Joachim Audenaert
2015-Apr-16 11:12 UTC
[R] melt function chooses wrong id variable with large datasets
Hello, This is a part of my dataset: structure(list(januari = c(38.1, 32.4, 34.5, 20.7, 21.5, 23.1, 29.7, 36.6, 36.1, 20.6, 20.4, 30.1, 38.7, 41.4, 37, 36, 37, 38, 23, 26.7), februari = c(31.5, 36.2, 38.2, 26.4, 20.9, 21.5, 30.2, 33.4, 32.6, 22.2, 21.7, 30, 35.7, 32.8, 39.3, 25.5, 23, 19.9, 21.3, 20.8), maart = c(34.2, 27, 24.2, 19.9, 19.7, 21.5, 30.6, 30, 19, 19.6, 20.6, 23.6, 17.9, 17.3, 21.4, 24.1, 20.9, 30.1, 32.6, 21.3), april = c(26.3, 29.6, 30.3, 23.6, 28.4, 20.7, 24.1, 27.3, 23.2, 18.3, 24.6, 27.4, 20.4, 18.1, 25.2, 19.8, 21, 23.7, 19.6, 18.1), mei = c(23.7, 24, 17.2, 23.2, 25.2, 17.2, 16, 15.6, 13.4, 16, 16.8, 14.6, 19.4, 21, 19.5, 18.5, 13.3, 13.7, 14.3, 14.1), juni = c(17.7, 14.2, 16.6, 15.7, 13.7, 14.7, 13.1, 12.9, 15.4, 11.9, 15.2, 15.3, 16.5, 16.1, 11.7, 11.2, 11.5, 10.8, 16.1, 14.8), juli = c(15.7, 14.5, 10.8, 10.5, 13.4, 12.2, 13.2, 13, 12.4, 13.1, 9.8, 10.5, 13.4, 11, 13.1, 15, 16.7, 16.1, 18.2, 15.7), augustus = c(12.9, 12.8, 15.2, 14.5, 17.2, 14.5, 14.4, 11, 13.1, 13.6, 14.6, 12.7, 13.6, 12.7, 15.5, 17.4, 15.2, 14.2, 17.7, 19.2), september = c(15.6, 15.5, 15.9, 15.1, 16, 19.4, 21.5, 23.7, 18.7, 23.8, 18, 16.2, 18.5, 20.6, 18.3, 22.5, 26.9, 19.4, 15.9, 20.5), oktober = c(21.4, 20.8, 14, 17, 23, 26.4, 19.6, 22.7, 26.9, 14.7, 15.2, 19.8, 26.9, 20.2, 14.3, 14.8, 18.5, 21.7, 21.4, 21.8), november = c(24.7, 26.2, 29, 21.6, 17.1, 16.9, 19.1, 24.7, 25.4, 19.8, 18.2, 16.3, 17, 17.7, 15.5, 14.7, 15.8, 19.9, 20.4, 23.3), december = c(19.8, 27, 21, 33, 22.6, 28.3, 21.1, 19, 17.3, 27, 30.2, 24.8, 17.9, 17.9, 20.7, 30.9, 36.2, 21, 20.2, 21.3), norm = c("45.8713463281901", "24.047250681782984", "3.7533684144746324", "38.594241119279324", "26.391897460120358", "61.746470001194638", "6.8321020448487992", "11.933109250115226", "51.951891096493924", "37.424611852237945", "5.1587836676942374", "36.552835044409434", "31.781209673851027", "29.09146215582853", "4.856812959269508", "5.3982910143166514", "46.553976273304215", "17.566272518985429", "20.552451905814117", "61.894775704479279" )), .Names = c("januari", "februari", "maart", "april", "mei", "juni", "juli", "augustus", "september", "oktober", "november", "december", "norm"), row.names = c(NA, 20L), class = "data.frame") I transform my dataset with the following script: y <- melt(dataset,na.rm=TRUE) variable <- y[,1] value <- y[,2] and can then perform a levene test as follows: LEVENE <- leveneTest(value~variable,y) When the dataset is small, lets say less than 100 values per column everything works great. I get the message: No id variables; using all as measure variables When the dataset is much bigger I get the following message Using norm as id variables, why does this function pick norm as id variable? and how can I tell R that each column title is my variable Met vriendelijke groeten - With kind regards, Joachim Audenaert onderzoeker gewasbescherming - crop protection researcher PCS | proefcentrum voor sierteelt - ornamental plant research Schaessestraat 18, 9070 Destelbergen, Belgi? T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95 E: joachim.audenaert at pcsierteelt.be | W: www.pcsierteelt.be From: PIKAL Petr <petr.pikal at precheza.cz> To: Joachim Audenaert <Joachim.Audenaert at pcsierteelt.be>, "r-help at r-project.org" <r-help at r-project.org> Date: 16/04/2015 12:13 Subject: RE: [R] melt function chooses wrong id variable with large datasets Hi There is something weird with your data and melt function. AFAIK melt does not use first row as id.variables. What is result of str(dataset) Instead of melt(dataset,id.vars=dataset[1,], na.rm=TRUE) melt expects something like melt(dataset, id.vars=c("norm, "jaar"), na.rm=TRUE) If you want more specific answer you shall show us part of your data, preferably copy output of dput(dataset[1:20,]) into your mail. Cheers Petr> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Joachim > Audenaert > Sent: Thursday, April 16, 2015 11:37 AM > To: r-help at r-project.org > Subject: [R] melt