Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R
Dear Emmanual, Thank you again for your email. The answer to isSymmetric(matrix_dissim_Eucl) is indeed TRUE. Thus the pcoa input is symmetric and has no complex values, but still the error ‘Error in min(D.eig$values) : invalid ‘type’ (complex) of argument’ occurs. I hope that you or someone else can figure out why this error occurs. Kind regards, Coline From: Emmanuel Paradis [mailto:emmanuel.para...@ird.fr] Sent: Tuesday, 7 April 2020 05:15 To: Coline Boonman Cc: r-sig-phylo Subject: Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R Hi Coline, Matrix symmetry is not about row- and colnames but about testing, for a square matrix X, if X[i, j] == X[j, i] for all i and j = 1, ..., n. I've just had a look at the code of isSymmetrix.matrix() and this is done by testing equality of X and t(X), so effectively making a copy of X which seems to explain why you run out of memory for this test (apart from the fact that you may have memory-hungry applications running on your computer...) You may try this instead: matrix_dissim_Eucl <- as.matrix(mat_dissim_Eucl) rm(mat_dissim_Eucl) gc() isSymmetric(matrix_dissim_Eucl) If you still run out of memory, try to quit some applications (Web browsers of Office typically use a lot of memory). Anyway, it doesn't change the fact that daisy(), like dist(), returns only the lower triangle of the distance matrix, so as.matrix() should return a symmetric matrix with its diagonal set to 0. So the above check is just to be sure. Best, Emmanuel - Le 6 Avr 20, à 22:00, Coline Boonman < <mailto:c.boon...@science.ru.nl> c.boon...@science.ru.nl> a écrit : Dear Emmanual, Thank you for your response! I have checked your code, and I get the following: matrix_dissim_Eucl<-as.matrix(mat_dissim_Eucl) any(is.complex(matrix_dissim_Eucl)) #FALSE isSymmetric.matrix(matrix_dissim_Eucl) # Error: cannot allocate vector of size 811.1Mb So I checked by hand (I think it checks for row and column length, and for equal row and column names dim(matrix_dissim_Eucl) #14582 14582 summary(colnames(matrix_dissim_Eucl)==row.names(matrix_dissim_Eucl)) #TRUE 14582 So I guess this means that it is a symmetric matrix that enters the pcoa function, and that there are no complex values in the matrix. I hope there is one thing I did not think of yet, and you can help me figure it out. In any case, thank you for your help. I really appreciated it. Kind regards, Coline From: Emmanuel Paradis [mailto:emmanuel.para...@ird.fr] Sent: Monday, 6 April 2020 16:47 To: Coline Boonman mailto:c.boon...@science.ru.nl> > Cc: r-sig-phylo mailto:r-sig-phylo@r-project.org> > Subject: Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R Hi Coline, Actually the test would be: any(is.complex(mat_dissim_Eucl)) And you may also test: isSymmetric(as.matrix(mat_dissim_Eucl)) But it'd very surprising this 2nd test returns FALSE. So if your matrix is real and symmetric, I don't see why you have complex eigenvalues from its decomposition. Best, Emmanuel - Le 6 Avr 20, à 21:16, Coline Boonman < <mailto:c.boon...@science.ru.nl> c.boon...@science.ru.nl> a écrit : Dear Emmanual, Thank you for your email. I have been trying to understand what is going on and if your suggestion is correct. However, if I test for complex numbers in my dissimilarity matrix (converted to a matrix: is.complex(as.matrix(mat_dissim_Eucl)) ) R gives me the result FALSE. That means that there are no complex numbers in the input for the pcoa, right? I hope you or someone else has another suggestion on why I get this error. Kind regards, Coline From: Emmanuel Paradis [mailto:emmanuel.para...@ird.fr] Sent: Thursday, 2 April 2020 07:43 To: Coline Boonman mailto:c.boon...@science.ru.nl> > Cc: r-sig-phylo mailto:r-sig-phylo@r-project.org> > Subject: Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R Hi Coline, This is strange: you calculate a distance matrix with daisy(), so the as.matrix() operation should return a symmetric matrix. Symmetric (real) matrices have all their eigenvalues real numbers. Maybe some complex values were produced by daisy()? Best, Emmanuel - Le 30 Mar 20, à 22:58, Coline Boonman < <mailto:c.boon...