Stefano Sofia
2015-Dec-10 10:08 UTC
[R] matrix which results singular but at the same time positive definite
Dear list users,
through the "matrixcalc" package I am performing some checks of
variance matrices (which must be positive definite).
In this example, it happens that the matrix A here reported is singular but
positive definite. Is it possible?
[,1] [,2] [,3] [,4]
[1,] 1.904255e-12 -1.904255e-12 -8.238960e-13 -1.240294e-12
[2,] -1.904255e-12 3.637979e-12 1.364242e-12 1.818989e-12
[3,] -8.238960e-13 1.364242e-12 4.809988e+00 7.742369e-01
[4,] -1.240294e-12 1.818989e-12 7.742369e-01 1.090411e+00
print(is.non.singular.matrix(A, tol = 1e-18))
FALSE
print(is.positive.definite(A, tol=1e-18))
TRUE
Is there something wrong with this matrix?
Any comment will be appreciated.
Stefano
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Rolf Turner
2015-Dec-10 10:38 UTC
[R] matrix which results singular but at the same time positive definite
On 10/12/15 23:08, Stefano Sofia wrote:> Dear list users, > through the "matrixcalc" package I am performing some checks of variance matrices (which must be positive definite). > In this example, it happens that the matrix A here reported is singular but positive definite. Is it possible? > > [,1] [,2] [,3] [,4] > [1,] 1.904255e-12 -1.904255e-12 -8.238960e-13 -1.240294e-12 > [2,] -1.904255e-12 3.637979e-12 1.364242e-12 1.818989e-12 > [3,] -8.238960e-13 1.364242e-12 4.809988e+00 7.742369e-01 > [4,] -1.240294e-12 1.818989e-12 7.742369e-01 1.090411e+00 > > print(is.non.singular.matrix(A, tol = 1e-18)) > FALSE > print(is.positive.definite(A, tol=1e-18)) > TRUE > > Is there something wrong with this matrix? > Any comment will be appreciated.There is nothing wrong with A (at least nothing that either a nice bowl of chicken soup or a bloody good swim wouldn't cure). Look at the code for the two functions. The tests use the tolerance in very different ways. My initial reaction is that the code for these functions is rather naive. cheers, Rolf Turner -- Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276
Fox, John
2015-Dec-10 13:41 UTC
[R] matrix which results singular but at the same time positive definite
Dear Stefano, You've already had a couple of informative responses directly addressing your question, but are you aware how ill-conditioned the matrix is (one of the responses alluded to this)?> kappa(X, exact=TRUE)[1] 7.313338e+12> eigen(X)$values[1] 4.964711e+00 9.356881e-01 4.863392e-12 6.788344e-13 Two of the variables have variances around 10^0 and the other two around 10^-12. Of course, you haven't said anything about the context, but does it really make sense to analyze the data on these scales? Best, John ----------------------------- John Fox, Professor McMaster University Hamilton, Ontario Canada L8S 4M4 Web: socserv.mcmaster.ca/jfox> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Stefano Sofia > Sent: December 10, 2015 5:08 AM > To: r-help at r-project.org > Subject: [R] matrix which results singular but at the same time positive definite > > Dear list users, > through the "matrixcalc" package I am performing some checks of variance > matrices (which must be positive definite). > In this example, it happens that the matrix A here reported is singular but > positive definite. Is it possible? > > [,1] [,2] [,3] [,4] > [1,] 1.904255e-12 -1.904255e-12 -8.238960e-13 -1.240294e-12 [2,] - > 1.904255e-12 3.637979e-12 1.364242e-12 1.818989e-12 [3,] -8.238960e-13 > 1.364242e-12 4.809988e+00 7.742369e-01 [4,] -1.240294e-12 1.818989e-12 > 7.742369e-01 1.090411e+00 > > print(is.non.singular.matrix(A, tol = 1e-18)) FALSE print(is.positive.definite(A, > tol=1e-18)) TRUE > > Is there something wrong with this matrix? > Any comment will be appreciated. > Stefano > > > ________________________________ > > AVVISO IMPORTANTE: Questo messaggio di posta elettronica pu? contenere > informazioni confidenziali, pertanto ? destinato solo a persone autorizzate alla > ricezione. I messaggi di posta elettronica per i client di Regione Marche > possono contenere informazioni confidenziali e con privilegi legali. Se non si ? il > destinatario specificato, non leggere, copiare, inoltrare o archiviare questo > messaggio. Se si ? ricevuto questo messaggio per errore, inoltrarlo al mittente > ed eliminarlo completamente dal sistema del proprio computer. Ai sensi > dell?art. 6 della DGR n. 1394/2008 si segnala che, in caso di necessit? ed > urgenza, la risposta al presente messaggio di posta elettronica pu? essere > visionata da persone estranee al destinatario. > IMPORTANT NOTICE: This e-mail message is intended to be received only by > persons entitled to receive the confidential information it may contain. E-mail > messages to clients of Regione Marche may contain information that is > confidential and legally privileged. Please do not read, copy, forward, or store > this message unless you are an intended recipient of it. If you have received > this message in error, please forward it to the sender and delete it completely > from your computer system. > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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.
