[R] Error while using register from fda package
Hi all, I think I've run into an error caused by my computer's having too little computational power, but I'm not sure. I used the following code to perform continuous registration on two functional objects: lambda1 - 10E-2 norder=8 samples-seq(0,780,length=781) nbasis - length(samples)+norder-2 mybasis-create.bspline.basis(c(0,780),nbasis,norder) myfdPar-fdPar(mybasis,4,lambda1) myfd.unemployment - smooth.basis(samples,unemployment.rate,myfdPar)$fd myfd.unemployment.squared - smooth.basis(samples,unemp.squared,myfdPar)$fd lambda2-10E-2 myfdPar-fdPar(mybasis,4,lambda2) myfd.inflation - smooth.basis(samples,inflation.rate,myfdPar,)$fd myfd.inflation.squared - smooth.basis(samples,inflation.squared,myfdPar)$fd plot(myfd.inflation) #register lambda=1 nbasis=myfd.unemployment$basis$nbasis ntrial=1 y0fd=mean(myfd.inflation) yfd=myfd.unemployment coef0-matrix(0,nbasis,ntrial) wfd-fd(coef0,mybasis) wfdPar=fdPar(coef0,2,lambda) reglist-register.fd(y0fd,yfd,wfdPar,iterlim=10,dbglev=1) I get the following error after the last command: Error in matrix(0, length(x), nbaspr) : too many elements specified Is this error associated with my computer's not having sufficient power to perform the registration? I can't think of what else that might be going on... Thanks, Zoe Richards [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Inverse function using FDA
Hi, Does anyone know how (or whether or not it's possible) to output an inverse of a functional object? I haven't found a way, but since derivatives etc. can be computed using the fda package it seems like this should be possible using this package or another designed for functional data analysis. Thanks, Zoe Richards [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Inverse function using FDA
I am trying to register unemployment rate and inverse of inflation rate to investigate the phillips curvehttp://www.econlib.org/library/Enc/PhillipsCurve.html by looking at the resulting warping function. On Wed, Mar 6, 2013 at 5:17 PM, Peter Ehlers ehl...@ucalgary.ca wrote: On 2013-03-06 12:54, zoe richards wrote: Hi, Does anyone know how (or whether or not it's possible) to output an inverse of a functional object? I haven't found a way, but since derivatives etc. can be computed using the fda package it seems like this should be possible using this package or another designed for functional data analysis. Thanks, Zoe Richards What does your question mean? Possibly, you could 'invert' a mean function, but I have no idea what that would accomplish. Can you provide an example of just what you want to do? Peter Ehlers [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] predict.smooth.Pspline function not found
I have a simple question that irritatingly I haven't been able to figure out on my own. It seems that some functions from the Pspline package are successfully installed while others are not. The code with which I'm working is more complicated, but the following highlights my problem. If I run the following code tt - seq (0,1,length=20) xt - tt^3 fit - smooth.Pspline (tt, xt, norder=3,spar=0.0001, method=1) pred- predict.smooth.Pspline (fit, tt, nderiv=0) I get this error: Error: could not find function predict.smooth.Pspline So it seems like smooth.Pspline is loading but predict.smooth.Pspline isn't. Any ideas about why this might be the case? -Zoe Richards [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R error: system is computationally singular when building GMM model
Dear, I built the generalized method of moments model to estimate the sales rank in the bookstore using plm package in R. The equation is: data1.gmm - pgmm(dynformula(lnsales_rank ~ ln_price + avg_ham_rate + avg_spam_rate + num_of_ham+ num_of_spam + ship_code2 +ship_code3 +ship_code4+ ship_code5+ ship_code6 + ship_ code7, lag = list(0, 0, 0, 0,0,0,0,0,0,0,0,0), log =FALSE), data=data, effect = individual, model = twosteps, transformation = ld,gmm.inst = ~ ln_price, lag.gmm =2) However, error message: Error in solve.default(Reduce(+, A1)) : system is computationally singular: reciprocal condition number = 6.36689e-23 shown. I found that skipping one of the ship_code variables (dummy variable) can generate result. But don't know the reason. I found some books about using R, but no one can answer me. Please help. Thanks much. Zoe [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to map new data to the existing cluster assignments in R mclust?
