[R] Select rows of a data frame according to values of vector in a list
Hi there !! I have a list like as follows : >lis $lis1 [1] 1 3 5 $lis2 [1] 2 4 6 8 9 I have another data frame like as follows >df 1 10 110 2 15 120 3 20 130 4 25 140 5 30 150 6 35 160 7 40 150 8 45 180 9 50 190 Now i want to select the rows of data frame by the value of list and the output will be as list and as follows >dat $lis1 1 10 110 3 20 130 5 30 150 $lis2 2 15 120 4 25 140 6 35 160 8 45 180 9 50 190 Any help will be very much appreciated. !! Best regards ... Tanvir Ahamed Göteborg, Sweden [[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.
Re: [R] Select rows of a data frame according to values of vector in a list
Hello, Try the following. lapply(lis, function(i) df[i, ]) Hope this helps, Rui Barradas Em 03-01-2014 09:04, Mohammad Tanvir Ahamed escreveu: Hi there !! I have a list like as follows : lis $lis1 [1] 1 3 5 $lis2 [1] 2 4 6 8 9 I have another data frame like as follows df 1 10 110 2 15 120 3 20 130 4 25 140 5 30 150 6 35 160 7 40 150 8 45 180 9 50 190 Now i want to select the rows of data frame by the value of list and the output will be as list and as follows dat $lis1 1 10 110 3 20 130 5 30 150 $lis2 2 15 120 4 25 140 6 35 160 8 45 180 9 50 190 Any help will be very much appreciated. !! Best regards ... Tanvir Ahamed Göteborg, Sweden [[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-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.
Re: [R] Select rows of a data frame according to values of vector in a list
Thanks !! Best regards ... Tanvir Ahamed Göteborg, Sweden From: Rui Barradas -h...@r-project.org> Sent: Friday, 3 January 2014, 10:58 Subject: Re: [R] Select rows of a data frame according to values of vector in a list Hello, Try the following. lapply(lis, function(i) df[i, ]) Hope this helps, Rui Barradas Em 03-01-2014 09:04, Mohammad Tanvir Ahamed escreveu: > Hi there !! > > I have a list like as follows : >> lis > $lis1 > [1] 1 3 5 > > $lis2 > [1] 2 4 6 8 9 > > I have another data frame like as follows >> df > 1 10 110 > 2 15 120 > 3 20 130 > 4 25 140 > 5 30 150 > 6 35 160 > 7 40 150 > 8 45 180 > 9 50 190 > > Now i want to select the rows of data frame by the value of list and the > output will be as list and as follows > >> dat > $lis1 > 1 10 110 > 3 20 130 > 5 30 150 > > $lis2 > 2 15 120 > 4 25 140 > 6 35 160 > 8 45 180 > 9 50 190 > [[elided Yahoo spam]] > > > Best regards > > > ... > Tanvir Ahamed > Göteborg, Sweden > [[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. > [[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] Ordering the rows of a data frame
Dear R users, I have two files of seasonal rainfall data (more than 10,000 rows each); here the first 8 rows of each file are reported. Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station 2000,1952,12,1,0,0,1953,3,1,0,0,307.20,90,100.0,1510 2000,1953,3,1,0,0,1953,6,1,0,0,153.60,92,100.0,1510 2000,1953,6,1,0,0,1953,9,1,0,0,181.00,92,100.0,1510 2000,1953,9,1,0,0,1953,12,1,0,0,202.40,91,100.0,1510 2000,1953,12,1,0,0,1954,3,1,0,0,153.80,90,100.0,1510 2000,1954,3,1,0,0,1954,6,1,0,0,286.20,92,100.0,1510 2000,1954,6,1,0,0,1954,9,1,0,0,142.80,92,100.0,1510 2000,1954,9,1,0,0,1954,12,1,0,0,186.60,91,100.0,1510 ... Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station 1056,2004,12,1,0,0,2005,3,1,0,0,93.60,2833,32.8,15 1056,2005,3,1,0,0,2005,6,1,0,0,149.80,4406,49.9,15 1056,2005,6,1,0,0,2005,9,1,0,0,52.80,1440,16.3,15 1056,2005,9,1,0,0,2005,12,1,0,0,191.80,1201,13.7,15 1056,2005,12,1,0,0,2006,3,1,0,0,26.40,336,3.9,15 1056,2006,12,1,0,0,2007,3,1,0,0,59.00,3604,41.7,15 1056,2007,3,1,0,0,2007,6,1,0,0,181.16,4414,50.0,15 1056,2007,6,1,0,0,2007,9,1,0,0,96.00,7337,83.1,15 ... I have to load them as data frames, to merge them and sort them by (Y_init,M_init,D_init,Code_Raingouge). I wrote a short function where I first load the two files as data frames df_1 <- read.csv(file="prec_all_19521201_19821201.csv", sep=",") df_2 <- read.csv(file="prec_all_19821201_20111201.csv", sep=",") then I merge them by df_final <- merge(df_1, df_2, all=TRUE) and finally I try to order df_final through df_final <- df_final[order(Y_init, M_init, D_init, Code_Raingouge), ] but this returns only the first row. I read the manual carefully and I saw some examples, but I have not been able to do this simple task. I spent quite a long time and now I decided to ask the list. Could please somebody help me to show me where the mistake is? Thank you Stefano AVVISO IMPORTANTE: Questo messaggio di posta elettronica può contenere informazioni confidenziali, pertanto è 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 è il destinatario specificato, non leggere, copiare, inoltrare o archiviare questo messaggio. Se si è ricevuto questo messaggio per errore, inoltrarlo al mittente ed eliminarlo completamente dal sistema del proprio computer. Ai sensi dellâart. 6 della DGR n. 1394/2008 si segnala che, in caso di necessità ed urgenza, la risposta al presente messaggio di posta elettronica può 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@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] Package LaplacesDemon information
Dear R-group I can not install the package LaplacesDemon in version 3.0.2 of R. I ask whether it is possible or, alternatively, signs for a equivalent package. Thanks you and best regards. Vittorio Colagrande [[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.