function chooses wrong id variable with large > datasets > > Hello all, > > I'm using a large dataset consisting of 2 groups of data, 2 columns in > excel with a header (group name) and 15 000 rows of data. I would like > like to compare this data, so I transform my dataset with the melt > function to get 1 column of data and 1 column of ID variables, then I > can apply different statistical tests. With small datasets this works > great, the melt function automatically chooses the name in row 1 as ID > variable and melts the data, thus giving me a matrix with all ID > variables in column one and the data accordingly in column 2. > With this big dataset however it chooses the whole first column as ID > variables in stead of the first row. Is there a reason why this happens > and how can I make sure the first row is chosen as ID variabele and the > lower rows as data? > > If I specify that I want the first row to be the id variable I also get > error. > > melt(dataset,id.vars=dataset[1,], na.rm=TRUE) > > Error: id variables not found in data: norm, jaar > > Are there alternative ways to create a good reshaped dataset? > > Met vriendelijke groeten - With kind regards, > > Joachim Audenaert > onderzoeker gewasbescherming - crop protection researcher > > PCS | proefcentrum voor sierteelt - ornamental plant research > > Schaessestraat 18, 9070 Destelbergen, Belgi > T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95 > E: joachim.audenaert at pcsierteelt.be | W: www.pcsierteelt.be > > Heb je je individuele begeleiding bemesting (CVBB) al aangevraagd? | > Het PCS op LinkedIn Disclaimer | Please consider the environment before > printing. Think green, keep it on the screen! > [[alternative HTML version deleted]]________________________________ 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. Heb je je individuele begeleiding bemesting (CVBB) al aangevraagd? | Het PCS op LinkedIn Disclaimer | Please consider the environment before printing. Think green, keep it on the screen! [[alternative HTML version deleted]]
PIKAL Petr
2015-Apr-16 11:41 UTC
[R] melt function chooses wrong id variable with large datasets
Hi With this dataset I get> dd.m0<-melt(dataset, na.rm=T)Using norm as id variables> head(dd.m0)norm variable value 1 45.8713463281901 januari 38.1 2 24.047250681782984 januari 32.4 3 3.7533684144746324 januari 34.5 4 38.594241119279324 januari 20.7 5 26.391897460120358 januari 21.5 6 61.746470001194638 januari 23.1>or dd.m<-melt(dataset, id.vars=NULL, na.rm=T)> head(dd.m)variable value 1 januari 38.1 2 januari 32.4 3 januari 34.5 4 januari 20.7 5 januari 21.5 6 januari 23.1> tail(dd.m)variable value 255 norm 4.856812959269508 256 norm 5.3982910143166514 257 norm 46.553976273304215 258 norm 17.566272518985429 259 norm 20.552451905814117 260 norm 61.894775704479279 The latter will put norm to the same column as months. Is it intended? Maybe you want> dd.m1<-melt(dataset[,-13], na.rm=T)No id variables; using all as measure variables> head(dd.m1)variable value 1 januari 38.1 2 januari 32.4 3 januari 34.5 4 januari 20.7 5 januari 21.5 6 januari 23.1> tail(dd.m1)variable value 235 december 20.7 236 december 30.9 237 december 36.2 238 december 21.0 239 december 20.2 240 december 21.3 Cheers Petr From: Joachim Audenaert [mailto:Joachim.Audenaert at pcsierteelt.be] Sent: Thursday, April 16, 2015 1:13 PM To: PIKAL Petr Cc: r-help at r-project.org Subject: RE: [R] melt function chooses wrong id variable with large datasets Hello, This is a part of my dataset: structure(list(januari = c(38.1, 32.4, 34.5, 20.7, 21.5, 23.1, 29.7, 36.6, 36.1, 20.6, 20.4, 30.1, 38.7, 41.4, 37, 36, 37, 38, 23, 26.7), februari = c(31.5, 36.2, 38.2, 26.4, 20.9, 21.5, 30.2, 33.4, 32.6, 22.2, 21.7, 30, 35.7, 32.8, 39.3, 25.5, 23, 19.9, 21.3, 20.8), maart = c(34.2, 27, 24.2, 19.9, 19.7, 21.5, 30.6, 30, 19, 19.6, 20.6, 23.6, 17.9, 17.3, 21.4, 24.1, 20.9, 30.1, 32.6, 21.3), april = c(26.3, 29.6, 30.3, 23.6, 28.4, 20.7, 24.1, 27.3, 23.2, 18.3, 24.6, 27.4, 20.4, 18.1, 25.2, 19.8, 21, 23.7, 19.6, 18.1), mei = c(23.7, 24, 17.2, 