Thanks Nicolas for the info! Elodie Camprasse 6/187 Auburn Road Hawthorn, VIC 3122 Australia
Email: elodie.campra...@gmail.com Website: http://hors-des-sentiers-battus.e-monsite.com/ Mobile: (+61) 049 794 0793 -----Original Message----- From: AniMov [mailto:animov-boun...@faunalia.it] On Behalf Of animov-requ...@faunalia.it Sent: Tuesday, 8 July 2014 9:46 PM To: animov@faunalia.it Subject: AniMov Digest, Vol 101, Issue 8 Send AniMov mailing list submissions to animov@faunalia.it To subscribe or unsubscribe via the World Wide Web, visit http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov or, via email, send a message with subject or body 'help' to animov-requ...@faunalia.it You can reach the person managing the list at animov-ow...@faunalia.it When replying, please edit your Subject line so it is more specific than "Re: Contents of AniMov digest..." Today's Topics: 1. Re: AniMov Digest, Vol 101, Issue 4 (Morellet Nicolas) 2. Re: AniMov Digest, Vol 101, Issue 7 (stefano anile) ---------------------------------------------------------------------- Message: 1 Date: Tue, 08 Jul 2014 13:34:21 +0200 From: Morellet Nicolas <nicolas.morel...@toulouse.inra.fr> To: Animal Movement <animov@faunalia.it> Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 4 Message-ID: <53bbd73d.9020...@toulouse.inra.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed You can add arbitray one second for example, but it could also be an erroneous location. For GPS data, it is not possible for example. See you, Nicolas. Le 08/07/2014 13:31, Elodie Camprasse a ?crit : > Stef, Nicolas, > Thanks for your help! I think I found the problem: when I was running the > code I posted, I still add the " dataset_multiple_trips_LB.csv" in the > working directory so the filelist and rbind functions were probably taking > it into account and messing up with the rest of the code. Because by > removing the previous versions of this file I got it to work now. Just out > of curiosity though, what should you do if you happen to have dates/times > that are exactly the same between individuals, and you do not want to remove > those points? > Elodie > > Elodie Camprasse > 6/187 Auburn Road > Hawthorn, VIC 3122 > Australia > > Email: elodie.campra...@gmail.com > Website: http://hors-des-sentiers-battus.e-monsite.com/ > Mobile: (+61) 049 794 0793 > > -----Original Message----- > From: AniMov [mailto:animov-boun...@faunalia.it] On Behalf Of > animov-requ...@faunalia.it > Sent: Tuesday, 8 July 2014 8:26 PM > To: animov@faunalia.it > Subject: AniMov Digest, Vol 101, Issue 4 > > Send AniMov mailing list submissions to > animov@faunalia.it > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov > or, via email, send a message with subject or body 'help' to > animov-requ...@faunalia.it > > You can reach the person managing the list at > animov-ow...@faunalia.it > > When replying, please edit your Subject line so it is more specific than > "Re: Contents of AniMov digest..." > > > Today's Topics: > > 1. Re: AniMov Digest, Vol 101, Issue 2 (stefano anile) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 8 Jul 2014 11:26:03 +0100 > From: stefano anile <stefanoan...@yahoo.it> > To: "animov@faunalia.it" <animov@faunalia.it> > Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 2 > Message-ID: > <1404815163.60370.yahoomail...@web171506.mail.ir2.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Elodie,? > about the date issue, this happened to me when there were more than one fix > with the same exactly date.? > Hope it can help. > Stef > > > Il Marted? 8 Luglio 2014 12:00, "animov-requ...@faunalia.it" > <animov-requ...@faunalia.it> ha scritto: > > > > Send AniMov mailing list submissions to > ??? animov@faunalia.it > > To subscribe or unsubscribe via the World Wide Web, visit ??? > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov > or, via email, send a message with subject or body 'help' to ??? > animov-requ...@faunalia.it > > You can reach the person managing the list at ??? animov-ow...@faunalia.it > > When replying, please edit your Subject line so it is more specific than > "Re: Contents of AniMov digest..." > > > Today's Topics: > > ? 1. Re: AniMov Digest, Vol 101, Issue 1 (Elodie Camprasse) ? 2. Re: > AniMov Digest, Vol 101, Issue 1 (Morellet Nicolas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 8 Jul 2014 19:31:42 +1000 > From: "Elodie Camprasse" <elodie.campra...@gmail.com> > To: <animov@faunalia.it> > Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 1 > Message-ID: <01b201cf9a8f$6f6eb1c0$4e4c1540$@gmail.com> > Content-Type: text/plain;??? charset="iso-8859-1" > > Nicolas, > Thanks heaps for the quick reply! Turns out, in the meantime I finally > realized that my id column for some reasons contained 21 levels instead of > 20 (I have 20 individuals) (the problem occurred because one of the level > was "id", ie the column name, even though I am not sure how that > happened...). So I fixed this problem and now my id column is alright (with > 20 levels as I wanted); however, now when I run the code again, it comes up > with a new error: " Error in as.ltraj(xy = data[, c("X.Latitude", > "X.Longitude")], date = data$timestamp,? :? non unique dates for a given > burst". > I have looked at the forums and saw that this situation could occur when the > date format was not set right (e.g. %y instead of %y) but I carefully > checked my format and cannot see any mistake there! > > Here is my new code > > #set working directory > setwd("C:/Users/Elodie/Documents/Deakin/Data analysis/GPS data > analysis/Processed LB multiple