Re: [R] Ordering the rows of a data frame
On Fri, Jan 3, 2014 at 9:41 AM, Stefano Sofia wrote: > > Dear R users, > I have two files of seasonal rainfall data (more than 10,000 rows each); here > the first 8 rows of each file are reported. > > Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station > 2000,1952,12,1,0,0,1953,3,1,0,0,307.20,90,100.0,1510 > 2000,1953,3,1,0,0,1953,6,1,0,0,153.60,92,100.0,1510 > 2000,1953,6,1,0,0,1953,9,1,0,0,181.00,92,100.0,1510 > 2000,1953,9,1,0,0,1953,12,1,0,0,202.40,91,100.0,1510 > 2000,1953,12,1,0,0,1954,3,1,0,0,153.80,90,100.0,1510 > 2000,1954,3,1,0,0,1954,6,1,0,0,286.20,92,100.0,1510 > 2000,1954,6,1,0,0,1954,9,1,0,0,142.80,92,100.0,1510 > 2000,1954,9,1,0,0,1954,12,1,0,0,186.60,91,100.0,1510 > ... > > Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station > 1056,2004,12,1,0,0,2005,3,1,0,0,93.60,2833,32.8,15 > 1056,2005,3,1,0,0,2005,6,1,0,0,149.80,4406,49.9,15 > 1056,2005,6,1,0,0,2005,9,1,0,0,52.80,1440,16.3,15 > 1056,2005,9,1,0,0,2005,12,1,0,0,191.80,1201,13.7,15 > 1056,2005,12,1,0,0,2006,3,1,0,0,26.40,336,3.9,15 > 1056,2006,12,1,0,0,2007,3,1,0,0,59.00,3604,41.7,15 > 1056,2007,3,1,0,0,2007,6,1,0,0,181.16,4414,50.0,15 > 1056,2007,6,1,0,0,2007,9,1,0,0,96.00,7337,83.1,15 > ... > > I have to load them as data frames, to merge them and sort them by > (Y_init,M_init,D_init,Code_Raingouge). > > I wrote a short function where I first load the two files as data frames > > df_1 <- read.csv(file="prec_all_19521201_19821201.csv", sep=",") > df_2 <- read.csv(file="prec_all_19821201_20111201.csv", sep=",") > > then I merge them by > > df_final <- merge(df_1, df_2, all=TRUE) > > and finally I try to order df_final through > > df_final <- df_final[order(Y_init, M_init, D_init, Code_Raingouge), ] You probably need df_final <- df_final[order(df_final$Y_init, df_final$M_init, df_final$D_init, df_final$Code_Raingouge), ] or df_final <- df_final[with(df_final, order(Y_init, M_init, D_init, Code_Raingouge)), ] > > but this returns only the first row. That is strange; do you have copies of Y_init, M_init etc. in your workspace? > > I read the manual carefully and I saw some examples, but I have not been able > to do this simple task. I can see how the data.frame sorting examples in ?order would lead to this confusion, as they are limited to the special case where the variables you want to sort by are in the workspace rather than (as is more often the case) variables in the data.frame itself. > I spent quite a long time and now I decided to ask the list. > Could please somebody help me to show me where the mistake is? > > Thank you > Stefano > > > > > AVVISO IMPORTANTE: Questo messaggio di posta elettronica può contenere > informazioni confidenziali, pertanto è 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 è il destinatario specificato, non leggere, copiare, inoltrare o > archiviare questo messaggio. Se si è 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 necessità ed urgenza, la risposta al presente messaggio di posta > elettronica può 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@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-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.
Re: [R] Ordering the rows of a data frame
Hi Sofia! You need to attach the data file before sorting: attach(df_final) or just use full qualified names (like df_final$Y_init) Dmitry On 03/01/2014 16:41, Stefano Sofia wrote: > Dear R users, > I have two files of seasonal rainfall data (more than 10,000 rows each); here > the first 8 rows of each file are reported. > > Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station > 2000,1952,12,1,0,0,1953,3,1,0,0,307.20,90,100.0,1510 > 2000,1953,3,1,0,0,1953,6,1,0,0,153.60,92,100.0,1510 > 2000,1953,6,1,0,0,1953,9,1,0,0,181.00,92,100.0,1510 > 2000,1953,9,1,0,0,1953,12,1,0,0,202.40,91,100.0,1510 > 2000,1953,12,1,0,0,1954,3,1,0,0,153.80,90,100.0,1510 > 2000,1954,3,1,0,0,1954,6,1,0,0,286.20,92,100.0,1510 > 2000,1954,6,1,0,0,1954,9,1,0,0,142.80,92,100.0,1510 > 2000,1954,9,1,0,0,1954,12,1,0,0,186.60,91,100.0,1510 > ... > > Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station > 1056,2004,12,1,0,0,2005,3,1,0,0,93.60,2833,32.8,15 > 1056,2005,3,1,0,0,2005,6,1,0,0,149.80,4406,49.9,15 > 1056,2005,6,1,0,0,2005,9,1,0,0,52.80,1440,16.3,15 > 1056,2005,9,1,0,0,2005,12,1,0,0,191.80,1201,13.7,15 > 1056,2005,12,1,0,0,2006,3,1,0,0,26.40,336,3.9,15 > 1056,2006,12,1,0,0,2007,3,1,0,0,59.00,3604,41.7,15 > 1056,2007,3,1,0,0,2007,6,1,0,0,181.16,4414,50.0,15 > 1056,2007,6,1,0,0,2007,9,1,0,0,96.00,7337,83.1,15 > ... > > I have to load them as data frames, to merge them and sort them by > (Y_init,M_init,D_init,Code_Raingouge). > > I wrote a short function where I first load the two files as data frames > > df_1 <- read.csv(file="prec_all_19521201_19821201.csv", sep=",") > df_2 <- read.csv(file="prec_all_19821201_20111201.csv", sep=",") > > then I merge them by > > df_final <- merge(df_1, df_2, all=TRUE) > > and finally I try to order df_final through > > df_final <- df_final[order(Y_init, M_init, D_init, Code_Raingouge), ] > > but this returns only the first row. > > I read the manual carefully and I saw some examples, but I have not been able > to do this simple task. > I spent quite a long time and now I decided to ask the list. > Could please somebody help me to show me where the mistake is? > > Thank you > Stefano > > > > > AVVISO IMPORTANTE: Questo messaggio di posta elettronica può contenere > informazioni confidenziali, pertanto è 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 è il destinatario specificato, non leggere, copiare, inoltrare o > archiviare questo messaggio. Se si è ricevuto questo messaggio per errore, > inoltrarlo al mittente ed eliminarlo completamente dal sistema del proprio > computer. Ai sensi dellâEUR^(TM)art. 6 della DGR n. 1394/2008 si segnala che, > in caso di necessità ed urgenza, la risposta al presente messaggio di posta > elettronica può 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@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. [[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] Linear transformation of multivariate normal