@science.ru.nl> c.boon...@science.ru.nl> a écrit : Dear reader, I am working with the pcoa function of ape in R and I got the error message: “min(D.eig$values) : invalid 'type' (complex) of argument” . My input data is a distance matrix, which pcoa first converts to a matrix in the first line within the code of the function. The error occurs when it wants to check for negative eigenvalues at the line ‘ min.eig <- min(D.eig$values)’ I checked D.eig$values and indeed they are
Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R
Hi Coline, Matrix symmetry is not about row- and colnames but about testing, for a square matrix X, if X[i, j] == X[j, i] for all i and j = 1, ..., n. I've just had a look at the code of isSymmetrix.matrix() and this is done by testing equality of X and t(X), so effectively making a copy of X which seems to explain why you run out of memory for this test (apart from the fact that you may have memory-hungry applications running on your computer...) You may try this instead: matrix_dissim_Eucl <- as.matrix(mat_dissim_Eucl) rm(mat_dissim_Eucl) gc() isSymmetric(matrix_dissim_Eucl) If you still run out of memory, try to quit some applications (Web browsers of Office typically use a lot of memory). Anyway, it doesn't change the fact that daisy(), like dist(), returns only the lower triangle of the distance matrix, so as.matrix() should return a symmetric matrix with its diagonal set to 0. So the above check is just to be sure. Best, Emmanuel - Le 6 Avr 20, à 22:00, Coline Boonman a écrit : > Dear Emmanual, > Thank you for your response! I have checked your code, and I get the > following: > matrix_dissim_Eucl<-as.matrix(mat_dissim_Eucl) > any(is.complex(matrix_dissim_Eucl)) > #FALSE > isSymmetric.matrix(matrix_dissim_Eucl) > # Error: cannot allocate vector of size 811.1Mb > So I checked by hand (I think it checks for row and column length, and for > equal > row and column names > dim(matrix_dissim_Eucl) > #14582 14582 > summary(colnames(matrix_dissim_Eucl)==row.names(matrix_dissim_Eucl)) > #TRUE 14582 > So I guess this means that it is a symmetric matrix that enters the pcoa > function, and that there are no complex values in the matrix. > I hope there is one thing I did not think of yet, and you can help me figure > it > out. In any case, thank you for your help. I really appreciated it. > Kind regards, > Coline > From: Emmanuel Paradis [mailto:emmanuel.para...@ird.fr] > Sent: Monday, 6 April 2020 16:47 > To: Coline Boonman > Cc: r-sig-phylo > Subject: Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of > ape > in R > Hi Coline, > Actually the test would be: > any(is.complex(mat_dissim_Eucl)) > And you may also test: > isSymmetric(as.matrix(mat_dissim_Eucl)) > But it'd very surprising this 2nd test returns FALSE. > So if your matrix is real and symmetric, I don't see why you have complex > eigenvalues from its decomposition. > Best, > Emmanuel > - Le 6 Avr 20, à 21:16, Coline Boonman < [ mailto:c.boon...@science.ru.nl > | > c.boon...@science.ru.nl ] > a écrit : >> Dear Emmanual, >> Thank you for your email. I have been trying to understand what is going on >> and >> if your suggestion is correct. However, if I test for complex numbers in my >> dissimilarity matrix (converted to a matrix: >> is.complex(as.matrix(mat_dissim_Eucl)) ) R gives me the result FALSE. That >> means that there are no complex numbers in the input for the pcoa, right? >> I hope you or someone else has another suggestion on why I get this error. >> Kind regards, >> Coline >> From: Emmanuel Paradis [ [ mailto:emmanuel.para...@ird.fr | >> mailto:emmanuel.para...@ird.fr ] ] >> Sent: Thursday, 2 April 2020 07:43 >> To: Coline Boonman < [ mailto:c.boon...@science.ru.nl | >> c.boon...