tracks") > file_list<-list.files(pattern="*.csv", full.names=TRUE) > require(data.table) > dataset = rbindlist(lapply( file_list, fread )) write.csv(dataset, file = > "dataset_multiple_trips_LB.csv", row.names = F) > > data<-read.csv("dataset_multiple_trips_LB.csv", header=T) ## FOR SOME > REASON, I do not understand why R as automoatically put an "X" > in front of some column names (like Date, Time, Latitude, Longitude) but not > in front of all of #them (the column name for id stayed as is...) so I just > used the names as they appeared in my data frame... > timestamp <- as.POSIXct(strptime(as.character(paste(data$X.Date, > data$X.Time)),"%Y/%m/%d %H:%M:%S"), "GMT") data <- data.frame(data, > timestamp = timestamp) everybody<-as.ltraj(xy = > data[,c("X.Latitude","X.Longitude")], date = data$timestamp, id = data$id) > > Perhaps it could help if I included some of the data so you can see how it > looks like: > id??? Index??? X.Date??? X.Time??? X.Latitude??? X.Longitude??? X.Speed > X.Course??? X.Distance??? X.EHPE??? timestamp LB-LP0009-(2)??? 38??? > 2013/10/15??? 05:09:35??? -38.621288 142.933365??? 0??? 348??? 0??? 5072??? > 15/10/2013 5:09 LB-LP0009-(2)??? 39??? 2013/10/15??? 05:11:39??? > -38.618813 142.935715??? 0??? 36??? 342.725368??? 4768??? 15/10/2013 5:11 > LB-LP0009-(2)??? 40??? 2013/10/15??? 05:13:49??? -38.619331 142.9366??? > 7344??? 243??? 96.122993??? 4768??? 15/10/2013 5:13 > > Thanks for letting me know if you can think of a way to fix this! > > P-S: Fyi, when I apply the drop_level on the code as it was before I fixed > the number of levels, I got this: > warnings() > Warning messages: > 1: In Ops.factor(x1$x, x2$x) : - not meaningful for factors > 2: In Ops.factor(x1$y, x2$y) : - not meaningful for factors > 3: In Ops.factor(x$x, x$x[1]) : - not meaningful for factors > 4: In Ops.factor(x$y, x$y[1]) : - not meaningful for factors > 5: In Ops.factor(x1$x, x2$x) : - not meaningful for factors > 6: In Ops.factor(x1$y, x2$y) : - not meaningful for factors...... There were > 50 or more warnings. > > Elodie Camprasse > 6/187 Auburn Road > Hawthorn, VIC 3122 > Australia > > Email:?elodie.campra...@gmail.com > Website:?http://hors-des-sentiers-battus.e-monsite.com/ > Mobile:?(+61) 049 794 0793? > > -----Original Message----- > From: AniMov [mailto:animov-boun...@faunalia.it] On Behalf Of > animov-requ...@faunalia.it > Sent: Tuesday, 8 July 2014 7:07 PM > To: animov@faunalia.it > Subject: AniMov Digest, Vol 101, Issue 1 > > Send AniMov mailing list submissions to > ??? animov@faunalia.it > > To subscribe or unsubscribe via the World Wide Web, visit ??? > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov > or, via email, send a message with subject or body 'help' to ??? > animov-requ...@faunalia.it > > You can reach the person managing the list at ??? animov-ow...@faunalia.it > > When replying, please edit your Subject line so it is more specific than > "Re: Contents of AniMov digest..." > > > Today's Topics: > > ? 1. Cannot create ltraj object (Elodie Camprasse) ? 2. Re: Cannot create > ltraj object (Morellet Nicolas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 8 Jul 2014 18:21:40 +1000 > From: "Elodie Camprasse" <elodie.campra...@gmail.com> > To: <animov@faunalia.it> > Subject: [AniMov] Cannot create ltraj object > Message-ID: <019c01cf9a85$a6f314b0$f4d93e10$@gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Folks, > > I have been encountering a problem when using the adehabitatLT package and > specifically the function as.ltraj and I was hoping someone could give me a > clue on how to solve the problem! > > I am working with GPS data. I have got 20 different files with tracks that I > have merged together; it looks like I have successfully created a POSIXct > column that I added to the dataframe and I have one column with latitude and > one with longitude, as well as an ID column that has the ID of my individual > birds; however, when I use the as.ltraj function, I get the following error: > "Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date = > data_used$timestamp,? : > > ? some id's are not present in the data" > > I tried different things (without naming the columns first and with column > names, with or without "-" in the ID numbers, using just the relevant > columns with no additional information.) and nothing is fixing the problem. > I also do not understand the error message because when I check the length > of the relevant columns, there are the same. > > Here is my code: > > > > setwd("C:/Users/Elodie/Documents/Deakin/Data analysis/GPS data > analysis/Processed LB multiple tracks") > > file_list<-list.files(pattern="*.csv", full.names=TRUE) > > require(data.table) > > #merge all the files in the working directory in one dataframe > > dataset = rbindlist(lapply( file_list, fread )) > > write.csv(dataset, file = "dataset_multiple_trips_LB.csv", row.names = F) > > data<-read.csv("dataset_multiple_trips_LB.csv", header=F) > > data_used<-data[-1,] > > #V3 is the Date column, V4 is the Time column > > timestamp <- as.POSIXct(strptime(as.character(paste(data_used$V3, > data_used$V4)),"%Y/%m/%d %H:%M:%S"), "GMT") > > data_used <- data.frame(data_used, V11 = timestamp) > > colnames(data_used)<-c("id", "index", "date", "time", "latitude", > "longitude", "speed", "course", "distance", "EHPE", "timestamp") > > everybody<-as.ltraj(xy = data_used[,c("latitude","longitude")], date = > data_used$timestamp, id = data_used$id) > > Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date = > data_used$timestamp,? : > ? some id's are not present in the data > > > > If I do the following code, I get the following results > >> length(data_used$id) > [1] 14444 >> length(data_used$timestamp) > [1] 14444 >> length(data_used$longitude) > [1] 14444 >> length(data_used$latitude) > [1] 14444. > > > > Thanks in advance for pointing me in the right direction! > Elodie > > > > Elodie Camprasse > > 6/187 Auburn Road > > Hawthorn, VIC 3122 > > Australia > > > > Email:? <mailto:elodie.campra...