Hello, Colleges! I'm having a problem with illustration of linear transformation of multivariate gaussian RV using R. According to the theory, if X ~ N(0, I), then CX ~ N(0,CC'). But the code below doesn't illustrate this. Please could you help me to find a mistake require(tmvtnorm) C = matrix(c(2,0,1,1), 2,2) x = c(1,2) pmvnorm(lower=rep(-Inf,2),upper=x, sigma=diag(2)) [1] 0.822204 attr(,"error") [1] 1e-15 attr(,"msg") [1] "Normal Completion" pmvnorm(lower=rep(-Inf,2),upper=as.vector(C%*%x), sigma=C %*% t(C)) [1] 0.9452332 attr(,"error") [1] 1e-15 attr(,"msg") [1] "Normal Completion" Dmitry __ 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] multitaper power analysis
Dear all, I have a big problem with R. I want to make a multitaper power spectrum analysis of a time series using 3 tapers and a resolution of two years with robust background noise estimation. I try different packages but unsuccessful. library(multitaper) d<-spec.mtm(CAMstd, nw=2, k=3,deltat=1/12,dtUnits="year") library(psd) dB<-Years dd<-pilot_spec(CAMstd, x.frequency = 2,log="dB", ntap = 3, remove.AR = 0, plot = T, verbose = FALSE) Please give a solution to succeed with this analysis. Thank you very much! -- --- Catalin-Constantin ROIBU Lecturer PhD, Forestry engineer Forestry Faculty of Suceava Str. Universitatii no. 13, Suceava, 720229, Romania office phone +4 0230 52 29 78, ext. 531 mobile phone +4 0745 53 18 01 +4 0766 71 76 58 FAX:+4 0230 52 16 64 silvic.usv.ro [[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.
Re: [R] Ordering the rows of a data frame
Inline Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." H. Gilbert Welch On Fri, Jan 3, 2014 at 7:08 AM, Dmitry Pavlyuk wrote: > Hi Sofia! > > You need to attach the data file before sorting: This is false! -- and generally a bad idea. See ?with Please do not give advice without checking whether it is correct. -- Bert > > attach(df_final) > > or just use full qualified names (like df_final$Y_init) > > Dmitry > > On 03/01/2014 16:41, Stefano Sofia wrote: >> Dear R users, >> I have two files of seasonal rainfall data (more than 10,000 rows each); >> here the first 8 rows of each file are reported. >> >> Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station >> 2000,1952,12,1,0,0,1953,3,1,0,0,307.20,90,100.0,1510 >> 2000,1953,3,1,0,0,1953,6,1,0,0,153.60,92,100.0,1510 >> 2000,1953,6,1,0,0,1953,9,1,0,0,181.00,92,100.0,1510 >> 2000,1953,9,1,0,0,1953,12,1,0,0,202.40,91,100.0,1510 >> 2000,1953,12,1,0,0,1954,3,1,0,0,153.80,90,100.0,1510 >> 2000,1954,3,1,0,0,1954,6,1,0,0,286.20,92,100.0,1510 >> 2000,1954,6,1,0,0,1954,9,1,0,0,142.80,92,100.0,1510 >> 2000,1954,9,1,0,0,1954,12,1,0,0,186.60,91,100.0,1510 >> ... >> >> Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station >> 1056,2004,12,1,0,0,2005,3,1,0,0,93.60,2833,32.8,15 >> 1056,2005,3,1,0,0,2005,6,1,0,0,149.80,4406,49.9,15 >> 1056,2005,6,1,0,0,2005,9,1,0,0,52.80,1440,16.3,15 >> 1056,2005,9,1,0,0,2005,12,1,0,0,191.80,1201,13.7,15 >> 1056,2005,12,1,0,0,2006,3,1,0,0,26.40,336,3.9,15 >> 1056,2006,12,1,0,0,2007,3,1,0,0,59.00,3604,41.7,15 >> 1056,2007,3,1,0,0,2007,6,1,0,0,181.16,4414,50.0,15 >> 1056,2007,6,1,0,0,2007,9,1,0,0,96.00,7337,83.1,15 >> ... >> >> I have to load them as data frames, to merge them and sort them by >> (Y_init,M_init,D_init,Code_Raingouge). >> >> I wrote a short function where I first load the two files as data frames >> >> df_1 <- read.csv(file="prec_all_19521201_19821201.csv", sep=",") >> df_2 <- read.csv(file="prec_all_19821201_20111201.csv", sep=",") >> >> then I merge them by >> >> df_final <- merge(df_1, df_2, all=TRUE) >> >> and finally I try to order df_final through >> >> df_final <- df_final[order(Y_init, M_init, D_init, Code_Raingouge), ] >> >> but this returns only the first row. >> >> I read the manual carefully and I saw some examples, but I have not been >> able to do this simple task. >> I spent quite a long time and now I decided to ask the list. >> Could please somebody help me to show me where the mistake is? >> >> Thank you >> Stefano >> >> >> >> >> AVVISO IMPORTANTE: Questo messaggio di posta elettronica può contenere >> informazioni confidenziali, pertanto è 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 è il destinatario specificato, non leggere, copiare, inoltrare o >> archiviare questo messaggio. Se si è ricevuto questo messaggio per errore, >> inoltrarlo al mittente ed eliminarlo completamente dal sistema del proprio >> computer. Ai sensi dellâEUR^(TM)art. 6 della DGR n. 1394/2008 si segnala >> che, in caso di necessità ed urgenza, la risposta al presente messaggio di >> posta elettronica può 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@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. > > > [[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-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-containe
[R] (no subject)