I need to map new data to the existing cluster assignments in R. For clustering was used mclust. I need to find which cluster the new data belong to. Asking for a help :) -- View this message in context: http://r.789695.n4.nabble.com/How-to-map-new-data-to-the-existing-cluster-assignments-in-R-mclust-tp4650702.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] remove from the R mailing list
I would like to be removed from the R mailing list. Thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help with Merge - unexpected loss of factor level
Hi, Thanks in advance for any advice you can give me, I am very stumped on this
problem...
I use R every day and consider myself a confident user, but this seems to be an
elementary problem..
Outline of problem: I am analysing the results of a study on protein expression
in cancer tissues. I have raw intensities from 2 different types of cancer and
normal tissue, which can be taken from several different parts of the cell, as
well as patient information. Part of the analysis calls for a fold-change
calculation. In order to do this I am sub-setting the dataset by cancer type,
merging each cancer dataset with the data from the Normal tissue, then
calculating fold change for matching individuals and cell section.
The problem is that I have been tracking one factor in particular ('branch',
values 2 or 3) and once the final merge occurs, the second level of this factor
seems to disappear in the last dataset, even though it was present before.
See code output below:
dim(tma)
names(tma)
[1] Code marker cell tumourAtumourEXP int
stain tumourPERC branch
levels(tma$tumourA)
[1] DCIS LN Metastasis Normal
Primary Invasive Carcinoma
#split into cancer and normal tissue
tma1-subset(tma, tumourA==Primary Invasive Carcinoma)
tma2-subset(tma, tumourA==LN Metastasis)
tmaN-subset(tma, tumourA==Normal)
#size of datasets
dim(tma1)
[1] 587 9
dim(tma2)
[1] 323 9
dim(tmaN)
[1] 142 9
#merge back with normal type
tma1.1-merge(tmaN, tma1, by=Code)
tma2.1-merge(tmaN, tma2, by=Code)
#new dimensions (seem excessively large)
dim(tma1.1)
[1] 2439 17
dim(tma2.1)
[1] 625 17
#progression of branch: factor in datasets. Note last one where it
disappears...
table(tma$branch)
2 3
450 613
table(tma1$branch)
2 3
314 273
table(tma2$branch)
2 3
39 284
table(tmaN$branch)
2 3
91 51
table(tma1.1$branch.x)
23
1806 633
table(tma2.1$branch.x)
3
625
Please, can someone tell me what's going on?
Thanks you very much,
Zoe van Havre
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Plotting Moa clustering result
Hi all, Is there a way of plotting a 'decision tree' from the results of Mona in the cluster package. The default bannerplot is not quite what I'm after - I would like a plot of the binary decision tree. Thanks Zoë __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Plotting Mona clustering result
Hi all, Is there a way of plotting a 'decision tree' from the results of Mona in the cluster package. The default bannerplot is not quite what I'm after - I would like a plot of the binary decision tree. Thanks Zoë [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] 3d Scatterplot using rgl
Hi, I am trying to plot a 3d scatter plot using the rgl package but am having trouble. I have a matrix containing x, y and z co-ordinates and a fourth element related to a count variable. I would like to plot the points using plot3d with the sizes of the points related to the fourth element in the matrix. Is this possible with plot3d or do I need to use something else? I include a small example of what I am trying to do swadt A B Crun1 run2 run3 run4 run5 run6 93 96 51 0.1 NA 0.1 NA NA NA 93 97 50 0.3 NA NA 0.1 NA NA 93 98 49 0.1 NA NA NA NA NA 94 95 51 NA NA NA NA NA 0.1 94 100 46 0.1 NA NA NA NA NA 94 96 50 2.1 0.1 1.0 0.7 0.8 0.4 94 97 49 3.2 0.9 1.9 1.9 1.6 1.6 94 98 48 0.9 NA 0.3 0.4 0.5 0.1 95 94 51 NA NA NA 0.1 0.1 NA 95 95 50 3.4 0.7 2.8 2.4 2.9 2.3 95 96 49 12.5 13.4 13.6 15.0 15.3 17.1 95 97 48 10.2 10.8 8.9 10.8 8.7 9.3 95 98 47 1.5 NA 0.9 0.7 0.8 0.1 96 93 51 0.1 NA NA NA NA NA If I use plot3d(swadt[,1],swadt[,2],swadt[,3],size=swadt[,4]) I get the following error Error in rgl.numeric(size) : size must be a single numeric value Is there a way of plotting this? Thanks Zoe Hoare [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