@gmail.com> elodie.campra...@gmail.com > > Website:? <http://hors-des-sentiers-battus.e-monsite.com/> > http://hors-des-sentiers-battus.e-monsite.com/ > > Mobile:? <tel:%28%2B61%29%20049%20794%200793> (+61) 049 794 0793 > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.faunalia.it/pipermail/animov/attachments/20140708/180cd72f/att > achment-0001.html> > > ------------------------------ > > Message: 2 > Date: Tue, 08 Jul 2014 11:06:54 +0200 > From: Morellet Nicolas <nicolas.morel...@toulouse.inra.fr> > To: animov@faunalia.it > Subject: Re: [AniMov] Cannot create ltraj object > Message-ID: <53bbb4ae.9000...@toulouse.inra.fr> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hello Elodie, > > Could you try ? > data_used = droplevels(data_used) > Maybe some individuals are present in the id variable (if this is a factor > variable) but with missing component(s). > > Cheers, > Nicolas. > > > Le 08/07/2014 10:21, Elodie Camprasse a ?crit : >> Folks, >> >> I have been encountering a problem when using the adehabitatLT package >> and specifically the function as.ltraj and I was hoping someone could >> give me a clue on how to solve the problem! >> >> I am working with GPS data. I have got 20 different files with tracks >> that > I have merged together; it looks like I have successfully created a POSIXct > column that I added to the dataframe and I have one column with latitude and > one with longitude, as well as an ID column that has the ID of my individual > birds; however, when I use the as.ltraj function, I get the following error: > "Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date = > data_used$timestamp,? : >> ? some id's are not present in the data" >> >> I tried different things (without naming the columns first and with >> column names, with or without "-" in the ID numbers, using just the >> relevant columns with no additional information...) and nothing is >> fixing the problem. I also do not understand the error message because >> when I check the length of the relevant columns, there are the same. >> >> Here is my code: >> >> setwd("C:/Users/Elodie/Documents/Deakin/Data analysis/GPS data >> analysis/Processed LB multiple tracks") >> >> file_list<-list.files(pattern="*.csv", full.names=TRUE) >> >> require(data.table) >> >> #merge all the files in the working directory in one dataframe >> >> dataset = rbindlist(lapply( file_list, fread )) >> >> write.csv(dataset, file = "dataset_multiple_trips_LB.csv", row.names = >> F) >> >> data<-read.csv("dataset_multiple_trips_LB.csv", header=F) >> >> data_used<-data[-1,] >> >> #V3 is the Date column, V4 is the Time column >> >> timestamp <- as.POSIXct(strptime(as.character(paste(data_used$V3, >> data_used$V4)),"%Y/%m/%d %H:%M:%S"), "GMT") >> >> data_used <- data.frame(data_used, V11 = timestamp) >> >> colnames(data_used)<-c("id", "index", "date", "time", "latitude", >> "longitude", "speed", "course", "distance", "EHPE", "timestamp") >> >> everybody<-as.ltraj(xy = data_used[,c("latitude","longitude")], date = >> data_used$timestamp, id = data_used$id) >> >> Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date = > data_used$timestamp,? : >> ? ? some id's are not present in the data >> >> If I do the following code, I get the following results >> >>> length(data_used$id) >> [1] 14444 >>> length(data_used$timestamp) >> [1] 14444 >>> length(data_used$longitude) >> [1] 14444 >>> length(data_used$latitude) >> [1] 14444. >> >> Thanks in advance for pointing me in the right direction! >> Elodie >> >> Elodie Camprasse >> >> 6/187 Auburn Road >> >> Hawthorn, VIC 3122 >> >> Australia >> >> Email: elodie.campra...@gmail.com <mailto:elodie.campra...@gmail.com> >> >> Website: http://hors-des-sentiers-battus.e-monsite.com/ >> >> Mobile: (+61) 049 794 0793 <tel:%28%2B61%29%20049%20794%200793> >> >> >> >> _______________________________________________ >> AniMov mailing list >> AniMov@faunalia.it >> http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov > -- ********************************************************** Nicolas MORELLET I.N.R.A. - Centre de Recherches de Toulouse Comportement et ?cologie de la Faune Sauvage (C.E.F.S.) BP 52627 - 31326 Castanet-Tolosan cedex (France) Tel : 05.61.28.51.28 Fax : 05.61.28.55.00 ********************************************************** --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com ------------------------------ Message: 2 Date: Tue, 8 Jul 2014 12:45:39 +0100 From: stefano anile <stefanoan...@yahoo.it> To: "animov@faunalia.it" <animov@faunalia.it> Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 7 Message-ID: <1404819939.32496.yahoomail...@web171502.mail.ir2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Hi Elodie,? the issue about time/dates occurs only if there are duplicates (clearly the same identical fix) within the same individual not between individuals. Stef? Il Marted? 8 Luglio 2014 13:31, "animov-requ...@faunalia.it" <animov-requ...@faunalia.it> ha scritto: Send AniMov mailing list submissions to ??? animov@faunalia.it To subscribe or unsubscribe via the World Wide Web, visit ??? http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov or, via email, send a message with subject or body 'help' to ??? animov-requ...