23.2, 25.2, 17.2, 16, 15.6, 13.4, 16, 16.8, 14.6, 19.4, 21, 19.5, 18.5, 13.3, 13.7, 14.3, 14.1), juni = c(17.7, 14.2, 16.6, 15.7, 13.7, 14.7, 13.1, 12.9, 15.4, 11.9, 15.2, 15.3, 16.5, 16.1, 11.7, 11.2, 11.5, 10.8, 16.1, 14.8), juli = c(15.7, 14.5, 10.8, 10.5, 13.4, 12.2, 13.2, 13, 12.4, 13.1, 9.8, 10.5, 13.4, 11, 13.1, 15, 16.7, 16.1, 18.2, 15.7), augustus = c(12.9, 12.8, 15.2, 14.5, 17.2, 14.5, 14.4, 11, 13.1, 13.6, 14.6, 12.7, 13.6, 12.7, 15.5, 17.4, 15.2, 14.2, 17.7, 19.2), september = c(15.6, 15.5, 15.9, 15.1, 16, 19.4, 21.5, 23.7, 18.7, 23.8, 18, 16.2, 18.5, 20.6, 18.3, 22.5, 26.9, 19.4, 15.9, 20.5), oktober = c(21.4, 20.8, 14, 17, 23, 26.4, 19.6, 22.7, 26.9, 14.7, 15.2, 19.8, 26.9, 20.2, 14.3, 14.8, 18.5, 21.7, 21.4, 21.8), november = c(24.7, 26.2, 29, 21.6, 17.1, 16.9, 19.1, 24.7, 25.4, 19.8, 18.2, 16.3, 17, 17.7, 15.5, 14.7, 15.8, 19.9, 20.4, 23.3), december = c(19.8, 27, 21, 33, 22.6, 28.3, 21.1, 19, 17.3, 27, 30.2, 24.8, 17.9, 17.9, 20.7, 30.9, 36.2, 21, 20.2, 21.3), norm = c("45.8713463281901", "24.047250681782984", "3.7533684144746324", "38.594241119279324", "26.391897460120358", "61.746470001194638", "6.8321020448487992", "11.933109250115226", "51.951891096493924", "37.424611852237945", "5.1587836676942374", "36.552835044409434", "31.781209673851027", "29.09146215582853", "4.856812959269508", "5.3982910143166514", "46.553976273304215", "17.566272518985429", "20.552451905814117", "61.894775704479279" )), .Names = c("januari", "februari", "maart", "april", "mei", "juni", "juli", "augustus", "september", "oktober", "november", "december", "norm"), row.names = c(NA, 20L), class = "data.frame") I transform my dataset with the following script: y <- melt(dataset,na.rm=TRUE) variable <- y[,1] value <- y[,2] and can then perform a levene test as follows: LEVENE <- leveneTest(value~variable,y) When the dataset is small, lets say less than 100 values per column everything works great. I get the message: No id variables; using all as measure variables When the dataset is much bigger I get the following message Using norm as id variables, why does this function pick norm as id variable? and how can I tell R that each column title is my variable Met vriendelijke groeten - With kind regards, Joachim Audenaert onderzoeker gewasbescherming - crop protection researcher PCS | proefcentrum voor sierteelt - ornamental plant research ________________________________ Schaessestraat 18, 9070 Destelbergen, Belgi? T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95 E: joachim.audenaert at pcsierteelt.be<mailto:joachim.audenaert at pcsierteelt.be> | W: www.pcsierteelt.be<http://www.pcsierteelt.be/> From: PIKAL Petr <petr.pikal at precheza.cz<mailto:petr.pikal at precheza.cz>> To: Joachim Audenaert <Joachim.Audenaert at pcsierteelt.be<mailto:Joachim.Audenaert at pcsierteelt.be>>, "r-help at r-project.org<mailto:r-help at r-project.org>" <r-help at r-project.org<mailto:r-help at r-project.org>> Date: 16/04/2015 12:13 Subject: RE: [R] melt function chooses wrong id variable with large datasets ________________________________ Hi There is something weird with your data and melt function. AFAIK melt does not use first row as id.variables. What is result of str(dataset) Instead of melt(dataset,id.vars=dataset[1,], na.rm=TRUE) melt expects something like melt(dataset, id.vars=c("norm, "jaar"), na.rm=TRUE) If you want more specific answer you shall show us part of your data, preferably copy output of dput(dataset[1:20,]) into your mail. Cheers Petr> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Joachim > Audenaert > Sent: Thursday, April 16, 2015 11:37 AM > To: r-help at r-project.org<mailto:r-help at r-project.org> > Subject: [R] melt function chooses wrong id variable with large > datasets > > Hello all, > > I'm using a large dataset consisting of 2 groups of data, 2 columns in > excel with a header (group name) and 15 000 rows of data. I would like > like to compare this data, so I transform my dataset with the melt > function to get 1 column of data and 1 column of ID variables, then I > can apply