@science.ru.nl >> ] > >> Cc: r-sig-phylo < [ mailto:r-sig-phylo@r-project.org | >> r-sig-phylo@r-project.org >> ] > >> Subject: Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of >> ape >> in R >> Hi Coline, >> This is strange: you calculate a distance matrix with daisy(), so the >> as.matrix() operation should return a symmetric matrix. Symmetric (real) >> matrices have all their eigenvalues real numbers. Maybe some complex values >> were produced by daisy()? >> Best, >> Emmanuel >> - Le 30 Mar 20, à 22:58, Coline Boonman < [ >> mailto:c.boon...@science.ru.nl | >> c.boon...@science.ru.nl ] > a écrit : >>> Dear reader, >>> I am working with the pcoa function of ape in R and I got the error message: >>> “min(D.eig$values) : invalid 'type' (complex) of argument” . >>> My input data is a distance matrix, which pcoa first converts to a matrix >>> in the >>> first line within the code of the function. The error occurs when it wants >>> to >>> check for negative eigenvalues at the line ‘ min.eig <- min(D.eig$values)’ >>> I checked D.eig$values and indeed they are complex numbers (imaginary >>> numbers). >>> What I don’t understand is why these are created. I never had any issues >>
Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R
Dear Emmanual, Thank you for your response! I have checked your code, and I get the following: matrix_dissim_Eucl<-as.matrix(mat_dissim_Eucl) any(is.complex(matrix_dissim_Eucl)) #FALSE isSymmetric.matrix(matrix_dissim_Eucl) # Error: cannot allocate vector of size 811.1Mb So I checked by hand (I think it checks for row and column length, and for equal row and column names dim(matrix_dissim_Eucl) #14582 14582 summary(colnames(matrix_dissim_Eucl)==row.names(matrix_dissim_Eucl)) #TRUE 14582 So I guess this means that it is a symmetric matrix that enters the pcoa function, and that there are no complex values in the matrix. I hope there is one thing I did not think of yet, and you can help me figure it out. In any case, thank you for your help. I really appreciated it. Kind regards, Coline From: Emmanuel Paradis [mailto:emmanuel.para...@ird.fr] Sent: Monday, 6 April 2020 16:47 To: Coline Boonman Cc: r-sig-phylo Subject: Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R Hi Coline, Actually the test would be: any(is.complex(mat_dissim_Eucl)) And you may also test: isSymmetric(as.matrix(mat_dissim_Eucl)) But it'd very surprising this 2nd test returns FALSE. So if your matrix is real and symmetric, I don't see why you have complex eigenvalues from its decomposition. Best, Emmanuel - Le 6 Avr 20, à 21:16, Coline Boonman mailto:c.boon...@science.ru.nl> > a écrit : Dear Emmanual, Thank you for your email. I have been trying to understand what is going on and if your suggestion is correct. However, if I test for complex numbers in my dissimilarity matrix (converted to a matrix: is.complex(as.matrix(mat_dissim_Eucl)) ) R gives me the result FALSE. That means that there are no complex numbers in the input for the pcoa, right? I hope you or someone else has another suggestion on why I get this error. Kind regards, Coline From: Emmanuel Paradis [mailto:emmanuel.para...@ird.fr] Sent: Thursday, 2 April 2020 07:43 To: Coline Boonman mailto:c.boon...@science.ru.nl> > Cc: r-sig-phylo mailto:r-sig-phylo@r-project.org> > Subject: Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R Hi Coline, This is strange: you calculate a distance matrix with daisy(), so the as.matrix() operation should return a symmetric matrix. Symmetric (real) matrices have all their eigenvalues real numbers. Maybe some complex values were produced by daisy()? Best, Emmanuel - Le 30 Mar 20, à 22:58, Coline Boonman mailto:c.boon...