@faunalia.it You can reach the person managing the list at ??? animov-ow...@faunalia.it When replying, please edit your Subject line so it is more specific than "Re: Contents of AniMov digest..." Today's Topics: ? 1. Re: AniMov Digest, Vol 101, Issue 4 (Elodie Camprasse) ---------------------------------------------------------------------- Message: 1 Date: Tue, 8 Jul 2014 21:31:04 +1000 From: "Elodie Camprasse" <elodie.campra...@gmail.com> To: <animov@faunalia.it> Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 4 Message-ID: <01ce01cf9aa0$1c47b4e0$54d71ea0$@gmail.com> Content-Type: text/plain;??? charset="iso-8859-1" Stef, Nicolas, Thanks for your help! I think I found the problem: when I was running the code I posted, I still add the " dataset_multiple_trips_LB.csv" in the working directory so the filelist and rbind functions were probably taking it into account and messing up with the rest of the code. Because by removing the previous versions of this file I got it to work now. Just out of curiosity though, what should you do if you happen to have dates/times that are exactly the same between individuals, and you do not want to remove those points? Elodie Elodie Camprasse 6/187 Auburn Road Hawthorn, VIC 3122 Australia Email:?elodie.campra...@gmail.com Website:?http://hors-des-sentiers-battus.e-monsite.com/ Mobile:?(+61) 049 794 0793? -----Original Message----- From: AniMov [mailto:animov-boun...@faunalia.it] On Behalf Of animov-requ...@faunalia.it Sent: Tuesday, 8 July 2014 8:26 PM To: animov@faunalia.it Subject: AniMov Digest, Vol 101, Issue 4 Send AniMov mailing list submissions to ??? animov@faunalia.it To subscribe or unsubscribe via the World Wide Web, visit ??? http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov or, via email, send a message with subject or body 'help' to ??? animov-requ...@faunalia.it You can reach the person managing the list at ??? animov-ow...@faunalia.it When replying, please edit your Subject line so it is more specific than "Re: Contents of AniMov digest..." Today's Topics: ? 1. Re: AniMov Digest, Vol 101, Issue 2 (stefano anile) ---------------------------------------------------------------------- Message: 1 Date: Tue, 8 Jul 2014 11:26:03 +0100 From: stefano anile <stefanoan...@yahoo.it> To: "animov@faunalia.it" <animov@faunalia.it> Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 2 Message-ID: ??? <1404815163.60370.yahoomail...@web171506.mail.ir2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Hi Elodie,? about the date issue, this happened to me when there were more than one fix with the same exactly date.? Hope it can help. Stef Il Marted? 8 Luglio 2014 12:00, "animov-requ...@faunalia.it" <animov-requ...@faunalia.it> ha scritto: Send AniMov mailing list submissions to ??? animov@faunalia.it To subscribe or unsubscribe via the World Wide Web, visit ??? http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov or, via email, send a message with subject or body 'help' to ??? animov-requ...@faunalia.it You can reach the person managing the list at ??? animov-ow...@faunalia.it When replying, please edit your Subject line so it is more specific than "Re: Contents of AniMov digest..." Today's Topics: ?? 1. Re: AniMov Digest, Vol 101, Issue 1 (Elodie Camprasse) ?? 2. Re: AniMov Digest, Vol 101, Issue 1 (Morellet Nicolas) ---------------------------------------------------------------------- Message: 1 Date: Tue, 8 Jul 2014 19:31:42 +1000 From: "Elodie Camprasse" <elodie.campra...@gmail.com> To: <animov@faunalia.it> Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 1 Message-ID: <01b201cf9a8f$6f6eb1c0$4e4c1540$@gmail.com> Content-Type: text/plain;??? charset="iso-8859-1" Nicolas, Thanks heaps for the quick reply! Turns out, in the meantime I finally realized that my id column for some reasons contained 21 levels instead of 20 (I have 20 individuals) (the problem occurred because one of the level was "id", ie the column name, even though I am not sure how that happened...). So I fixed this problem and now my id column is alright (with 20 levels as I wanted); however, now when I run the code again, it comes up with a new error: " Error in as.ltraj(xy = data[, c("X.Latitude", "X.Longitude")], date = data$timestamp,? :?? non unique dates for a given burst". I have looked at the forums and saw that this situation could occur when the date format was not set right (e.g. %y instead of %y) but I carefully checked my format and cannot see any mistake there! Here is my new code #set working directory setwd("C:/Users/Elodie/Documents/Deakin/Data analysis/GPS data analysis/Processed LB multiple tracks") file_list<-list.files(pattern="*.csv", full.names=TRUE) require(data.table) dataset = rbindlist(lapply( file_list, fread )) write.csv(dataset, file = "dataset_multiple_trips_LB.csv", row.names = F) data<-read.csv("dataset_multiple_trips_LB.csv", header=T) ## FOR SOME REASON, I do not understand why R as automoatically put an "X" in front of some column names (like Date, Time, Latitude, Longitude) but not in front of all of #them (the column name for id stayed as is...) so I just used the names as they appeared in my data frame... timestamp <- as.POSIXct(strptime(as.character(paste(data$X.Date, data$X.Time)),"%Y/%m/%d %H:%M:%S"), "GMT") data <- data.frame(data, timestamp = timestamp) everybody<-as.ltraj(xy = data[,c("X.Latitude","X.Longitude")], date = data$timestamp, id = data$id) Perhaps it could help if I included some of the data so you can see how it looks like: id??? Index??? X.Date??? X.Time??? X.Latitude??? X.Longitude??? X.Speed X.Course??? X.Distance??? X.EHPE??? timestamp LB-LP0009-(2)??? 