debra ragland
2015-Jul-01 13:23 UTC
[R] applying coda package effectiveSize function to a list
Please help,I am spinning my wheels behind what should be a pretty simple solution. I found a solution by asking another question on here but it seems to not be effective on all my files of similar make up to the test case. I am simply trying to read data into R, group/order it by chain and atom number (V2 and V3 in the test data) and apply the effectiveSize function from the coda package to the grouped data. Previously I have tried splitting the data, and then applying the function over the new list, which, as I previously stated, only works in the test case.sapply(lst, function(x) coda::effectiveSize(x["variable"])) see comments?Apply a function from a specific R package to all files in folderI have tried aggregate, ddply, and a host of other commands/packages to no avail.My data files are very large so I am hoping that someone willing to help can retrieve a file from hereI cannot interpret the error I that I am getting, that seems to pop up no matter what I do.Error in ar.yw.default(x, aic = aic, order.max = order.max, na.action = na.action, : 'order.max' must be >= 1One dataset is here?https://drive.google.com/open?id=0B0I4hNiJD0ErZWR5UDZjd1BiNm [[alternative HTML version deleted]]
PIKAL Petr
2015-Jul-01 14:40 UTC
[R] applying coda package effectiveSize function to a list
Hi Please no HTML posting. It is almost unreadable. Do not post twice the same question, it is unnecessary. I do not know coda package but without further info you probably do not get sensible answer. Is your splits data mcmc or mcmc.list object? How does objects for which the function works differ from your other tested objects? Just a wild guess - some part of an object for which effectivSize throws error has dimension 1 or 0. Cheers Petr> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of debra > ragland via R-help > Sent: Wednesday, July 01, 2015 3:23 PM > To: r-help at r-project.org > Subject: [R] applying coda package effectiveSize function to a list > > Please help,I am spinning my wheels behind what should be a pretty > simple solution. I found a solution by asking another question on here > but it seems to not be effective on all my files of similar make up to > the test case. I am simply trying to read data into R, group/order it > by chain and atom number (V2 and V3 in the test data) and apply the > effectiveSize function from the coda package to the grouped data. > Previously I have tried splitting the data, and then applying the > function over the new list, which, as I previously stated, only works > in the test case.sapply(lst, function(x) > coda::effectiveSize(x["variable"])) see comments Apply a function from > a specific R package to all files in folderI have tried aggregate, > ddply, and a host of other commands/packages to no avail.My data files > are very large so I am hoping that someone willing to help can retrieve > a file from hereI cannot interpret the error I that I am getting, that > seems to pop up no matter what I do.Error in ar.yw.default(x, aic > aic, order.max = order.max, na.action = na.action, : 'order.max' must > be >= 1One dataset is > here https://drive.google.com/open?id=0B0I4hNiJD0ErZWR5UDZjd1BiNm > [[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.________________________________ Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu. V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce s dodatkem ?i odchylkou. - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient.
PIKAL Petr
2015-Jul-01 15:06 UTC
[R] applying coda package effectiveSize function to a list
Hi> -----Original Message----- > From: Debra Ragland [mailto:ragland.debra at yahoo.com] > Sent: Wednesday, July 01, 2015 4:53 PM > To: PIKAL Petr > Subject: Re: [R] applying coda package effectiveSize function to a list > > Hi Petr, > > How do I remove a post?AFAIK, no way. Why? Instead of removing speculating about removing your post you shall add some additional info so as knowledgable guys can find out an answer. Petr> > Sent from my iPhone > > > On Jul 1, 2015, at 10:40 AM, PIKAL Petr <petr.pikal at precheza.cz> > wrote: > > > > Hi > > > > Please no HTML posting. It is almost unreadable. > > > > Do not post twice the same question, it is unnecessary. > > > > I do not know coda package but without further info you probably do > not get sensible answer. > > > > Is your splits data mcmc or mcmc.list object? > > > > How does objects for which the function works differ from your other > tested objects? > > > > Just a wild guess - some part of an object for which effectivSize > throws error has dimension 1 or 0. > > > > Cheers > > Petr > > > > > > > > > > > >> -----Original Message----- > >> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of > debra > >> ragland via R-help > >> Sent: Wednesday, July 01, 2015 3:23 PM > >> To: r-help at r-project.org > >> Subject: [R] applying coda package effectiveSize function to a list > >> > >> Please help,I am spinning my wheels behind what should be a pretty > >> simple solution. I found a solution by asking another question on > >> here but it seems to not be effective on all my files of similar > make > >> up to the test case. I am simply trying to read data into R, > >> group/order it by chain and atom number (V2 and V3 in the test data) > >> and apply the effectiveSize function from the coda package to the > grouped data. > >> Previously I have tried splitting the data, and then applying the > >> function over the new list, which, as I previously stated, only > works > >> in the