[R] plots of ACF
Hello. I have one Model (M3) fitted using the lme package, and I have checked the correlation structure of within-group errors using plot(ACF (M3,maxLag=10),alpha=0.05) But now I am not sure how to interpret this plot for the empirical autocorrelation function. The problem is that I am used to see/interpret diagrams in which all the autocorrelation Lags, except lag-1, are inside the confidence envelopes, or those plots where only Lags 1 and 2 are outside those envelopes. But how should I interpret my ACF plot, where Lags 1, 7, 8 and 9, are those outside those envelopes? Is there any correlation structure? Which one might that be? AR1()? Also, I have used the plot of the empirical ACF of the normalized residuals, but it gives exactly the same results. Could you please help me? Best regards Sara Mouro Sara Maltez Mouro Centro de Ecologia Funcional Departamento de Botânica Universidade de Coimbra [EMAIL PROTECTED] www.uc.pt/ecology/saramaltezmouro Sara Maltez Mouro Centro de Ecologia Funcional Departamento de Botânica Universidade de Coimbra [EMAIL PROTECTED] www.uc.pt/ecology/saramaltezmouro [[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] different ACF results
Dear all, I have one Model (M3) fitted using the lme package, and I have checked the correlation structure of within-group errors using plot(ACF (M3,maxLag=10),alpha=0.05) But now I am not sure how to interpret this plot for the empirical autocorrelation function. The problem is that I am used to see/interpret diagrams in which all the autocorrelation Lags, except lag-1, are inside the confidence envelopes, or those plots where only Lags 1 and 2 are outside those envelopes. But how should I interpret my ACF plot, where Lags 1, 7, 8 and 9, are those outside those envelopes? Is there any correlation structure? Which one might that be? AR1()? Also, I have used the plot of the empirical ACF of the normalized residuals, but it gives exactly the same results. Could you please help me? Best regards Sara Mouro Sara Maltez Mouro Centro de Ecologia Funcional Departamento de Botânica Universidade de Coimbra [EMAIL PROTECTED] www.uc.pt/ecology/saramaltezmouro [[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 join these two models?
Dear R users, I have this 2 models that fit to my data: M3varI - update (M3, weights=varIdent(form= ~ 1|SITE)) M3AR1-update(M3,correlation=corAR1()) The first one, updates my M3 so that I can account for the variance structure of random erros. The second one, updates my M3 so that I can account for the correlation structure of random errors. How can I put them toghether in one final model? I have tryed it using gls but I could not do it. Could you please help me o this? Bets regards, Sara Maltez Mouro Centro de Ecologia Funcional Departamento de Botânica Universidade de Coimbra [EMAIL PROTECTED] www.uc.pt/ecology/saramaltezmouro [[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] uninitialized pdMat object
Dear all, I am using the nlme package and trying to modelate the variance- covariance matrix of random effects. However, I do not understand why do I get this error message: M4CompSym - update(M4,random=A~pdCompSymm(~CED)) Error in pdMatrix.pdCompSymm(x) : Cannot extract the matrix from an uninitialized pdMat object Can anyone please help me? How do I update one Model using one of the pre-defined matrixes? Regards, Sara Mouro Sara Maltez Mouro Centro de Ecologia Funcional Departamento de Botânica Universidade de Coimbra [EMAIL PROTECTED] www.uc.pt/ecology/saramaltezmouro [[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] random parameters in nlme