38??? 2013/10/15???? 05:09:35??? -38.621288 142.933365??? 0??? 348??? 0??? 5072??? 15/10/2013 5:09 LB-LP0009-(2)??? 39???? 2013/10/15???? 05:11:39??? -38.618813 142.935715??? 0??? 36??? 342.725368??? 4768??? 15/10/2013 5:11 LB-LP0009-(2)??? 40???? 2013/10/15???? 05:13:49??? -38.619331 142.9366??? 7344??? 243??? 96.122993??? 4768??? 15/10/2013 5:13 Thanks for letting me know if you can think of a way to fix this! P-S: Fyi, when I apply the drop_level on the code as it was before I fixed the number of levels, I got this: warnings() Warning messages: 1: In Ops.factor(x1$x, x2$x) : - not meaningful for factors 2: In Ops.factor(x1$y, x2$y) : - not meaningful for factors 3: In Ops.factor(x$x, x$x[1]) : - not meaningful for factors 4: In Ops.factor(x$y, x$y[1]) : - not meaningful for factors 5: In Ops.factor(x1$x, x2$x) : - not meaningful for factors 6: In Ops.factor(x1$y, x2$y) : - not meaningful for factors...... There were 50 or more warnings. Elodie Camprasse 6/187 Auburn Road Hawthorn, VIC 3122 Australia Email:?elodie.campra...@gmail.com Website:?http://hors-des-sentiers-battus.e-monsite.com/ Mobile:?(+61) 049 794 0793? -----Original Message----- From: AniMov [mailto:animov-boun...@faunalia.it] On Behalf Of animov-requ...@faunalia.it Sent: Tuesday, 8 July 2014 7:07 PM To: animov@faunalia.it Subject: AniMov Digest, Vol 101, Issue 1 Send AniMov mailing list submissions to ??? animov@faunalia.it To subscribe or unsubscribe via the World Wide Web, visit ??? http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov or, via email, send a message with subject or body 'help' to ??? animov-requ...@faunalia.it You can reach the person managing the list at ??? animov-ow...@faunalia.it When replying, please edit your Subject line so it is more specific than "Re: Contents of AniMov digest..." Today's Topics: ?? 1. Cannot create ltraj object (Elodie Camprasse) ?? 2. Re: Cannot create ltraj object (Morellet Nicolas) ---------------------------------------------------------------------- Message: 1 Date: Tue, 8 Jul 2014 18:21:40 +1000 From: "Elodie Camprasse" <elodie.campra...@gmail.com> To: <animov@faunalia.it> Subject: [AniMov] Cannot create ltraj object Message-ID: <019c01cf9a85$a6f314b0$f4d93e10$@gmail.com> Content-Type: text/plain; charset="us-ascii" Folks, I have been encountering a problem when using the adehabitatLT package and specifically the function as.ltraj and I was hoping someone could give me a clue on how to solve the problem! I am working with GPS data. I have got 20 different files with tracks that I have merged together; it looks like I have successfully created a POSIXct column that I added to the dataframe and I have one column with latitude and one with longitude, as well as an ID column that has the ID of my individual birds; however, when I use the as.ltraj function, I get the following error: "Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date = data_used$timestamp,? : ? some id's are not present in the data" I tried different things (without naming the columns first and with column names, with or without "-" in the ID numbers, using just the relevant columns with no additional information.) and nothing is fixing the problem. I also do not understand the error message because when I check the length of the relevant columns, there are the same. Here is my code: setwd("C:/Users/Elodie/Documents/Deakin/Data analysis/GPS data analysis/Processed LB multiple tracks") file_list<-list.files(pattern="*.csv", full.names=TRUE) require(data.table) #merge all the files in the working directory in one dataframe dataset = rbindlist(lapply( file_list, fread )) write.csv(dataset, file = "dataset_multiple_trips_LB.csv", row.names = F) data<-read.csv("dataset_multiple_trips_LB.csv", header=F) data_used<-data[-1,] #V3 is the Date column, V4 is the Time column timestamp <- as.POSIXct(strptime(as.character(paste(data_used$V3, data_used$V4)),"%Y/%m/%d %H:%M:%S"), "GMT") data_used <- data.frame(data_used, V11 = timestamp) colnames(data_used)<-c("id", "index", "date", "time", "latitude", "longitude", "speed", "course", "distance", "EHPE", "timestamp") everybody<-as.ltraj(xy = data_used[,c("latitude","longitude")], date = data_used$timestamp, id = data_used$id) Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date = data_used$timestamp,? : ? some id's are not present in the data If I do the following code, I get the following results > length(data_used$id) [1] 14444 > length(data_used$timestamp) [1] 14444 > length(data_used$longitude) [1] 14444 > length(data_used$latitude) [1] 14444. Thanks in advance for pointing me in the right direction! Elodie Elodie Camprasse 6/187 Auburn Road Hawthorn, VIC 3122 Australia Email:? <mailto:elodie.campra...@gmail.com> elodie.campra...@gmail.com Website:? <http://hors-des-sentiers-battus.e-monsite.com/> http://hors-des-sentiers-battus.e-monsite.com/ Mobile:? <tel:%28%2B61%29%20049%20794%200793> (+61) 049 794 0793 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.faunalia.it/pipermail/animov/attachments/20140708/180cd72f/att achment-0001.html> ------------------------------ Message: 2 Date: Tue, 08 Jul 2014 11:06:54 +0200 From: Morellet Nicolas <nicolas.morel...@toulouse.inra.fr> To: animov@faunalia.it Subject: Re: [AniMov] Cannot create ltraj object Message-ID: <53bbb4ae.9000...