different statistical tests. With small datasets this works > great, the melt function automatically chooses the name in row 1 as ID > variable and melts the data, thus giving me a matrix with all ID > variables in column one and the data accordingly in column 2. > With this big dataset however it chooses the whole first column as ID > variables in stead of the first row. Is there a reason why this happens > and how can I make sure the first row is chosen as ID variabele and the > lower rows as data? > > If I specify that I want the first row to be the id variable I also get > error. > > melt(dataset,id.vars=dataset[1,], na.rm=TRUE) > > Error: id variables not found in data: norm, jaar > > Are there alternative ways to create a good reshaped dataset? > > Met vriendelijke groeten - With kind regards, > > Joachim Audenaert > onderzoeker gewasbescherming - crop protection researcher > > PCS | proefcentrum voor sierteelt - ornamental plant research > > Schaessestraat 18, 9070 Destelbergen, Belgi > T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95 > E: joachim.audenaert at pcsierteelt.be<mailto:joachim.audenaert at pcsierteelt.be> | W: www.pcsierteelt.be > > Heb je je individuele begeleiding bemesting (CVBB) al aangevraagd? | > Het PCS op LinkedIn Disclaimer | Please consider the environment before > printing. Think green, keep it on the screen! > [[alternative HTML version deleted]]________________________________ 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. Heb je je individuele begeleiding bemesting (CVBB) al aangevraagd?<http://www.pcsierteelt.be/hosting/pcs/pcs_site.nsf/0/32795D6E62E2F6A8C1257DCE002F4A44?opendocument> | Het PCS op LinkedIn<http://www.linkedin.com/company/proefcentrum-voor-sierteelt> Disclaimer<http://www.pcsierteelt.be/hosting/pcs/pcs_site.nsf/0/EABE6EFE9E0C1C55C1257AD100322499> | Please consider the environment before printing. Think green, keep it on the screen! ________________________________ 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. 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Joachim Audenaert
2015-Apr-16 11:59 UTC
[R] melt function chooses wrong id variable with large datasets
Thanks, indeed norm should be in the same group as as the months. everything works fine when the number of data is quite small, but with big datasets (15 000 values) things seem to go wrong and I can't explain why. It puts norm as an individual column in stead of in the group of months as it does when the dataset is small. Met vriendelijke groeten - With kind regards, Joachim Audenaert onderzoeker gewasbescherming - crop protection researcher PCS | proefcentrum voor sierteelt - ornamental plant research Schaessestraat 18, 9070 Destelbergen, Belgi? T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95 E: joachim.audenaert at pcsierteelt.be | W: www.pcsierteelt.be From: PIKAL Petr <petr.pikal at precheza.cz> To: Joachim Audenaert <Joachim.Audenaert at pcsierteelt.be> Cc: "r-help at r-project.org" <r-help at r-project.org> Date: 16/04/2015 13:41 Subject: RE: [R] melt function chooses wrong id variable with large datasets Hi With this dataset I get> dd.m0<-melt(dataset, na.rm=T)Using norm as id variables> head(dd.m0)norm variable value 1 45.8713463281901 januari 38.1 2 24.047250681782984 januari 32.4 3 3.7533684144746324 januari 34.5 4 38.594241119279324 januari 20.7 5 26.391897460120358 januari 21.5 6 61.746470001194638 januari 23.1>or dd.m<-melt(dataset, id.vars=NULL, na.rm=T)> head(dd.m)variable value 1 januari 38.1 2 januari 32.4 3 januari 34.5 4 januari 20.7 5 januari 21.5 6 januari 23.1> tail(dd.m)variable value 255 norm 4.856812959269508 256 norm 5.3982910143166514 257 norm 46.553976273304215 258 norm 17.566272518985429 259 norm 20.552451905814117 260 norm 61.894775704479279 The latter will put norm to the same column as months. Is it intended? Maybe you want> dd.m1<-melt(dataset[,-13], na.rm=T)No id variables; using all as measure variables> head(dd.m1)variable value 1 januari 38.1 2 januari 32.4 3 januari 34.5 4 januari 20.7 5 januari 21.5 6 januari 