Stefano Sofia
2015-Dec-10 15:41 UTC
[R] matrix which results singular but at the same time positive definite
Dear John, thank you for your considerations. This matrix (which is a variance matrix) is part of an algorithm for forward-filtering and backward-sampling of Dynamic Linear Models (West and Harrison, 1997), applied to DLM representation of ARIMA processes (Petris, Petrone, Campagnoli). It is therefore very difficult to explain why this variance matrix becomes so ill conditioned. This already happens at the first iteration of the algorithm. I will try to work on initial conditions and some fixed parameters. Thank you again Stefano ________________________________________ Da: Fox, John [jfox at mcmaster.ca] Inviato: gioved? 10 dicembre 2015 14.41 A: Stefano Sofia; r-help at r-project.org Oggetto: RE: matrix which results singular but at the same time positive definite Dear Stefano, You've already had a couple of informative responses directly addressing your question, but are you aware how ill-conditioned the matrix is (one of the responses alluded to this)?> kappa(X, exact=TRUE)[1] 7.313338e+12> eigen(X)$values[1] 4.964711e+00 9.356881e-01 4.863392e-12 6.788344e-13 Two of the variables have variances around 10^0 and the other two around 10^-12. Of course, you haven't said anything about the context, but does it really make sense to analyze the data on these scales? Best, John ----------------------------- John Fox, Professor McMaster University Hamilton, Ontario Canada L8S 4M4 Web: socserv.mcmaster.ca/jfox> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Stefano Sofia > Sent: December 10, 2015 5:08 AM > To: r-help at r-project.org > Subject: [R] matrix which results singular but at the same time positive definite > > Dear list users, > through the "matrixcalc" package I am performing some checks of variance > matrices (which must be positive definite). > In this example, it happens that the matrix A here reported is singular but > positive definite. Is it possible? > > [,1] [,2] [,3] [,4] > [1,] 1.904255e-12 -1.904255e-12 -8.238960e-13 -1.240294e-12 [2,] - > 1.904255e-12 3.637979e-12 1.364242e-12 1.818989e-12 [3,] -8.238960e-13 > 1.364242e-12 4.809988e+00 7.742369e-01 [4,] -1.240294e-12 1.818989e-12 > 7.742369e-01 1.090411e+00 > > print(is.non.singular.matrix(A, tol = 1e-18)) FALSE print(is.positive.definite(A, > tol=1e-18)) TRUE > > Is there something wrong with this matrix? > Any comment will be appreciated. > Stefano > > > ________________________________ > > AVVISO IMPORTANTE: Questo messaggio di posta elettronica pu? contenere > informazioni confidenziali, pertanto ? destinato solo a persone autorizzate alla > ricezione. I messaggi di posta elettronica per i client di Regione Marche > possono contenere informazioni confidenziali e con privilegi legali. Se non si ? il > destinatario specificato, non leggere, copiare, inoltrare o archiviare questo > messaggio. Se si ? ricevuto questo messaggio per errore, inoltrarlo al mittente > ed eliminarlo completamente dal sistema del proprio computer. Ai sensi > dell?art. 6 della DGR n. 1394/2008 si segnala che, in caso di necessit? ed > urgenza, la risposta al presente messaggio di posta elettronica pu? essere > visionata da persone estranee al destinatario. > IMPORTANT NOTICE: This e-mail message is intended to be received only by > persons entitled to receive the confidential information it may contain. E-mail > messages to clients of Regione Marche may contain information that is > confidential and legally privileged. Please do not read, copy, forward, or store > this message unless you are an intended recipient of it. If you have received > this message in error, please forward it to the sender and delete it completely > from your computer system. > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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.________________________________ AVVISO IMPORTANTE: Questo messaggio di posta elettronica pu? contenere informazioni confidenziali, pertanto ? destinato solo a persone autorizzate alla ricezione. I messaggi di posta elettronica per i client di Regione Marche possono contenere informazioni confidenziali e con privilegi legali. Se non si ? il destinatario specificato, non leggere, copiare, inoltrare o archiviare questo messaggio. Se si ? ricevuto questo messaggio per errore, inoltrarlo al mittente ed eliminarlo completamente dal sistema del proprio computer. Ai sensi dell?art. 6 della DGR n. 1394/2008 si segnala che, in caso di necessit? ed urgenza, la risposta al presente messaggio di posta elettronica pu? essere visionata da persone estranee al destinatario. IMPORTANT NOTICE: This e-mail message is intended to be received only by persons entitled to receive the confidential information it may contain. E-mail messages to clients of Regione Marche may contain information that is confidential and legally privileged. Please do not read, copy, forward, or store this message unless you are an intended recipient of it. If you have received this message in error, please forward it to the sender and delete it completely from your computer system.