@toulouse.inra.fr> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" Hello Elodie, Could you try ? data_used = droplevels(data_used) Maybe some individuals are present in the id variable (if this is a factor variable) but with missing component(s). Cheers, Nicolas. Le 08/07/2014 10:21, Elodie Camprasse a ?crit : > > Folks, > > I have been encountering a problem when using the adehabitatLT package > and specifically the function as.ltraj and I was hoping someone could > give me a clue on how to solve the problem! > > I am working with GPS data. I have got 20 different files with tracks > that I have merged together; it looks like I have successfully created a POSIXct column that I added to the dataframe and I have one column with latitude and one with longitude, as well as an ID column that has the ID of my individual birds; however, when I use the as.ltraj function, I get the following error: "Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date = data_used$timestamp,? : > >?? some id's are not present in the data" > > I tried different things (without naming the columns first and with > column names, with or without "-" in the ID numbers, using just the > relevant columns with no additional information...) and nothing is > fixing the problem. I also do not understand the error message because > when I check the length of the relevant columns, there are the same. > > Here is my code: > > setwd("C:/Users/Elodie/Documents/Deakin/Data analysis/GPS data > analysis/Processed LB multiple tracks") > > file_list<-list.files(pattern="*.csv", full.names=TRUE) > > require(data.table) > > #merge all the files in the working directory in one dataframe > > dataset = rbindlist(lapply( file_list, fread )) > > write.csv(dataset, file = "dataset_multiple_trips_LB.csv", row.names = > F) > > data<-read.csv("dataset_multiple_trips_LB.csv", header=F) > > data_used<-data[-1,] > > #V3 is the Date column, V4 is the Time column > > timestamp <- as.POSIXct(strptime(as.character(paste(data_used$V3, > data_used$V4)),"%Y/%m/%d %H:%M:%S"), "GMT") > > data_used <- data.frame(data_used, V11 = timestamp) > > colnames(data_used)<-c("id", "index", "date", "time", "latitude", > "longitude", "speed", "course", "distance", "EHPE", "timestamp") > > everybody<-as.ltraj(xy = data_used[,c("latitude","longitude")], date = > data_used$timestamp, id = data_used$id) > > Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date = data_used$timestamp,? : >? ? some id's are not present in the data > > If I do the following code, I get the following results > > >length(data_used$id) > [1] 14444 > >length(data_used$timestamp) > [1] 14444 > >length(data_used$longitude) > [1] 14444 > >length(data_used$latitude) > [1] 14444. > > Thanks in advance for pointing me in the right direction! > Elodie > > Elodie Camprasse > > 6/187 Auburn Road > > Hawthorn, VIC 3122 > > Australia > > Email: elodie.campra...@gmail.com <mailto:elodie.campra...@gmail.com> > > Website: http://hors-des-sentiers-battus.e-monsite.com/ > > Mobile: (+61) 049 794 0793 <tel:%28%2B61%29%20049%20794%200793> > > > > _______________________________________________ > AniMov mailing list > AniMov@faunalia.it > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov -- ********************************************************** ? ? ? ? ? ? ? ? ? ? Nicolas MORELLET I.N.R.A. - Centre de Recherches de Toulouse Comportement et ?cologie de la Faune Sauvage (C.E.F.S.) BP 52627 - 31326 Castanet-Tolosan cedex (France) ? ? ? ? ? ? ?? Tel :? 05.61.28.51.28 ? ? ? ? ? ? ?? Fax :? 05.61.28.55.00 ********************************************************** --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.faunalia.it/pipermail/animov/attachments/20140708/23f6544d/att achment.html> ------------------------------ Subject: Digest Footer _______________________________________________ AniMov mailing list AniMov@faunalia.it http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov ------------------------------ End of AniMov Digest, Vol 101, Issue 1 ************************************** ------------------------------ Message: 2 Date: Tue, 08 Jul 2014 11:43:59 +0200 From: Morellet Nicolas <nicolas.morel...@toulouse.inra.fr> To: Animal Movement <animov@faunalia.it> Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 1 Message-ID: <53bbbd5f.3000...@toulouse.inra.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Elodie, I guess you have not very "clean data". I suspect that the type of your variables is not well defined. You should use str(data) to see the type of your data. In particular, latitudes and longitude should not be factor variables. In general R add some X and Y for columns with repeated names, but I wonder what happen here. Maybe if you need more help, you could send a short part of your file to the list or directly to me. I could have a look with the code and the file. It is up to you. Cheers, Nicolas Le 08/07/2014 11:31, Elodie Camprasse a ?crit : > Nicolas, > Thanks heaps for the quick reply! Turns out, in the meantime I finally > realized that my id column for some reasons contained 21 levels > instead of > 20 (I have 20 individuals) (the problem occurred because one of the > level was "id", ie the column name, even though I am not sure how that > happened...). So I fixed this problem and now my id column is alright > (with > 20 levels as I wanted); however, now when I run the code again, it > comes up with a new error: " Error in as.ltraj(xy = data[, > c("X.Latitude", "X.Longitude")], date = data$timestamp,? :?? non > unique dates for a given burst". > I have looked at the forums and saw that this situation could occur > when the date format was not set right (e.g. %y instead of %y) but I > carefully checked my format and cannot see