@science.ru.nl> > a écrit : Dear reader, I am working with the pcoa function of ape in R and I got the error message: “min(D.eig$values) : invalid 'type' (complex) of argument” . My input data is a distance matrix, which pcoa first converts to a matrix in the first line within the code of the function. The error occurs when it wants to check for negative eigenvalues at the line ‘ min.eig <- min(D.eig$values)’ I checked D.eig$values and indeed they are complex numbers (imaginary numbers). What I don’t understand is why these are created. I never had any issues with the pcoa function before, and now I change my dataset and this happens. The distance matrix values range from 0 to 47 and I have species names as rownames and column names. In the attachment I include a small piece of the dataset and the code I run. I checked when the error occurs, and I don’t see why the extra line (2063) gives the error. I hope someone can help me. Kind regards, Coline Boonman -- PhD student Department of Environmental Science Faculty of Science Radboud University Nijmegen P.O. Box 9010, NL-6500 GL Nijmegen E: c.boon...@science.ru.nl <mailto:c.boon...@science.ru.nl> T: + 31 (0)243653270 / + 31 (0)243653281 (secr.) http://www.ru.nl/environmentalscience ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org <mailto:R-sig-phylo@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R
Hi Coline, Actually the test would be: any(is.complex(mat_dissim_Eucl)) And you may also test: isSymmetric(as.matrix(mat_dissim_Eucl)) But it'd very surprising this 2nd test returns FALSE. So if your matrix is real and symmetric, I don't see why you have complex eigenvalues from its decomposition. Best, Emmanuel - Le 6 Avr 20, à 21:16, Coline Boonman a écrit : Dear Emmanual, Thank you for your email. I have been trying to understand what is going on and if your suggestion is correct. However, if I test for complex numbers in my dissimilarity matrix (converted to a matrix: is.complex(as.matrix(mat_dissim_Eucl)) ) R gives me the result FALSE. That means that there are no complex numbers in the input for the pcoa, right? I hope you or someone else has another suggestion on why I get this error. Kind regards, Coline From: Emmanuel Paradis [mailto:emmanuel.para...@ird.fr] Sent: Thursday, 2 April 2020 07:43 To: Coline Boonman Cc: r-sig-phylo Subject: Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R Hi Coline, This is strange: you calculate a distance matrix with daisy(), so the as.matrix() operation should return a symmetric matrix. Symmetric (real) matrices have all their eigenvalues real numbers. Maybe some complex values were produced by daisy()? Best, Emmanuel - Le 30 Mar 20, à 22:58, Coline Boonman < [ mailto:c.boon...@science.ru.nl | c.boon...@science.ru.nl ] > a écrit : BQ_BEGIN Dear reader, I am working with the pcoa function of ape in R and I got the error message: “min(D.eig$values) : invalid 'type' (complex) of argument” . My input data is a distance matrix, which pcoa first converts to a matrix in the first line within the code of the function. The error occurs when it wants to check for negative eigenvalues at the line ‘ min.eig <- min(D.eig$values)’ I checked D.eig$values and indeed they are complex numbers (imaginary numbers). What I don’t understand is why these are created. I never had any issues with the pcoa function before, and now I change my dataset and this happens. The distance matrix values range from 0 to 47 and I have species names as rownames and column names. In the attachment I include a small piece of the dataset and the code I run. I checked when the error occurs, and I don’t see why the extra line (2063) gives the error. I hope someone can help me. Kind regards, Coline Boonman -- PhD student Department of Environmental Science Faculty of Science Radboud University Nijmegen P.O. Box 9010, NL-6500 GL Nijmegen E: [ mailto:c.boon...@science.ru.nl | c.boon...@science.ru.nl ] T: + 31 (0)243653270 / + 31 (0)243653281 (secr.) [ http://www.ru.nl/environmentalscience | http://www.ru.nl/environmentalscience ] ___ R-sig-phylo mailing list - [ mailto:R-sig-phylo@r-project.org | R-sig-phylo@r-project.org ] [ https://stat.ethz.ch/mailman/listinfo/r-sig-phylo | https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ] Searchable archive at [ http://www.mail-archive.com/r-sig-phylo@r-project.org/ | http://www.mail-archive.com/r-sig-phylo@r-project.org/ ] BQ_END [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R