Hi I have a factor in two level and a continues variable nested in one of the factor A levels. Does it nested ancova model? Please guide me Regards, [[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] APA two-way bar-chart
Dear R-users, I'm struggling with APA formatted two way BAR-charts according to apa-style i should have the legend in the background of my plot (so above the bars and not beside the picture/plot itself) and the background should be completely white without gridlines or what so ever. Could any one give me a hint or solution? See Below for my commands thank you so much, Benjamin Telkamp (Email: inzichtel...@gmail.com, The Netherlands) these are the commands used so far which just didn't give me what i wanted library(ggplot2) library(foreign) install.packages("Hmisc") DATA1 <- read.spss(file=DATA1, use.value.labels=TRUE, to.data.frame=TRUE) Bar_PD <- ggplot(DATA1, aes(Age_group, IRI_PD )) Bar_PD + stat_summary(fun.y = mean, geom = "bar", fill = "Purple") + stat_summary(fun.data = mean_cl_normal, geom = "errorbar", width = 0.2) + labs (x = "Leeftijdsgroep", y = "IRI PD") + theme(plot.background = element_rect(colour= "White")) __ If you reply to this email, your message will be added to the discussion below: http://r.789695.n4.nabble.com/APA-two-way-bar-chart-tp4683046.html This email was sent by Benjamin Telkamp (via Nabble) To receive all replies by email, subscribe to this discussion: http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=subscribe_by_code&node=4683046&code=ci1oZWxwQHItcHJvamVjdC5vcmd8NDY4MzA0NnwtNzg0MjM1NTA4 [[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.
Re: [R] Ordering the rows of a data frame
Bert, why do you think that "attach" is not working in this case? Did you check it before your advice? :) I agree about "generally bad approach", but it is quite convenient for work with one data set. Dmitry On 03/01/2014 18:28, Bert Gunter wrote: Inline Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." H. Gilbert Welch On Fri, Jan 3, 2014 at 7:08 AM, Dmitry Pavlyuk wrote: Hi Sofia! You need to attach the data file before sorting: This is false! -- and generally a bad idea. See ?with Please do not give advice without checking whether it is correct. -- Bert attach(df_final) or just use full qualified names (like df_final$Y_init) Dmitry On 03/01/2014 16:41, Stefano Sofia wrote: Dear R users, I have two files of seasonal rainfall data (more than 10,000 rows each); here the first 8 rows of each file are reported. Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station 2000,1952,12,1,0,0,1953,3,1,0,0,307.20,90,100.0,1510 2000,1953,3,1,0,0,1953,6,1,0,0,153.60,92,100.0,1510 2000,1953,6,1,0,0,1953,9,1,0,0,181.00,92,100.0,1510 2000,1953,9,1,0,0,1953,12,1,0,0,202.40,91,100.0,1510 2000,1953,12,1,0,0,1954,3,1,0,0,153.80,90,100.0,1510 2000,1954,3,1,0,0,1954,6,1,0,0,286.20,92,100.0,1510 2000,1954,6,1,0,0,1954,9,1,0,0,142.80,92,100.0,1510 2000,1954,9,1,0,0,1954,12,1,0,0,186.60,91,100.0,1510 ... Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station 1056,2004,12,1,0,0,2005,3,1,0,0,93.60,2833,32.8,15 1056,2005,3,1,0,0,2005,6,1,0,0,149.80,4406,49.9,15 1056,2005,6,1,0,0,2005,9,1,0,0,52.80,1440,16.3,15 1056,2005,9,1,0,0,2005,12,1,0,0,191.80,1201,13.7,15 1056,2005,12,1,0,0,2006,3,1,0,0,26.40,336,3.9,15 1056,2006,12,1,0,0,2007,3,1,0,0,59.00,3604,41.7,15 1056,2007,3,1,0,0,2007,6,1,0,0,181.16,4414,50.0,15 1056,2007,6,1,0,0,2007,9,1,0,0,96.00,7337,83.1,15 ... I have to load them as data frames, to merge them and sort them by (Y_init,M_init,D_init,Code_Raingouge). I wrote a short function where I first load the two files as data frames df_1 <- read.csv(file="prec_all_19521201_19821201.csv", sep=",") df_2 <- read.csv(file="prec_all_19821201_20111201.csv", sep=",") then I merge them by df_final <- merge(df_1, df_2, all=TRUE) and finally I try to order df_final through df_final <- df_final[order(Y_init, M_init, D_init, Code_Raingouge), ] but this returns only the first row. I read the manual carefully and I saw some examples, but I have not been able to do this simple task. I spent quite a long time and now I decided to ask the list. Could please somebody help me to show me where the mistake is? Thank you Stefano AVVISO IMPORTANTE: Questo messaggio di posta elettronica può contenere informazioni confidenziali, pertanto è 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 è il destinatario specificato, non leggere, copiare, inoltrare o archiviare questo messaggio. Se si è ricevuto questo messaggio per errore, inoltrarlo al mittente ed eliminarlo completamente dal sistema del proprio computer. Ai sensi dellâEUR^(TM)art. 6 della DGR n. 1394/2008 si segnala che, in caso di necessità ed urgenza, la risposta al presente messaggio di posta elettronica può 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@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. [[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-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,
Re: [R] Ordering the rows of a data frame