any mistake there! > > Here is my new code > > #set working directory > setwd("C:/Users/Elodie/Documents/Deakin/Data analysis/GPS data > analysis/Processed LB multiple tracks") > file_list<-list.files(pattern="*.csv", full.names=TRUE) > require(data.table) > dataset = rbindlist(lapply( file_list, fread )) write.csv(dataset, > file = "dataset_multiple_trips_LB.csv", row.names = F) > > data<-read.csv("dataset_multiple_trips_LB.csv", header=T) ## FOR SOME > REASON, I do not understand why R as automoatically put an "X" > in front of some column names (like Date, Time, Latitude, Longitude) > but not in front of all of #them (the column name for id stayed as > is...) so I just used the names as they appeared in my data frame... > timestamp <- as.POSIXct(strptime(as.character(paste(data$X.Date, > data$X.Time)),"%Y/%m/%d %H:%M:%S"), "GMT") data <- data.frame(data, > timestamp = timestamp) everybody<-as.ltraj(xy = > data[,c("X.Latitude","X.Longitude")], date = data$timestamp, id = > data$id) > > Perhaps it could help if I included some of the data so you can see > how it looks like: > id??? Index??? X.Date??? X.Time??? X.Latitude??? X.Longitude??? > X.Speed X.Course??? X.Distance??? X.EHPE??? timestamp LB-LP0009-(2)??? > 38???? 2013/10/15???? 05:09:35??? -38.621288 142.933365??? 0??? 348??? > 0??? 5072??? 15/10/2013 5:09 LB-LP0009-(2)??? 39???? 2013/10/15???? > 05:11:39??? -38.618813 142.935715??? 0??? 36??? 342.725368??? 4768??? > 15/10/2013 5:11 LB-LP0009-(2)??? 40???? 2013/10/15???? 05:13:49??? > -38.619331 142.9366??? 7344??? 243??? 96.122993??? 4768??? 15/10/2013 > 5:13 > > Thanks for letting me know if you can think of a way to fix this! > > P-S: Fyi, when I apply the drop_level on the code as it was before I > fixed the number of levels, I got this: > warnings() > Warning messages: > 1: In Ops.factor(x1$x, x2$x) : - not meaningful for factors > 2: In Ops.factor(x1$y, x2$y) : - not meaningful for factors > 3: In Ops.factor(x$x, x$x[1]) : - not meaningful for factors > 4: In Ops.factor(x$y, x$y[1]) : - not meaningful for factors > 5: In Ops.factor(x1$x, x2$x) : - not meaningful for factors > 6: In Ops.factor(x1$y, x2$y) : - not meaningful for factors...... > There were > 50 or more warnings. > > Elodie Camprasse > 6/187 Auburn Road > Hawthorn, VIC 3122 > Australia > > Email: elodie.campra...@gmail.com > Website: http://hors-des-sentiers-battus.e-monsite.com/ > Mobile: (+61) 049 794 0793 > > -----Original Message----- > From: AniMov [mailto:animov-boun...@faunalia.it] On Behalf Of > animov-requ...@faunalia.it > Sent: Tuesday, 8 July 2014 7:07 PM > To: animov@faunalia.it > Subject: AniMov Digest, Vol 101, Issue 1 > > Send AniMov mailing list submissions to ??? animov@faunalia.it > > To subscribe or unsubscribe via the World Wide Web, visit ??? > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov > or, via email, send a message with subject or body 'help' to ??? > animov-requ...@faunalia.it > > You can reach the person managing the list at ??? > animov-ow...@faunalia.it > > When replying, please edit your Subject line so it is more specific > than > "Re: Contents of AniMov digest..." > > > Today's Topics: > >? ?? 1. Cannot create ltraj object (Elodie Camprasse) ? ?? 2. Re: >Cannot create ltraj object (Morellet Nicolas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 8 Jul 2014 18:21:40 +1000 > From: "Elodie Camprasse" <elodie.campra...@gmail.com> > To: <animov@faunalia.it> > Subject: [AniMov] Cannot create ltraj object > Message-ID: <019c01cf9a85$a6f314b0$f4d93e10$@gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Folks, > > I have been encountering a problem when using the adehabitatLT package > and specifically the function as.ltraj and I was hoping someone could > give me a clue on how to solve the problem! > > I am working with GPS data. I have got 20 different files with tracks > that I have merged together; it looks like I have successfully created > a POSIXct column that I added to the dataframe and I have one column > with latitude and one with longitude, as well as an ID column that has > the ID of my individual birds; however, when I use the as.ltraj function, I get the following error: > "Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date > = data_used$timestamp,? : > >? ? some id's are not present in the data" > > I tried different things (without naming the columns first and with > column names, with or without "-" in the ID numbers, using just the > relevant columns with no additional information.) and nothing is fixing the problem. > I also do not understand the error message because when I check the > length of the relevant columns, there are the same. > > Here is my code: > >? > > setwd("C:/Users/Elodie/Documents/Deakin/Data analysis/GPS data > analysis/Processed LB multiple tracks") > > file_list<-list.files(pattern="*.csv", full.names=TRUE) > > require(data.table) > > #merge all the files in the working directory in one dataframe > > dataset = rbindlist(lapply( file_list, fread )) > > write.csv(dataset, file = "dataset_multiple_trips_LB.csv", row.names = > F) > > data<-read.csv("dataset_multiple_trips_LB.csv", header=F) > > data_used<-data[-1,] > > #V3 is the Date column, V4 is the Time column > > timestamp <- as.POSIXct(strptime(as.character(paste(data_used$V3, > data_used$V4)),"%Y/%m/%d %H:%M:%S"), "GMT") > > data_used <- data.frame(data_used, V11 = timestamp) > > colnames(data_used)<-c("id", "index", "date", "time", "latitude", > "longitude", "speed", "course", "distance", "EHPE", "timestamp") > > everybody<-as.ltraj(xy = data_used[,c("latitude","longitude")], date = > data_used$timestamp, id = data_used$id) > > Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date =? >data_used$timestamp,? : >? ? some id's are not present in the data > >? > > If I do the following code, I get the following results > >> length(data_used$id) > [1] 14444 >> length(data_used$timestamp) > [1] 14444 >> length(data_used$longitude) > [1] 14444 >> length(data_used$latitude) > [1] 14444. > >? > > Thanks in advance for pointing me in the right direction! > Elodie > >? > > Elodie Camprasse > > 6/187 Auburn Road > > Hawthorn, VIC 3122 > > Australia > >? > > Email:? <mailto:elodie.campra...