Dear all, I am using the nlme package to find the best model using non-linear mixed effects model. After the all the other things needed, I did M1- nlme(NShrubs~A*exp(-B*CED),data=DataSg,fixed=list (A~SITE,B~1), random=B~1,start=list(fixed=c (1.66,1.66,1.66,1.66,1.66,1.66,1.66,1.66,0.0038)),control=lmc) and it was ok. However, the data showed to need random parameters at both the intercept and the slope. And I can not understand why do I always get an error message like: Error in parse(text = paste(~, paste(nVal, collapse = /))) : unexpected end of input in ~ or Error in nlme.formula(NShrubs ~ A * exp(-B * CED), data = DataSg, fixed = list(A ~ : random formula must be a formula or list of formulae Could you please tell me where/what am I doing wrong (in any of the following options I have uses)? M1- nlme(NShrubs~A*exp(-B*CED),data=DataSg,fixed=list (A~SITE,B~1), random=list(B~1),start=list(fixed=c (1.66,1.66,1.66,1.66,1.66,1.66,1.66,1.66,0.0038)),control=lmc) M1- nlme(NShrubs~A*exp(-B*CED),data=DataSg,fixed=list (A~SITE,B~1), random=list(B~1(SITE)),start=list(fixed=c (1.66,1.66,1.66,1.66,1.66,1.66,1.66,1.66,0.0038)),control=lmc) M1- nlme(NShrubs~A*exp(-B*CED),data=DataSg,fixed=list (A~SITE,B~1), random=~CED,start=list(fixed=c (1.66,1.66,1.66,1.66,1.66,1.66,1.66,1.66,0.0038)),control=lmc) M1- nlme(NShrubs~A*exp(-B*CED),data=DataSg,fixed=list (A~SITE,B~1), random=list(A~I,B~I),start=list(fixed=c (1.66,1.66,1.66,1.66,1.66,1.66,1.66,1.66,0.0038)),control=lmc) M1- nlme(NShrubs~A*exp(-B*CED),data=DataSg,fixed=list (A~SITE,B~1), random=~1,start=list(fixed=c (1.66,1.66,1.66,1.66,1.66,1.66,1.66,1.66,0.0038)),control=lmc) M1- nlme(NShrubs~A*exp(-B*CED),data=DataSg,fixed=list (A~SITE,B~1), random=~1|SITE,start=list(fixed=c (1.66,1.66,1.66,1.66,1.66,1.66,1.66,1.66,0.0038)),control=lmc) M1- nlme(NShrubs~A*exp(-B*CED),data=DataSg,fixed=list (A~SITE,B~1), random=~1|SITE/T,start=list(fixed=c (1.66,1.66,1.66,1.66,1.66,1.66,1.66,1.66,0.0038)),control=lmc) I would be really greatful if you can please help me on this. Best regards, Sara Maltez Mouro Centro de Ecologia Funcional Departamento de Botânica Universidade de Coimbra [EMAIL PROTECTED] www.uc.pt/ecology/saramaltezmouro [[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] memory problems (not me. my pc!)
Dear R users, I have got an error message related with memory size, but I could not understand if and how to solve it. Could you please help me? I was using the source quickPCNM-761.R, for a space matrix with 12572 rows (with X and Y (UTM) coordinates), and an Y matrix containing response data, with 10 variables (with lots of zero values). When I run: resPCNM-quickPCNM(dados1,coordXY) I got: Error: cannot allocate vector of size 602.9 Mb In addition: Warning messages: 1: In vector(double, length) : Reached total allocation of 254Mb: see help(memory.size) 2: In vector(double, length) : Reached total allocation of 254Mb: see help(memory.size) 3: In vector(double, length) : Reached total allocation of 254Mb: see help(memory.size) 4: In vector(double, length) : Reached total allocation of 254Mb: see help(memory.size) Afterwards I have used memory.size as follows: memory.size() [1] 14.10536 memory.size(TRUE) [1] 19.1875 round(memory.limit(), 2) [1] 254.98 How could I solve this problem? With another (i.e. with more memory) PC? How much memory do I nedd? 602.9? Best regards, Sara Mouro PS- I have also used the option range=TRUE, and thus I think the memory problems have nothing to do with the (high) UTM values. PS2- I hope the zero values in response variables are not a problem for PCNM analysis?! __ 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 compile sources?
Dear all, I have read the on-line explanations I have found about Building R from sources, and istalling Packages from sources... Also, I have installed gcc4.0 and the gfrotran-4.2.1.dmg. However, I still do not know how to use them to compile one Source (in particular packfor_0.0-7.tar.gz) so that I can use it in R (for MAC OS X). Could someone please explain it to me in an easiest way (i.e. to someone who has already suffered enough to learn R for herself, and knows little about programming)? Thank you in advance! Best regards, Sara Mouro __ 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.