You misunderstand = I was not sufficiently clear. What is false is your statement that "you **need** to attach the data file before sorting." You do not. with()/within() can be used to avoid using the fully qualified names without attaching. I did not claim that attaching first would not work, only that it was not **necessary** and is generally unwise. -- Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." H. Gilbert Welch On Fri, Jan 3, 2014 at 9:21 AM, Dmitry Pavlyuk wrote: > Bert, why do you think that "attach" is not working in this case? Did you > check it before your advice? :) > I agree about "generally bad approach", but it is quite convenient for work > with one data set. > > Dmitry > > On 03/01/2014 18:28, Bert Gunter wrote: >> >> Inline >> >> Bert Gunter >> Genentech Nonclinical Biostatistics >> (650) 467-7374 >> >> "Data is not information. Information is not knowledge. And knowledge >> is certainly not wisdom." >> H. Gilbert Welch >> >> >> >> >> On Fri, Jan 3, 2014 at 7:08 AM, Dmitry Pavlyuk >> wrote: >>> >>> Hi Sofia! >>> >>> You need to attach the data file before sorting: >> >> This is false! -- and generally a bad idea. See ?with >> Please do not give advice without checking whether it is correct. >> >> -- Bert >> >> >>> attach(df_final) >>> >>> or just use full qualified names (like df_final$Y_init) >>> >>> Dmitry >>> >>> On 03/01/2014 16:41, Stefano Sofia wrote: Dear R users, I have two files of seasonal rainfall data (more than 10,000 rows each); here the first 8 rows of each file are reported. Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station 2000,1952,12,1,0,0,1953,3,1,0,0,307.20,90,100.0,1510 2000,1953,3,1,0,0,1953,6,1,0,0,153.60,92,100.0,1510 2000,1953,6,1,0,0,1953,9,1,0,0,181.00,92,100.0,1510 2000,1953,9,1,0,0,1953,12,1,0,0,202.40,91,100.0,1510 2000,1953,12,1,0,0,1954,3,1,0,0,153.80,90,100.0,1510 2000,1954,3,1,0,0,1954,6,1,0,0,286.20,92,100.0,1510 2000,1954,6,1,0,0,1954,9,1,0,0,142.80,92,100.0,1510 2000,1954,9,1,0,0,1954,12,1,0,0,186.60,91,100.0,1510 ... Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station 1056,2004,12,1,0,0,2005,3,1,0,0,93.60,2833,32.8,15 1056,2005,3,1,0,0,2005,6,1,0,0,149.80,4406,49.9,15 1056,2005,6,1,0,0,2005,9,1,0,0,52.80,1440,16.3,15 1056,2005,9,1,0,0,2005,12,1,0,0,191.80,1201,13.7,15 1056,2005,12,1,0,0,2006,3,1,0,0,26.40,336,3.9,15 1056,2006,12,1,0,0,2007,3,1,0,0,59.00,3604,41.7,15 1056,2007,3,1,0,0,2007,6,1,0,0,181.16,4414,50.0,15 1056,2007,6,1,0,0,2007,9,1,0,0,96.00,7337,83.1,15 ... I have to load them as data frames, to merge them and sort them by (Y_init,M_init,D_init,Code_Raingouge). I wrote a short function where I first load the two files as data frames df_1 <- read.csv(file="prec_all_19521201_19821201.csv", sep=",") df_2 <- read.csv(file="prec_all_19821201_20111201.csv", sep=",") then I merge them by df_final <- merge(df_1, df_2, all=TRUE) and finally I try to order df_final through df_final <- df_final[order(Y_init, M_init, D_init, Code_Raingouge), ] but this returns only the first row. I read the manual carefully and I saw some examples, but I have not been able to do this simple task. I spent quite a long time and now I decided to ask the list. Could please somebody help me to show me where the mistake is? Thank you Stefano AVVISO IMPORTANTE: Questo messaggio di posta elettronica può contenere informazioni confidenziali, pertanto è 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 è il destinatario specificato, non leggere, copiare, inoltrare o archiviare questo messaggio. Se si è ricevuto questo messaggio per errore, inoltrarlo al mittente ed eliminarlo completamente dal sistema del proprio computer. Ai sensi dellâEUR^(TM)art. 6 della DGR n. 1394/2008 si segnala che, in caso di necessità ed urgenza, la risposta al presente messaggio di posta elettronica può 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 un
Re: [R] Package LaplacesDemon information
On Jan 3, 2014, at 6:45 AM, Vittorio Colagrande wrote: > Dear R-group > > > > I can not install the package LaplacesDemon in version 3.0.2 of R. > > I ask whether it is possible or, alternatively, signs for a equivalent > package. > > > > Thanks you and best regards. > > Vittorio Colagrande > > [[alternative HTML version deleted]] Please read the Posting Guide. You have offered precious little information about the causes of your failure. There are several specific requests in the Posting Guide that when you provide them will help people decode your mysteries. > > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html -- David Winsemius Alameda, CA, USA __ 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] robust definition of \code{} for a knitr-produced document
[Not sure if I should post this here, or on a another list, but will try here first...] For a book I'm writing using knitr .Rnw files, I would like to use \code{} to mark *all* R code, without having to escape special characters that appear in R names, formulas, etc. In the past, I've use the LaTeX definition of \code{} in the test file below, without problems. However, in the context of my book project, \code{y ~ (A + B)^2} fails, and I'm forced to use \verb|y ~ (A + B)^2|, or for other cases explicitly escape the special characters, as in \code{str\_length()} or \code{Arthritis\$sex}. Below is a test file that *works*. What I don't know is how to find out why it doesn't work in the context of my book project. --- begin code-test.tex --- \documentclass{article} \usepackage{url} \makeatletter \newcommand\code{\bgroup\@makeother\_\@makeother\~\@makeother\$\@makeother\^\@codex} \def\@codex#1{{\normalfont\ttfamily\hyphenchar\font=-1 #1}\egroup} \makeatother \begin{document} Testing use of code fragments with special characters without having to escape them. \begin{itemize} \item Formulas-- code: \code{y ~ (A + B)^2}; verb: \verb|y ~ (A + B)^2|; url: \url{y ~ (A + B)^2} \item Underscored names-- code: \code{str_length()}; verb: \verb|str_length()|; url: \url{str_length()} \item \$ names-- code: \code{Arthritis$sex}; verb: \verb|Arthritis$sex|; url: \url{Arthritis$sex} \end{itemize} \end{document} --- end code-test.tex -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. & Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ 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.
