similar to: GAM, GAMM and numerical integration, help please

(corrected version of previous posting) I fit a GAM to turtle growth data following methods in Limpus & Chaloupka 1997 (http://www.int-res.com/articles/meps/149/m149p023.pdf). I want to obtain figures similar to Fig 3 c & f in Limpus & Chaloupka (1997), which according to the figure legend are "expected size-at-age functions" obtained by numerically integrating

Hi All, I just used "dump" on Splus to transfer a pile of survival objects from Splus 3.4 on Solaris 7 to R 0.63.3 on Intel. The only trick is that survival objects contain an element holding the original call that generated the object. When Splus writes these out, it doesn't mark them in any way, so when R tries to read them in, it ends up trying to reevaluate the call. Not

Hi All, I just used "dump" on Splus to transfer a pile of survival objects from Splus 3.4 on Solaris 7 to R 0.63.3 on Intel. The only trick is that survival objects contain an element holding the original call that generated the object. When Splus writes these out, it doesn't mark them in any way, so when R tries to read them in, it ends up trying to reevaluate the call. Not

To get RSPython installed on my debian test box, I had to make a couple of changes not listed in ftp://www.omegahat.org/pub/Omega/RSPython/FAQ.html 1) I had to change $R_HOME/src/modules/X11 : $(R_X11_la): $(R_X11_la_OBJECTS) $(R_X11_la_DEPENDENCIES) $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS) $(R_X11_la_LIBADD) $(LIBS) to $(R_X11_la): $(R_X11_la_OBJECTS)

Hi All, I would like to use anonymous cvs, but it appears not to be working (again?). There was a discussion back in Jan-Feb about whether to continue supporting it, but it seemed that Tony Rossini got it working and the discussion left off there. Did someone decide to disable it, or is it just not working properly? Here's the details: $ cvs -d

This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_000_01C344B0.28BC0750 Content-Type: text/plain; charset="windows-1252" Summary: Currently R provides > dev.control(displaylist='inhbit') to turn *off* the recording of graphics operations in a device, but there is no

A colleague has seen a problem (with Samba 3.0), in using LDAP. A very simple version of the problem is as follows, where he tries to authenticate a user "grw" > > I am almost there... I get the following when I do a simple test to > > find the user 'grw' by attempting to change the password (even > > though I do not want Samba to change the pw, this

I'm new to all this Linux stuff and looking to download Wine. Is there a version that I should choose for Limpus?

Hi all, with PowerPoint and ThinkCell one can draw something they call waterfall chart and it looks like this: http://www.think-cell.com/products/images/waterfall.gif I found discussions on waterfall charts in the archive of this mailinglist, but unfortunately they looked totally different. Other names for this type of plot seem to be bridge chart, cascade chart, stair case chart, etc. but

Summary: patch to add environment parameter to load() to allow -------- specification of destination environment. --> Patch against R 0.63.2 appended at end of this message. <-- Story: ------ I've been running some rather long MCMC chains, which occasionally crash, either due to an "Invalid tag in name extraction" error, or due to the machine going down. (I'm playing

Hi, I have installed wine on Mandrake 8.1 (the RPM from the Mandrake CD), fixed the ~/.wine/config file (man wine.conf) but the wine still does not work. If I run what-ever application it does nothing, if I leave it long enough, it displays this.... [mypc]#wine notepad err:ntdll:RtlpWaitForCriticalSection Critical section 0x4011a610 wait timed out, retrying (60 sec) fs=024f

Per the discussion about the problems with prcomp() when n << p, which boils down to a problem with svd() when n << p, here is a patch to prcomp() which substitutes La.svd() instead of svd(). -Greg (This is really a feature enhancement, but submitted to R-bugs to make sure it doesn't get lost. ) *** R-1.6.0/src/library/mva/R/prcomp.R Mon Aug 13 17:41:50 2001 ---

Dear R-users, To obtain the percentage of deviance explained when fitting a gam model using the mgcv library is straightforward: summary(object.gam) $dev.expl or alternatively, using the deviance (deviance(object.gam)) of the null and the fitted models, and then using 1 minus the quotient of deviances. However, when a gamm (generalizad aditive mixed model) is fitted, the

Hi all, I would like to fit a gamm model of the form: Y~X+X*f(z) Where f is the smooth function and With random effects on X and on the intercept. So, I try to write it like this: gam.lme<- gamm(Y~ s(z, by=X) +X, random=list(groups=pdDiag(~1+X)) ) but I get the error message : Error in MEestimate(lmeSt, grps) : Singularity in backsolve at level 0, block 1

I am switching from Matlab to R, but I found that R is 200 times slower than matlab. Since I am newbie to R, I must be missing some important programming tips. Please help me out on this. Here is the function: ## make the full pair-wise permutation of a vector ## input_fc=c(1,2,3); ## output_fc=( 1 1 1 2 2 2 3 3 3 1 2 3 1 2 3 1 2 3 ); grw_permute = function(input_fc){ fc_vector = input_fc

I am having difficulty fitting a mgcv::gamm model that includes both a random smooth term (i.e. 'fs' smooth) and autoregressive errors. Standard smooth terms with a factor interaction using the 'by=' option work fine. Both on my actual data and a toy example (below) I am getting the same error so am inclined to wonder if this is either a bug or a model that gamm is simply unable

Try to fit a longitudinal dataset using generalized mixed effects models via the R function gamm() as follows: library(mgcv) gamm0.fit<- gamm(y ~ x+s(z,bs="cr"), random=list( x=~1, s(z,bs="cr")=~1 ), family = binomial, data =raw) the data is

Hello, I am trying to fit a gamm (package mgcv) model with a smooth term, a linear term, and an interaction between the two. The reason I am using gamm rather than gam is that there are repeated measures in time (which is the smooth term x1), so I am including an AR1 autocorrelation term. The model I have so far ended up with is of the type gamm(y ~ s(x1) + s(x1, by=x2), correlation =

Dear R users, I am trying to use "gamm" from package "mgcv" to model results from a mesocosm experiment. My model is of type M1 <- gamm(Resp ~ s(Day, k=8) + s(Day, by=C, k=8) + Flow + offset(LogVol), data=MyResp, correlation = corAR1(form= ~ Day|Mesocosm), family=poisson(link=log)) where the response variable is counts, offset by the

I want to use gamm to generate smoothed trend line for three groups identified by dummy variable genea and geneb. My question is how to add in an interaction term between the time and another dummy variable such as gender? fitm<-gamm(change_gfr~ genea+geneb+s(timea_n,bs="ps")+s(timeb_n,bs="ps")+s(timec_n,bs="ps"),data=mm,random=list(time_n=~1|PID)) -- View this