Dear Emmanual, Thank you for your email. I have been trying to understand what is going on and if your suggestion is correct. However, if I test for complex numbers in my dissimilarity matrix (converted to a matrix: is.complex(as.matrix(mat_dissim_Eucl)) ) R gives me the result FALSE. That means that there are no complex numbers in the input for the pcoa, right? I hope you or someone else has another suggestion on why I get this error. Kind regards, Coline From: Emmanuel Paradis [mailto:emmanuel.para...@ird.fr] Sent: Thursday, 2 April 2020 07:43 To: Coline Boonman Cc: r-sig-phylo Subject: Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R Hi Coline, This is strange: you calculate a distance matrix with daisy(), so the as.matrix() operation should return a symmetric matrix. Symmetric (real) matrices have all their eigenvalues real numbers. Maybe some complex values were produced by daisy()? Best, Emmanuel - Le 30 Mar 20, à 22:58, Coline Boonman mailto:c.boon...@science.ru.nl> > a écrit : Dear reader, I am working with the pcoa function of ape in R and I got the error message: “min(D.eig$values) : invalid 'type' (complex) of argument” . My input data is a distance matrix, which pcoa first converts to a matrix in the first line within the code of the function. The error occurs when it wants to check for negative eigenvalues at the line ‘ min.eig <- min(D.eig$values)’ I checked D.eig$values and indeed they are complex numbers (imaginary numbers). What I don’t understand is why these are created. I never had any issues with the pcoa function before, and now I change my dataset and this happens. The distance matrix values range from 0 to 47 and I have species names as rownames and column names. In the attachment I include a small piece of the dataset and the code I run. I checked when the error occurs, and I don’t see why the extra line (2063) gives the error. I hope someone can help me. Kind regards, Coline Boonman -- PhD student Department of Environmental Science Faculty of Science Radboud University Nijmegen P.O. Box 9010, NL-6500 GL Nijmegen E: c.boon...@science.ru.nl <mailto:c.boon...@science.ru.nl> T: + 31 (0)243653270 / + 31 (0)243653281 (secr.) http://www.ru.nl/environmentalscience ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org <mailto:R-sig-phylo@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Question on min(D.eig$values) in pcoa function of ape in R
Hi Coline, This is strange: you calculate a distance matrix with daisy(), so the as.matrix() operation should return a symmetric matrix. Symmetric (real) matrices have all their eigenvalues real numbers. Maybe some complex values were produced by daisy()? Best, Emmanuel - Le 30 Mar 20, à 22:58, Coline Boonman a écrit : > Dear reader, > I am working with the pcoa function of ape in R and I got the error message: > “min(D.eig$values) : invalid 'type' (complex) of argument” . > My input data is a distance matrix, which pcoa first converts to a matrix in > the > first line within the code of the function. The error occurs when it wants to > check for negative eigenvalues at the line ‘ min.eig <- min(D.eig$values)’ > I checked D.eig$values and indeed they are complex numbers (imaginary > numbers). > What I don’t understand is why these are created. I never had any issues with > the pcoa function before, and now I change my dataset and this happens. The > distance matrix values range from 0 to 47 and I have species names as rownames > and column names. In the attachment I include a small piece of the dataset and > the code I run. I checked when the error occurs, and I don’t see why the extra > line (2063) gives the error. > I hope someone can help me. > Kind regards, > Coline Boonman > -- > PhD student > Department of Environmental Science > Faculty of Science > Radboud University Nijmegen > P.O. Box 9010, NL-6500 GL Nijmegen > E: c.boon...@science.ru.nl > T: + 31 (0)243653270 / + 31 (0)243653281 (secr.) > http://www.ru.nl/environmentalscience > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