Re: [R] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)
Hi again and thank you all for the answers i need to add that im a relatively R neewb so i apologize in advance i started R with the --vanilla option and ran gc() this is the output i get: > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 182236 9.8 407500 21.8 35 18.7 Vcells 277896 2.2 786432 6.0 785897 6.0 also this is the memory.profile() > memory.profile() NULL symbolpairlist closure environment promise 15611 866952277 3144175 language special builtinchar logical integer 21636 44 63763614574 11089 double complex character ... anylist 782 1 20934 0 08023 expressionbytecode externalptr weakref raw S4 162711272 364 365 831 > im running on linux (arch linux) and 'free' shows this: zeltak@zuni ~ â³ free -h total used free sharedbuffers cached Mem: 251G99G 152G66G 249M84G -/+ buffers/cache:14G 237G Swap: 0B 0B 0B im not running any parrallel stuff at all milan: how does one know if the memory is fragmented? thank you all again i really appreciate the help best Z On Thu, Jan 2, 2014 at 10:35 PM, Ben Bolker wrote: > Xebar Saram gmail.com> writes: > > > > > Hi All, > > > > I have a terrible issue i cant seem to debug which is halting my work > > completely. I have R 3.02 installed on a linux machine (arch > linux-latest) > > which I built specifically for running high memory use models. the system > > is a 16 core, 256 GB RAM machine. it worked well at the start but in the > > recent days i keep getting errors and crashes regarding memory use, such > as > > "cannot create vector size of XXX, not enough memory" etc > > > > when looking at top (linux system monitor) i see i barley scrape the 60 > GB > > of ram (out of 256GB) > > > > i really don't know how to debug this and my whole work is halted due to > > this so any help would be greatly appreciated > > I'm very sympathetic, but it will be almost impossible to debug > this sort of a problem remotely, without a reproducible example. > The only guess that I can make, if you *really* are running *exactly* > the same code as you previously ran successfully, is that you might > have some very large objects hidden away in a saved workspace in a > .RData file that's being loaded automatically ... > > I would check whether gc(), memory.profile(), etc. give sensible results > in a clean R session (R --vanilla). > > Ben Bolker > > __ > 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. > [[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.
Re: [R] Ordering the rows of a data frame
Ah, ok, thank you for explanations! Dmitry On 03/01/2014 20:00, Bert Gunter wrote: You misunderstand = I was not sufficiently clear. What is false is your statement that "you **need** to attach the data file before sorting." You do not. with()/within() can be used to avoid using the fully qualified names without attaching. I did not claim that attaching first would not work, only that it was not **necessary** and is generally unwise. -- Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." H. Gilbert Welch On Fri, Jan 3, 2014 at 9:21 AM, Dmitry Pavlyuk wrote: Bert, why do you think that "attach" is not working in this case? Did you check it before your advice? :) I agree about "generally bad approach", but it is quite convenient for work with one data set. Dmitry On 03/01/2014 18:28, Bert Gunter wrote: Inline Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." H. Gilbert Welch On Fri, Jan 3, 2014 at 7:08 AM, Dmitry Pavlyuk wrote: Hi Sofia! You need to attach the data file before sorting: This is false! -- and generally a bad idea. See ?with Please do not give advice without checking whether it is correct. -- Bert attach(df_final) or just use full qualified names (like df_final$Y_init) Dmitry On 03/01/2014 16:41, Stefano Sofia wrote: Dear R users, I have two files of seasonal rainfall data (more than 10,000 rows each); here the first 8 rows of each file are reported. Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station 2000,1952,12,1,0,0,1953,3,1,0,0,307.20,90,100.0,1510 2000,1953,3,1,0,0,1953,6,1,0,0,153.60,92,100.0,1510 2000,1953,6,1,0,0,1953,9,1,0,0,181.00,92,100.0,1510 2000,1953,9,1,0,0,1953,12,1,0,0,202.40,91,100.0,1510 2000,1953,12,1,0,0,1954,3,1,0,0,153.80,90,100.0,1510 2000,1954,3,1,0,0,1954,6,1,0,0,286.20,92,100.0,1510 2000,1954,6,1,0,0,1954,9,1,0,0,142.80,92,100.0,1510 2000,1954,9,1,0,0,1954,12,1,0,0,186.60,91,100.0,1510 ... Code_Raingouge,Y_init,M_init,D_init,h_init,m_init,Y_fin,M_fin,D_fin,h_fin,m_fin,Rainfall,N_Values,Quality_Level,Code_Station 1056,2004,12,1,0,0,2005,3,1,0,0,93.60,2833,32.8,15 1056,2005,3,1,0,0,2005,6,1,0,0,149.80,4406,49.9,15 1056,2005,6,1,0,0,2005,9,1,0,0,52.80,1440,16.3,15 1056,2005,9,1,0,0,2005,12,1,0,0,191.80,1201,13.7,15 1056,2005,12,1,0,0,2006,3,1,0,0,26.40,336,3.9,15 1056,2006,12,1,0,0,2007,3,1,0,0,59.00,3604,41.7,15 1056,2007,3,1,0,0,2007,6,1,0,0,181.16,4414,50.0,15 1056,2007,6,1,0,0,2007,9,1,0,0,96.00,7337,83.1,15 ... I have to load them as data frames, to merge them and sort them by (Y_init,M_init,D_init,Code_Raingouge). I wrote a short function where I first load the two files as data frames df_1 <- read.csv(file="prec_all_19521201_19821201.csv", sep=",") df_2 <- read.csv(file="prec_all_19821201_20111201.csv", sep=",") then I merge them by df_final <- merge(df_1, df_2, all=TRUE) and finally I try to order df_final through df_final <- df_final[order(Y_init, M_init, D_init, Code_Raingouge), ] but this returns only the first row. I read the manual carefully and I saw some examples, but I have not been able to do this simple task. I spent quite a long time and now I decided to ask the list. Could please somebody help me to show me where the mistake is? Thank you Stefano AVVISO IMPORTANTE: Questo messaggio di posta elettronica può contenere informazioni confidenziali, pertanto è 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 è il destinatario specificato, non leggere, copiare, inoltrare o archiviare questo messaggio. Se si è ricevuto questo messaggio per errore, inoltrarlo al mittente ed eliminarlo completamente dal sistema del proprio computer. Ai sensi dellâEUR^(TM)art. 6 della DGR n. 1394/2008 si segnala che, in caso di necessità ed urgenza, la risposta al presente messaggio di posta elettronica può 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://ww
[R] Permutation test with raster data
Hello!  I am having two variables x and y (whereas y is a set of raster images) and want to quantify the correlation between x and y by calculating the Pearson Correlation Coefficient. In order to ensure how signficant the correlation results are, I am interested in getting the p-value (<0.1) for this two tailed student-t distribution. The problem now is: I have a very small number of observations and therefore would need to make a permutation test, which enables to simulate a high number of observations.  So far I did the Pearsons Correlation and Significance test, but without applying permutaton test. I used following formula for obtaining the p-values:  T = r*(sqrt(n-2))/sqrt(1-r²) p-value = 2 P [ T(n-2) ⥠|t|] r...Pearson correlation coefficient n...degree of freedom  Now I have to redo everything using a permutation test. I thought of implementing 'lmp' function in 'calc' function of raster package. The two variables I wanted to save within two lists. I am interested in getting the p-value for each pixel. Can this work?  I will very much appreaciate your help!                                                Dipl.-Ing. Stefan Mühlbauer, MSc Kaiser Strasse 85/2/15 A - 1070 Wien E-Mail: stefan.mue...@yahoo.de dattel_pa...@yahoo.de [[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.
Re: [R] Permutation test with raster data
See in-line below. cheers, Rolf Turner On 04/01/14 12:48, Stefan Mühlbauer wrote: Hello!  I am having two variables x and y (whereas y is a set of raster images) and want to quantify the correlation between x and y by calculating the Pearson Correlation Coefficient. In order to ensure how signficant the correlation results are, I am interested in getting the p-value (<0.1) for this two tailed student-t distribution. The problem now is: I have a very small number of observations and therefore would need to make a permutation test, which enables to simulate a high number of observations. You are deluding yourself.  So far I did the Pearsons Correlation and Significance test, but without applying permutaton test. I used following formula for obtaining the p-values:  T = r*(sqrt(n-2))/sqrt(1-r²) p-value = 2 P [ T(n-2) ≥ |t|] r...Pearson correlation coefficient n...degree of freedom  Now I have to redo everything using a permutation test. I thought of implementing 'lmp' function in 'calc' function of raster package. The two variables I wanted to save within two lists. I am interested in getting the p-value for each pixel. Can this work?  I will very much appreaciate your help! __ 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] Unstack a dataframe using RCommander
Hi, Looking to see how to unstack a dataframe using RCommander. The dataset I'm using is: http://www.sagepub.com/dsur/study/DSUR%20Data%20Files/Chapter%209/SpiderLong.dat I want to use RCommander to change it to this form: http://www.sagepub.com/dsur/study/DSUR%20Data%20Files/Chapter%209/SpiderWide.dat Possible? In R, I would just load the datafile into spiderLong, then run unstack(spiderLong,Anxiety~Group), but I am trying to find out if I can do the same just using RCommander. D. -- View this message in context: http://r.789695.n4.nabble.com/Unstack-a-dataframe-using-RCommander-tp4683072.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)
It would help to know the sizes of the objects that have in your workspace and also provide the 10 prior lines of your script at the point of the error so that we can see what you are trying to do. The following commands will list out the sizes of the objects: cbind(sapply(ls(), function(x){ object.size(get(x)) })) copy and paste it into the command line when the error occurs. Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it. On Fri, Jan 3, 2014 at 3:40 PM, Xebar Saram wrote: > Hi again and thank you all for the answers > > i need to add that im a relatively R neewb so i apologize in advance > > i started R with the --vanilla option and ran gc() > > this is the output i get: > >> gc() > used (Mb) gc trigger (Mb) max used (Mb) > Ncells 182236 9.8 407500 21.8 35 18.7 > Vcells 277896 2.2 786432 6.0 785897 6.0 > > also this is the memory.profile() > >> memory.profile() >NULL symbolpairlist closure environment promise > 15611 866952277 3144175 >language special builtinchar logical integer > 21636 44 63763614574 11089 > double complex character ... anylist > 782 1 20934 0 08023 > expressionbytecode externalptr weakref raw S4 > 162711272 364 365 831 >> > > im running on linux (arch linux) and 'free' shows this: > > > zeltak@zuni ~ ↳ free -h > total used free sharedbuffers cached > Mem: 251G99G 152G66G 249M84G > -/+ buffers/cache:14G 237G > Swap: 0B 0B 0B > > im not running any parrallel stuff at all > > milan: how does one know if the memory is fragmented? > > thank you all again i really appreciate the help > > best > > Z > > > > On Thu, Jan 2, 2014 at 10:35 PM, Ben Bolker wrote: > >> Xebar Saram gmail.com> writes: >> >> > >> > Hi All, >> > >> > I have a terrible issue i cant seem to debug which is halting my work >> > completely. I have R 3.02 installed on a linux machine (arch >> linux-latest) >> > which I built specifically for running high memory use models. the system >> > is a 16 core, 256 GB RAM machine. it worked well at the start but in the >> > recent days i keep getting errors and crashes regarding memory use, such >> as >> > "cannot create vector size of XXX, not enough memory" etc >> > >> > when looking at top (linux system monitor) i see i barley scrape the 60 >> GB >> > of ram (out of 256GB) >> > >> > i really don't know how to debug this and my whole work is halted due to >> > this so any help would be greatly appreciated >> >> I'm very sympathetic, but it will be almost impossible to debug >> this sort of a problem remotely, without a reproducible example. >> The only guess that I can make, if you *really* are running *exactly* >> the same code as you previously ran successfully, is that you might >> have some very large objects hidden away in a saved workspace in a >> .RData file that's being loaded automatically ... >> >> I would check whether gc(), memory.profile(), etc. give sensible results >> in a clean R session (R --vanilla). >> >> Ben Bolker >> >> __ >> 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. >> > > [[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-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] Parse character strings so they "align" (line up/match) properly
Dear listserv, I don't know if this question is more appropriate for the Bioconductor listserv or the general R listserv. I am asking it here because I believe this problem can be solved using regular R commands in the base package. I suspect you all will be very helpful. I have genetic sequence data in the following form. Each letter represents a nucleotide. ref.sequence <- "ATAGCCGCA" sequence1 <- "AT[G][C][C]AGCCG[T]CA" sequence2 <- "ATAGCCGC[C][A][C]A" sequence3 <- "AT[GCC]AGCCGCA" The brackets indicate nucleotide "insertions" relative to the reference sequence ("ref.sequence"). Some sequences may have some/all of the insertions, some may not. What I want is for all of the positions to "align" (line up) properly. Therefore, the sequences lacking a particular insertion should get scored with a dash (or dashes) at that position. I want to end up with this: ref.sequence should look like this: "AT---AGCCG-C---A" sequence1 should look like this: "AT[G][C][C]AGCCG[T]C---A" sequence2 should look like this: "AT---AGCCG-C[C][A][C]A" sequence3 should look like this: "AT[G][C][C]AGCCG-C---A" So how can I make this happen efficiently? Thanks very much in advance, --- Josh Banta, Ph.D Assistant Professor Department of Biology The University of Texas at Tyler Tyler, TX 75799 Tel: (903) 565-5655 http://plantevolutionaryecology.org [[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] p value of trends for odds ratios (or hazard ratios)
Dear Sir Many papers calculated the p value of trends for odds ratios of ordered category variables. I have found the tabodds command in Stata. But how to do it in R? Thanks *Yao Zhu* *Department of UrologyFudan University Shanghai Cancer CenterShanghai, China* [[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] [R-pkgs] caret version 6.0-21
The caret package (short for Classification And REgression Training) attempts to streamline the process for creating predictive models. The package contains tools for: - data splitting - pre-processing - feature selection - model tuning using resampling (with parallel processing) - variable importance estimation as well as other functionality. The package website has lengthy descriptions of functionality: http://caret.r-forge.r-project.org/ A new version, 6.0-21, was just released to CRAN and contains major improvements: - A new system for user-defined models has been added. See http://caret.r-forge.r-project.org/custom_models.html. - When creating the grid of tuning parameter values, the column names no longer need to be preceded by a period. Periods can still be used as before but are not required. - trainControl now has a 'method = "none"' resampling option that bypasses model tuning and fits the model to the entire training set. - Several new models were added, bringing the total number of models up to 149. - ggplot methods were added for several classes. Most changes are not user-visible so that the impact on current scripts should be minimal. For this caret update, the AppliedPredictiveModeling package will be brought up to date shortly with slightly modified scripts for the analyses contained in the text. Thanks to the R community and caret contributors: Jed Wing, Steve Weston, Andre Williams, Chris Keefer, Allan Engelhardt, Tony Cooper, Zachary Mayer and the R Core Team. Please contact me (max.k...@pfizer.com) with any comments, suggestions, questions or ideas for a good wedding toasts. Max ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ 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.