test case.sapply(lst, function(x) > >> coda::effectiveSize(x["variable"])) see comments Apply a function > >> from a specific R package to all files in folderI have tried > >> aggregate, ddply, and a host of other commands/packages to no > >> avail.My data files are very large so I am hoping that someone > >> willing to help can retrieve a file from hereI cannot interpret the > >> error I that I am getting, that seems to pop up no matter what I > >> do.Error in ar.yw.default(x, aic = aic, order.max = order.max, > >> na.action = na.action, : 'order.max' must be >= 1One dataset is > here > >> https://drive.google.com/open?id=0B0I4hNiJD0ErZWR5UDZjd1BiNm > >> [[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. > > > > ________________________________ > > Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a > jsou ur?eny pouze jeho adres?t?m. > > Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? > neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho > kopie vyma?te ze sv?ho syst?mu. > > Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento > email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. > > Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou > modifikacemi ?i zpo?d?n?m p?enosu e-mailu. > > > > V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: > > - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? > smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. > > - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? > p?ijmout; Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky > ze strany p??jemce s dodatkem ?i odchylkou. > > - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve > v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. > > - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za > spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? > zmocn?n nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly > adres?tovi tohoto emailu p??padn? osob?, kterou adres?t zastupuje, > p?edlo?eny nebo jejich existence je adres?tovi ?i osob? j?m zastoupen? > zn?m?. > > > > This e-mail and any documents attached to it may be confidential and > are intended only for its intended recipients. > > If you received this e-mail by mistake, please immediately inform its > sender. Delete the contents of this e-mail with all attachments and its > copies from your system. > > If you are not the intended recipient of this e-mail, you are not > authorized to use, disseminate, copy or disclose this e-mail in any > manner. > > The sender of this e-mail shall not be liable for any possible damage > caused by modifications of the e-mail or by delay with transfer of the > email. > > > > In case that this e-mail forms part of business dealings: > > - the sender reserves the right to end negotiations about entering > into a contract in any time, for any reason, and without stating any > reasoning. > > - if the e-mail contains an offer, the recipient is entitled to > immediately accept such offer; The sender of this e-mail (offer) > excludes any acceptance of the offer on the part of the recipient > containing any amendment or variation. > > - the sender insists on that the respective contract is concluded > only upon an express mutual agreement on all its aspects. > > - the sender of this e-mail informs that he/she is not authorized to > enter into any contracts on behalf of the company except for cases in > which he/she is expressly authorized to do so in writing, and such > authorization or power of attorney is submitted to the recipient or the > person represented by the recipient, or the existence of such > authorization is known to the recipient of the person represented by > the recipient.________________________________ Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a jsou ur?eny pouze jeho adres?t?m. Jestli?e jste obdr?el(a) tento e-mail omylem, informujte laskav? neprodlen? jeho odes?latele. Obsah tohoto emailu i s p??lohami a jeho kopie vyma?te ze sv?ho syst?mu. Nejste-li zam??len?m adres?tem tohoto emailu, nejste opr?vn?ni tento email jakkoliv u??vat, roz?i?ovat, kop?rovat ?i zve?ej?ovat. Odes?latel e-mailu neodpov?d? za eventu?ln? ?kodu zp?sobenou modifikacemi ?i zpo?d?n?m p?enosu e-mailu. V p??pad?, ?e je tento e-mail sou??st? obchodn?ho jedn?n?: - vyhrazuje si odes?latel pr?vo ukon?it kdykoliv jedn?n? o uzav?en? smlouvy, a to z jak?hokoliv d?vodu i bez uveden? d?vodu. - a obsahuje-li nab?dku, je adres?t opr?vn?n nab?dku bezodkladn? p?ijmout; Odes?latel tohoto e-mailu (nab?dky) vylu?uje p?ijet? nab?dky ze strany p??jemce s dodatkem ?i odchylkou. - trv? odes?latel na tom, ?e p??slu?n? smlouva je uzav?ena teprve v?slovn?m dosa?en?m shody na v?ech jej?ch n?le?itostech. - odes?latel tohoto emailu informuje, ?e nen? opr?vn?n uzav?rat za spole?nost ??dn? smlouvy s v?jimkou p??pad?, kdy k tomu byl p?semn? zmocn?n nebo p?semn? pov??en a takov? pov??en? nebo pln? moc byly adres?tovi tohoto emailu p??padn? osob?, kterou adres?t zastupuje, p?edlo?eny nebo jejich existence je adres?tovi ?i osob? j?m zastoupen? zn?m?. This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients. If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system. If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner. The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email. In case that this e-mail forms part of business dealings: - the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning. - if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation. - the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects. - the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient.