor (acoustic condtion: 3 levels) by bootstrapping my sampling distribution of F from the empirical sample distribution. I chose to resample because the sample distribution deviates from normality a lot. The overall F is significant and now I wish to decompose this with contrasts to ask if latencies to

I have some code that calls R's finalizer interface, e.g., .Call('R_RegisterFinalizerEx', object, function, TRUE) This worked pre 1.6, but now I get '.Call function name not in call table'. Are functions listed in Rinternals.h no longer available in .Call? Or is this a namespace issue? How do I reference the function? Thanks. Tim -- Timothy H. Keitt The University of

How to Ancova in R? I know this has got to be an FAQ, because I see it asked in the lists, but I haven't seen an answer to it. I see the R-sm has the ancova thing happening, but I kind of doubt that what I'm trying to do is "smoothing"... -- Pete Hurd phurd at uts.cc.utexas.edu http://www.zo.utexas.edu/research/phurd Section of Integrative Biology, University of Texas, Austin

Dear R friends, I was wondering if there were factorial and modulus functions out there that I've somehow overlooked? -P. -- Peter L. Hurd, Ph.D. phurd at uts.cc.utexas.edu http://www.zo.utexas.edu/research/phurd fax 512.471-3878 Section of Integrative Biology, University of Texas, Austin TX 78712 USA

Hi Folks, I have repeated measures for data on association time (under 2 acoustic condtions) in male and female frogs as they grow to adulthood (6 timepoints). Thus, two within-subject variables (Acoustic Condition: 2 levels, Timepoint: 6 levels) and one between-subject variable (Sex:male or female). I am pretty sure my distributions depart from normality but I would first like to simply run a

Hello R friends, I'm wondering why I get funny qqnorm() results. It seems that they should all be reflected in the normal qqline(). For instance: if I qqnorm() bimodal or uniform data I get a sigmoidal in which the qqnorm() points lie above the qqline() at -ve theoretical quantiles, and the qqnorm() points lie below the qqline() at +ve theoretical quantiles. Yet I expect such platykurtic

R-users - I must preface this question by saying that I'm a relative newbie to both R and mixed-modeling. I'm using lme fit an ANCOVA-like model. My data consist of bone length measurements for a developmental series of two capuchin monkey species. I'm interested in whether the rate of bone length scaling to body mass (i.e., growth) differs between species. My call to lme

-- R Help List -- I am looking for a bivariate normal cdf routine in R. I have some fortran routines for this, which appear to be based on 15-point quadrature. Any guidance/suggestions on making these in loadable R-functions would be appreciated. Thanks, Dan =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Daniel A. Powers, Ph.D. Department of Sociology University of Texas at Austin

I am trying to copy files to a password protected drive which is "Ranch" at TACC from another network drive. I am logged in to the source drive and can run R there. The following code does not even find the destination folder. file.copy("sourcedrive/file.tar", " username@ranch.tacc.utexas.edu/uniqueID/destinationfolder/file.tar", overwrite = FALSE) Thanks in

Hello world, I'm trying to do an anova on data in data.set, dependent variable is a column named "dep.var", grouping variable is in a column called "indep.var", and is.factor(indep.var) is TRUE... why can't I just do aov(dep.var ~ indep.var, data = data.set)? What have I done to deserve this?! What gives? Am I missing something totlly obvious? R-base-1.0.0-1,

Hi, I am not on this mailing list, but here is a terrible bug that has stopped me in my tracks. I am unable to remove observations from a data matrix. temp is the original matrix. Notice that there are 288 entries with a 104 in the first column. I attempt to remove these entries, but R does not do it. brad ACTUAL COMMANDS: > dim(temp) [1] 30528 11 > table(temp[,1]) 1 3 4