@gmail.com> elodie.campra...@gmail.com > > Website:? <http://hors-des-sentiers-battus.e-monsite.com/> > http://hors-des-sentiers-battus.e-monsite.com/ > > Mobile:? <tel:%28%2B61%29%20049%20794%200793> (+61) 049 794 0793 > >? > > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://lists.faunalia.it/pipermail/animov/attachments/20140708/180cd7 > 2f/att > achment-0001.html> > > ------------------------------ > > Message: 2 > Date: Tue, 08 Jul 2014 11:06:54 +0200 > From: Morellet Nicolas <nicolas.morel...@toulouse.inra.fr> > To: animov@faunalia.it > Subject: Re: [AniMov] Cannot create ltraj object > Message-ID: <53bbb4ae.9000...@toulouse.inra.fr> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hello Elodie, > > Could you try ? > data_used = droplevels(data_used) > Maybe some individuals are present in the id variable (if this is a > factor > variable) but with missing component(s). > > Cheers, > Nicolas. > > > Le 08/07/2014 10:21, Elodie Camprasse a ?crit : >> Folks, >> >> I have been encountering a problem when using the adehabitatLT >> package and specifically the function as.ltraj and I was hoping >> someone could give me a clue on how to solve the problem! >> >> I am working with GPS data. I have got 20 different files with tracks >> that > I have merged together; it looks like I have successfully created a > POSIXct column that I added to the dataframe and I have one column > with latitude and one with longitude, as well as an ID column that has > the ID of my individual birds; however, when I use the as.ltraj function, I get the following error: > "Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date > = data_used$timestamp,? : >>? ? some id's are not present in the data" >> >> I tried different things (without naming the columns first and with >> column names, with or without "-" in the ID numbers, using just the >> relevant columns with no additional information...) and nothing is >> fixing the problem. I also do not understand the error message >> because when I check the length of the relevant columns, there are the same. >> >> Here is my code: >> >> setwd("C:/Users/Elodie/Documents/Deakin/Data analysis/GPS data >> analysis/Processed LB multiple tracks") >> >> file_list<-list.files(pattern="*.csv", full.names=TRUE) >> >> require(data.table) >> >> #merge all the files in the working directory in one dataframe >> >> dataset = rbindlist(lapply( file_list, fread )) >> >> write.csv(dataset, file = "dataset_multiple_trips_LB.csv", row.names >> = >> F) >> >> data<-read.csv("dataset_multiple_trips_LB.csv", header=F) >> >> data_used<-data[-1,] >> >> #V3 is the Date column, V4 is the Time column >> >> timestamp <- as.POSIXct(strptime(as.character(paste(data_used$V3, >> data_used$V4)),"%Y/%m/%d %H:%M:%S"), "GMT") >> >> data_used <- data.frame(data_used, V11 = timestamp) >> >> colnames(data_used)<-c("id", "index", "date", "time", "latitude", >> "longitude", "speed", "course", "distance", "EHPE", "timestamp") >> >> everybody<-as.ltraj(xy = data_used[,c("latitude","longitude")], date >> = data_used$timestamp, id = data_used$id) >> >> Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date >> = > data_used$timestamp,? : >>? ?? some id's are not present in the data >> >> If I do the following code, I get the following results >> >>> length(data_used$id) >> [1] 14444 >>> length(data_used$timestamp) >> [1] 14444 >>> length(data_used$longitude) >> [1] 14444 >>> length(data_used$latitude) >> [1] 14444. >> >> Thanks in advance for pointing me in the right direction! >> Elodie >> >> Elodie Camprasse >> >> 6/187 Auburn Road >> >> Hawthorn, VIC 3122 >> >> Australia >> >> Email: elodie.campra...@gmail.com <mailto:elodie.campra...@gmail.com> >> >> Website: http://hors-des-sentiers-battus.e-monsite.com/ >> >> Mobile: (+61) 049 794 0793 <tel:%28%2B61%29%20049%20794%200793> >> >> >> >> _______________________________________________ >> AniMov mailing list >> AniMov@faunalia.it >> http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov > -- ********************************************************** ? ? ? ? ? ? ? ? ? ? Nicolas MORELLET I.N.R.A. - Centre de Recherches de Toulouse Comportement et ?cologie de la Faune Sauvage (C.E.F.S.) BP 52627 - 31326 Castanet-Tolosan cedex (France) ? ? ? ? ? ? ?? Tel :? 05.61.28.51.28 ? ? ? ? ? ? ?? Fax :? 05.61.28.55.00 ********************************************************** --- Ce courrier ?lectronique ne contient aucun virus ou logiciel malveillant parce que la protection avast! Antivirus est active. http://www.avast.com ------------------------------ Subject: Digest Footer _______________________________________________ AniMov mailing list AniMov@faunalia.it http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov ------------------------------ End of AniMov Digest, Vol 101, Issue 2 ************************************** -------------- next part -------------- An HTML attachment was scrubbed... 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