23.1> tail(dd.m1)variable value 235 december 20.7 236 december 30.9 237 december 36.2 238 december 21.0 239 december 20.2 240 december 21.3 Cheers Petr From: Joachim Audenaert [mailto:Joachim.Audenaert at pcsierteelt.be] Sent: Thursday, April 16, 2015 1:13 PM To: PIKAL Petr Cc: r-help at r-project.org Subject: RE: [R] melt function chooses wrong id variable with large datasets Hello, This is a part of my dataset: structure(list(januari = c(38.1, 32.4, 34.5, 20.7, 21.5, 23.1, 29.7, 36.6, 36.1, 20.6, 20.4, 30.1, 38.7, 41.4, 37, 36, 37, 38, 23, 26.7), februari = c(31.5, 36.2, 38.2, 26.4, 20.9, 21.5, 30.2, 33.4, 32.6, 22.2, 21.7, 30, 35.7, 32.8, 39.3, 25.5, 23, 19.9, 21.3, 20.8), maart = c(34.2, 27, 24.2, 19.9, 19.7, 21.5, 30.6, 30, 19, 19.6, 20.6, 23.6, 17.9, 17.3, 21.4, 24.1, 20.9, 30.1, 32.6, 21.3), april = c(26.3, 29.6, 30.3, 23.6, 28.4, 20.7, 24.1, 27.3, 23.2, 18.3, 24.6, 27.4, 20.4, 18.1, 25.2, 19.8, 21, 23.7, 19.6, 18.1), mei = c(23.7, 24, 17.2, 23.2, 25.2, 17.2, 16, 15.6, 13.4, 16, 16.8, 14.6, 19.4, 21, 19.5, 18.5, 13.3, 13.7, 14.3, 14.1), juni = c(17.7, 14.2, 16.6, 15.7, 13.7, 14.7, 13.1, 12.9, 15.4, 11.9, 15.2, 15.3, 16.5, 16.1, 11.7, 11.2, 11.5, 10.8, 16.1, 14.8), juli = c(15.7, 14.5, 10.8, 10.5, 13.4, 12.2, 13.2, 13, 12.4, 13.1, 9.8, 10.5, 13.4, 11, 13.1, 15, 16.7, 16.1, 18.2, 15.7), augustus = c(12.9, 12.8, 15.2, 14.5, 17.2, 14.5, 14.4, 11, 13.1, 13.6, 14.6, 12.7, 13.6, 12.7, 15.5, 17.4, 15.2, 14.2, 17.7, 19.2), september = c(15.6, 15.5, 15.9, 15.1, 16, 19.4, 21.5, 23.7, 18.7, 23.8, 18, 16.2, 18.5, 20.6, 18.3, 22.5, 26.9, 19.4, 15.9, 20.5), oktober = c(21.4, 20.8, 14, 17, 23, 26.4, 19.6, 22.7, 26.9, 14.7, 15.2, 19.8, 26.9, 20.2, 14.3, 14.8, 18.5, 21.7, 21.4, 21.8), november = c(24.7, 26.2, 29, 21.6, 17.1, 16.9, 19.1, 24.7, 25.4, 19.8, 18.2, 16.3, 17, 17.7, 15.5, 14.7, 15.8, 19.9, 20.4, 23.3), december = c(19.8, 27, 21, 33, 22.6, 28.3, 21.1, 19, 17.3, 27, 30.2, 24.8, 17.9, 17.9, 20.7, 30.9, 36.2, 21, 20.2, 21.3), norm = c("45.8713463281901", "24.047250681782984", "3.7533684144746324", "38.594241119279324", "26.391897460120358", "61.746470001194638", "6.8321020448487992", "11.933109250115226", "51.951891096493924", "37.424611852237945", "5.1587836676942374", "36.552835044409434", "31.781209673851027", "29.09146215582853", "4.856812959269508", "5.3982910143166514", "46.553976273304215", "17.566272518985429", "20.552451905814117", "61.894775704479279" )), .Names = c("januari", "februari", "maart", "april", "mei", "juni", "juli", "augustus", "september", "oktober", "november", "december", "norm"), row.names = c(NA, 20L), class = "data.frame") I transform my dataset with the following script: y <- melt(dataset,na.rm=TRUE) variable <- y[,1] value <- y[,2] and can then perform a levene test as follows: LEVENE <- leveneTest(value~variable,y) When the dataset is small, lets say less than 100 values per column everything works great. I get the message: No id variables; using all as measure variables When the dataset is much bigger I get the following message Using norm as id variables, why does this function pick norm as id variable? and how can I tell R that each column title is my variable Met vriendelijke groeten - With kind regards, Joachim Audenaert onderzoeker gewasbescherming - crop protection researcher PCS | proefcentrum voor sierteelt - ornamental plant research Schaessestraat 18, 9070 Destelbergen, Belgi? T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95 E: joachim.audenaert at pcsierteelt.be | W: www.pcsierteelt.be From: PIKAL Petr <petr.pikal at precheza.cz> To: Joachim Audenaert <Joachim.Audenaert at pcsierteelt.be>, " r-help at r-project.org" <r-help at r-project.org> Date: 16/04/2015 12:13 Subject: RE: [R] melt function chooses wrong id variable with large datasets Hi There is something weird with your data and melt function. AFAIK melt does not use first row as id.variables. What is result of str(dataset) Instead of melt(dataset,id.vars=dataset[1,], na.rm=TRUE) melt expects something like melt(dataset, id.vars=c("norm, "jaar"), na.rm=TRUE) If you want more specific answer you