similar to: R 2.6.0 Windows/lme4 Rblas load problem

Dear List, assume I want to make a minor local change in a package that is supplied as .rda. For example, I want to get rid of the non-verbose-protected "Iteration" message in GLMM/lme4. Probably I have to load / change / save the package, but could someone help me to get the syntax right? Dieter Menne

We have extracted parameters from physiological measurements by fitting SSlogis-like curves with nlsList and nlme. We presented residuals plot in a paper, but a referee argues that these cannot be included (too technical), and r-square values should be given instead to compare the goodness of fit with those of other authors. I remember that 30 years ago in my stat 101, I learned that r-square is

Dear List, I am struggling understanding S4 classes. For example, when GLMM summary(glmmML( whatever)) outputs the following line: Estimate Std. Error DF z value Pr(>|z|) (Intercept) 0.856 0.319 45 2.68 0.0073 How do I access the Pr column? Dieter

Is there an easy way to remove data frame columns by name instead of by index? The following gives the idea remove<-c("subj","drug") data[-remove] I found a solution with a few evals and substitutes, similar to that used in reshapeLong, but there must be an easier way out. Dieter --------------------------------------- Dr. Dieter Menne Biomed Software 72074 T?bingen Tel

I am confused by the logic of renaming: # Rename individual list items? Empl<-list(employee="Anna",spouse="Fred") names(Empl)<-c("empl","spo") names(Empl) #[1] "empl" "spo" # worked like a charm... but names(Empl[1])<-"newempl" # no error message, yet .... names(Empl) #[1] "empl" "spo" #

Hi Dieter, Sorry my mistake. I wanted to convert them into Decimal (not Hexadecimal). Given this string, the desired answer follows: > ascii_str <- "ORQ>IK" 79 82 81 62 73 75 > ascii_str2 <- "FDC" 70 68 67 - Gundala Viswanath Jakarta - Indonesia On Mon, Dec 22, 2008 at 5:49 PM, Dieter Menne <dieter.menne at menne-biomed.de> wrote: > Gundala

Dear R and lme4 users- I am trying to fit a mixed-effects model, with the glmer function in lme4, to right-skewed, zero-inflated, non-normal data representing understory grass and forb biomass (continuous) as a function of tree density (indicated by leaf-area). Thus, I have tried to specify a Gamma distribution with a log-link function but consistently receive an error as follows: >

Dear R-Listers, to measure the psychometric curve of pitch discrimination, one sequentially presents two tones of slightly different pitch to an observer (animal will do), and asks "which is higher". The pschometric curve is the fraction of correct responses plotted against the pitch difference. It passes through 50% (pure guessing) at zero and normally approaches 100% at large

Dear friends of nlme, Running quinModel (Pinheiro/Bates page 380) on R (current release, windows) gives: Nonlinear mixed-effects model fit by maximum likelihood Model: conc ~ quinModel(Subject, time, conc, dose, interval, lV, lKa, lCl) Data: Quinidine Log-likelihood: -497 Fixed: lV + lKa + lCl ~ 1 lV lKa lCl 5.382 -0.273 2.470 Random effects: Formula: list(lV ~ 1, lCl ~ 1)

Using a formula converted with as.formula with lme leads to an error message. Same works ok with lm, and with lme and a fixed formula. # demonstrates problems with lme and as.formula demo<-data.frame(x=1:20,y=(1:20)+rnorm(20),subj=as.factor(rep(1:2,10))) demo.lm1<-lme(y~x,data=demo,random=~1|subj) print(summary(demo.lm1)) newframe<-data.frame(x=1:5,subj=rep(1,5))

Hi Dieter and R community: I tried both of these three versions with ylim as suggested, none work: I am getting only single (pch = 16) not overlayed (pch =3) everytime. *vs 1* require(lattice) xyplot(Sepal.Length ~ Sepal.Width | Species , data= iris, panel= function(x, y, subscripts) { panel.xyplot(x, y, pch=16, col = "green4", ylim = c(0, 10)) panel.lmline(x, y, lty=4, col =

I have problem getting the concept of a nested fixed variable into the nlme scheme. I fear the question is very stupid. In the past I had asked this before, and never got a reply (in other cases, the response was within hours). I also checked the S-list, where several similar enquiries of other people are orphaned. We have a cross-over design, where patient are treated two weeks with placebo,

Dear friends of lmer, http://wiki.r-project.org/rwiki/doku.php?id=guides:lmer-tests I have put a transcript of the long thread on lmer/lme4 statistical test into the Wiki. For all those who missed it life, and for those like me, who don't like the special style of the R-list to keep full length quotes. Creating the text there was not much fun, waiting times are simply unacceptable and the

deriv seems to have problems with a minus-sign before a bracket. Below are four examples of the same function, the top one is wrong, all others are correct (hopefully). Rest of expression not shown, it is the same for all versions. _ platform i386-pc-mingw32 arch x86 os Win32 system x86, Win32 status major 1 minor 3.0 year 2001 month 06 day 22 language R

I have a two-dimensional loess fit, and need to calculate the gradient field from it. Even after looking at loess.c and loess.f, I don't understand the meaning of the returned polynomial coefficients. Or is the brute force method of using a tangential approx to the fitted values the way to go? Dieter Menne --------------------------------------- Dr. Dieter Menne Biomed Software 72074

Dieter Menne wrote: > Hi, Jim, > > there is a typo at the bottom of plotCI: there is an y.to.in which should be > x.to.in. > > See list for an example. > > http://article.gmane.org/gmane.comp.lang.r.general/147103 > > Should be: > nz <- (abs(ui - pmin(x + gap, ui)) * x.to.in) > 0.001 > > Dieter > > Hi Dieter, Thanks for the fix. I have

Thanks to Dieter Menne and Spencer Graves I started to get my way through lsoda() Now I need to use it in with nls() to assess parameters I have a go with a basic example dy/dt = K1*conc I try to assess the value of K1 from a simulated data set with a K1 close to 2. Here is (I think) the best code that I've done so far even though it crashes when I call nls()

Dear Mixed Effect Friends, Somehow, R(1021, Windows) seem to run differently from S Plus: The soybean example from Pinheiro/Bates on page 290 fails in R. (Soybean1 is Soybean with the NA and "critical" case removed. Same procedure with full Soybean). > fm1Soy.lis<-nlsList(weight~SSlogis(Time,Asym,xmid,scal),data=Soybean1) > fm1Soy.nlme<-nlme(fm1Soy.lis) Error: Singularity

Dear friends of lattice, I know how to position trellis plots with print(...,split,more=T) or (...position). Sometimes I wish I had something like the old "par(mfcol=2, mfrow=3)" mechanism, where the next free viewport is automatically chosen. I tried fiddling with grid-viewports, but could not find an easy solution. Did I miss something? Dieter Menne

I noticed a problem using R 2.7.1 on Windows XP SP2 with the precompiled Atlas Rblas.dll. Running the code below causes R to crash. I started R using Rgui --vanilla and am using the precompiled Atlas Rblas.dll from cran.fhcrc.org dated 17-Jul-2007 05:04 for Core2 Duo. The code that causes the crash: x <- rnorm(100) y <- rnorm(100) z <- rnorm(100) loess(z ~ x * y) loess(z ~ x) does