shall show us part of your data, preferably copy output of dput(dataset[1:20,]) into your mail. Cheers Petr> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Joachim > Audenaert > Sent: Thursday, April 16, 2015 11:37 AM > To: r-help at r-project.org > Subject: [R] melt function chooses wrong id variable with large > datasets > > Hello all, > > I'm using a large dataset consisting of 2 groups of data, 2 columns in > excel with a header (group name) and 15 000 rows of data. I would like > like to compare this data, so I transform my dataset with the melt > function to get 1 column of data and 1 column of ID variables, then I > can apply different statistical tests. With small datasets this works > great, the melt function automatically chooses the name in row 1 as ID > variable and melts the data, thus giving me a matrix with all ID > variables in column one and the data accordingly in column 2. > With this big dataset however it chooses the whole first column as ID > variables in stead of the first row. Is there a reason why this happens > and how can I make sure the first row is chosen as ID variabele and the > lower rows as data? > > If I specify that I want the first row to be the id variable I also get > error. > > melt(dataset,id.vars=dataset[1,], na.rm=TRUE) > > Error: id variables not found in data: norm, jaar > > Are there alternative ways to create a good reshaped dataset? > > Met vriendelijke groeten - With kind regards, > > Joachim Audenaert > onderzoeker gewasbescherming - crop protection researcher > > PCS | proefcentrum voor sierteelt - ornamental plant research > > Schaessestraat 18, 9070 Destelbergen, Belgi > T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95 > E: joachim.audenaert at pcsierteelt.be | W: www.pcsierteelt.be > > Heb je je individuele begeleiding bemesting (CVBB) al aangevraagd? | > Het PCS op LinkedIn Disclaimer | Please consider the environment before > printing. Think green, keep it on the screen! > [[alternative HTML version deleted]]________________________________ 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. 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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. Heb je je individuele begeleiding bemesting (CVBB) al aangevraagd? | Het PCS op LinkedIn Disclaimer | Please consider the environment before printing. Think green, keep it on the screen! 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. 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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. Heb je je individuele begeleiding bemesting (CVBB) al aangevraagd? | Het PCS op LinkedIn Disclaimer | Please consider the environment before printing. Think green, keep it on the screen! [[alternative HTML version deleted]]
PIKAL Petr
2015-Apr-17 09:07 UTC
[R] melt function chooses wrong id variable with large datasets
Yes It could be. But anyway, if you wanted to melt your frame and be sure to have norm column added to months column you shall use melt(dataset, id.vars=NULL, na.rm=TRUE) construction. Without it and considering data you sent I get> head(dd.m0)norm variable value 1 45.8713463281901 januari 38.1 2 24.047250681782984 januari 32.4 3 3.7533684144746324 januari 34.5 4 38.594241119279324 januari 20.7 5 26.391897460120358 januari 21.5 6 61.746470001194638 januari 23.1 ... without this id.vars=NULL parameter. Cheers Petr PS. Keep your post to Rhelp - others may learn from it and anothers can provide you with more elaborated explanation. From: Joachim Audenaert [mailto:Joachim.Audenaert at pcsierteelt.be] Sent: Friday, April 17, 2015 8:23 AM To: PIKAL Petr Subject: RE: [R] melt function chooses wrong id variable with large datasets Hello, I upgraded R tot version 3.1.3 and now everything in the script works perfectly. Could the troubles be due to the fact that I was running an older version? Met vriendelijke groeten - With kind regards, Joachim Audenaert onderzoeker gewasbescherming - crop protection researcher PCS | proefcentrum voor sierteelt - ornamental plant research ________________________________ Schaessestraat 18, 9070 Destelbergen, Belgi? T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95 E: joachim.audenaert at pcsierteelt.be<mailto:joachim.audenaert at pcsierteelt.be> | W: www.pcsierteelt.be<http://www.pcsierteelt.be/> From: PIKAL Petr <petr.pikal at precheza.cz<mailto:petr.pikal at precheza.cz>> To: Joachim Audenaert <Joachim.Audenaert at pcsierteelt.be<mailto:Joachim.Audenaert at pcsierteelt.be>> Cc: "r-help at r-project.org<mailto:r-help at r-project.org>" <r-help at r-project.org<mailto:r-help at r-project.org>> Date: 16/04/2015 13:41 Subject: RE: [R] melt function chooses wrong id variable with large datasets ________________________________ Hi With this dataset I get> dd.m0<-melt(dataset, na.rm=T)Using norm as id variables> head(dd.m0)norm variable value 1 45.8713463281901 januari 38.1 2 24.047250681782984 januari 32.4 3 3.7533684144746324 januari 34.5 4 38.594241119279324 januari 20.7 5 26.391897460120358 januari 21.5 6 61.746470001194638 januari 23.1>or dd.m<-melt(dataset, id.vars=NULL, na.rm=T)> head(dd.m)variable value 1 januari 38.1 2 januari 32.4 3 januari 34.5 4 januari 20.7 5 januari 21.5 6 januari 23.1> tail(dd.m)variable value 255 norm 4.856812959269508 256 norm 5.3982910143166514 257 norm 46.553976273304215 258 norm 17.566272518985429 259 norm 20.552451905814117 260 norm 61.894775704479279 The latter will put norm to the same column as months. Is it intended? Maybe you want> dd.m1<-melt(dataset[,-13], na.rm=T)No id variables; using all as measure variables> head(dd.m1)variable value 1 januari 38.1 2 januari 32.4 3 januari 34.5 4 januari 20.7 5 januari 21.5 6 januari 23.1> tail(dd.m1)variable value 235 december 20.7 236 december 30.9 237 december 36.2 238 december 21.0 239 december 20.2 240 december 21.3 Cheers Petr From: Joachim Audenaert [mailto:Joachim.Audenaert at pcsierteelt.be] Sent: Thursday, April 16, 2015 1:13 PM To: PIKAL Petr Cc: r-help at r-project.org<mailto:r-help at r-project.org> Subject: RE: [R] melt function chooses wrong id variable with large datasets Hello, This is a part of my dataset: structure(list(januari = c(38.1, 32.4, 34.5, 20.7, 21.5, 23.1, 29.7, 36.6, 36.1, 20.6, 20.4, 30.1, 38.7, 41.4, 37, 36, 37, 38, 23, 26.7), februari = c(31.5, 36.2, 38.2, 26.4, 20.9, 21.5, 30.2, 33.4, 32.6, 22.2, 21.7, 30, 35.7, 32.8, 39.3, 25.5, 23, 19.9, 21.3, 20.8), maart = c(34.2, 27, 24.2, 19.9, 19.7, 21.5, 30.6, 30, 19, 19.6, 20.6, 23.6, 17.9, 17.3, 21.4, 24.1, 20.9, 30.1, 32.6, 21.3), april = c(26.3, 29.6, 30.3, 23.6, 28.4, 20.7, 24.1, 27.3, 23.2, 18.3, 24.6, 27.4, 20.4, 18.1, 25.2, 19.8, 21, 23.7, 19.6, 18.1), mei = c(23.7, 24, 17.2, 23.2, 25.2, 17.2, 16, 15.6, 13.4, 16, 16.8, 14.6, 19.4, 21, 19.5, 18.5, 13.3, 13.7, 14.3, 14.1), juni = c(17.7, 14.2, 16.6, 15.7, 13.7, 14.7, 13.1, 12.9, 15.4, 11.9, 15.2, 15.3, 16.5, 16.1, 11.7, 11.2, 11.5, 10.8, 16.1, 14.8), juli = c(15.7, 14.5, 10.8, 10.5, 13.4, 12.2, 13.2, 13, 12.4, 13.1, 9.8, 10.5, 13.4, 11, 13.1, 15, 16.7, 16.1, 18.2, 15.7), augustus = c(12.9, 12.8, 15.2, 14.5, 17.2, 14.5, 14.4, 11, 13.1, 13.6, 14.6, 12.7, 13.6, 12.7, 15.5, 17.4, 15.2, 14.2, 17.7, 19.2), september = c(15.6, 15.5, 15.9, 15.1, 16, 19.4, 21.5, 23.7, 18.7, 23.8, 18, 16.2, 18.5, 20.6, 18.3, 22.5, 26.9, 19.4, 15.9, 20.5), oktober = c(21.4, 20.8, 14, 17, 23, 26.4, 19.6, 22.7, 26.9, 14.7, 15.2, 19.8, 26.9, 20.2, 14.3, 14.8, 18.5, 21.7, 21.4, 21.8), november = c(24.7, 26.2, 29, 21.6, 17.1, 16.9, 19.1, 24.7, 25.4, 19.8, 18.2, 16.3, 17, 17.7, 15.5, 14.7, 15.8, 19.9, 20.4, 23.3), december = c(19.8, 27, 21, 33, 22.6, 28.3, 21.1, 19, 17.3, 27, 30.2, 24.8, 17.9, 17.9, 20.7, 30.9, 36.2, 21, 20.2, 21.3), norm = c("45.8713463281901", "24.047250681782984", "3.7533684144746324", "38.594241119279324", "26.391897460120358", "61.746470001194638", "6.8321020448487992", "11.933109250115226", "51.951891096493924", "37.424611852237945", "5.1587836676942374", "36.552835044409434", "31.781209673851027", "29.09146215582853", "4.856812959269508", "5.3982910143166514", "46.553976273304215", "17.566272518985429", "20.552451905814117", "61.894775704479279" )), .Names = c("januari", "februari", "maart", "april", "mei", "juni", "juli", "augustus", "september", "oktober", "november", "december", "norm"), row.names = c(NA, 20L), class = "data.frame") I transform my dataset with the following script: y <- melt(dataset,na.rm=TRUE) variable <- y[,1] value <- y[,2] and can then perform a levene test as follows: LEVENE <- leveneTest(value~variable,y) When the dataset is small, lets say less than 100 values per column everything works great. I get the message: No id variables; using all as measure variables When the dataset is much bigger I get the following message Using norm as id variables, why does this function pick norm as id variable? and how can I tell R that each column title is my variable Met vriendelijke groeten - With kind regards, Joachim Audenaert onderzoeker gewasbescherming - crop protection researcher PCS | proefcentrum voor sierteelt - ornamental plant research ________________________________ Schaessestraat 18, 9070 Destelbergen, Belgi? T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95 E: joachim.audenaert at pcsierteelt.be<mailto:joachim.audenaert at pcsierteelt.be> | W: www.pcsierteelt.be<http://www.pcsierteelt.be/> From: PIKAL Petr <petr.pikal at precheza.cz<mailto:petr.pikal at precheza.cz>> To: Joachim Audenaert <Joachim.Audenaert at pcsierteelt.be<mailto:Joachim.Audenaert at pcsierteelt.be>>, "r-help at r-project.org<mailto:r-help at r-project.org>" <r-help at r-project.org<mailto:r-help at r-project.org>> Date: 16/04/2015 12:13 Subject: RE: [R] melt function chooses wrong id variable with large datasets ________________________________ Hi There is something weird with your data and melt function. AFAIK melt does not use first row as id.variables. What is result of str(dataset) Instead of melt(dataset,id.vars=dataset[1,], na.rm=TRUE) melt expects something like melt(dataset, id.vars=c("norm, "jaar"), na.rm=TRUE) If you want more specific answer you shall show us part of your data, preferably copy output of dput(dataset[1:20,]) into your mail. Cheers Petr> -----Original Message----- > From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Joachim > Audenaert > Sent: Thursday, April 16, 2015 11:37 AM > To: r-help at r-project.org<mailto:r-help at r-project.org> > Subject: [R] melt function chooses wrong id variable with large > datasets > > Hello all, > > I'm using a large dataset consisting of 2 groups of data, 2 columns in > excel with a header (group name) and 15 000 rows of data. I would like > like to compare this data, so I transform my dataset with the melt > function to get 1 column of data and 1 column of ID variables, then I > can apply different statistical tests. With small datasets this works > great, the melt function automatically chooses the name in row 1 as ID > variable and melts the data, thus giving me a matrix with all ID > variables in column one and the data accordingly in column 2. > With this big dataset however it chooses the whole first column as ID > variables in stead of the first row. Is there a reason why this happens > and how can I make sure the first row is chosen as ID variabele and the > lower rows as data? > > If I specify that I want the first row to be the id variable I also get > error. > > melt(dataset,id.vars=dataset[1,], na.rm=TRUE) > > Error: id variables not found in data: norm, jaar > > Are there alternative ways to create a good reshaped dataset? > > Met vriendelijke groeten - With kind regards, > > Joachim Audenaert > onderzoeker gewasbescherming - crop protection researcher > > PCS | proefcentrum voor sierteelt - ornamental plant research > > Schaessestraat 18, 9070 Destelbergen, Belgi > T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95 > E: joachim.audenaert at pcsierteelt.be<mailto:joachim.audenaert at pcsierteelt.be> | W: www.pcsierteelt.be > > Heb je je individuele begeleiding bemesting (CVBB) al aangevraagd? | > Het PCS op LinkedIn Disclaimer | Please consider the environment before > printing. 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