Thanks so much for having a look! I'll get working from there and try to see at what point the problems start occurring! Hopefully I can find the solution! Elodie
Elodie Camprasse 6/187 Auburn Road Hawthorn, VIC 3122 Australia Email: [email protected] Website: http://hors-des-sentiers-battus.e-monsite.com/ Mobile: (+61) 049 794 0793 -----Original Message----- From: AniMov [mailto:[email protected]] On Behalf Of [email protected] Sent: Tuesday, 8 July 2014 9:06 PM To: [email protected] Subject: AniMov Digest, Vol 101, Issue 5 Send AniMov mailing list submissions to [email protected] 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 [email protected] You can reach the person managing the list at [email protected] 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 (Morellet Nicolas) ---------------------------------------------------------------------- Message: 1 Date: Tue, 08 Jul 2014 13:05:31 +0200 From: Morellet Nicolas <[email protected]> To: [email protected] Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 2 Message-ID: <[email protected]> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" Hi, I have absolutely no problem with your short data frame. I wonder if you really need all these steps but I have no error. head(everybody) *********** List of class ltraj *********** Type of the traject: Type II (time recorded) Irregular traject. Variable time lag between two locs Characteristics of the bursts: id burst nb.reloc NAs date.begin date.end 1 A A 18 0 2013-10-15 05:09:35 2013-10-15 05:45:27 2 B B 18 0 2013-10-15 18:05:35 2013-10-15 18:49:31 3 C C 15 0 2013-11-19 18:11:01 2013-11-19 18:54:26 infolocs provided. The following variables are available: [1] "pkey" To check the repetition on the same date you can use: table(table(timestamp)>1) Cheers, Nicolas. Le 08/07/2014 12:23, Elodie Camprasse a ?crit : > Nicolas, > I have checked the latitude and longitude, they are not factors but numeric. > > I have made a sample of the data for you to look at if you have time. > It includes 3 individuals (A, B, C). Hopefully you can help me > understand what the problem is, because I have been at it for almost a > day and I still feel like I am not any closer to finding a solution!! > Thanks so much for your help! It's much appreciated! > Elodie > > > Elodie Camprasse > 6/187 Auburn Road > Hawthorn, VIC 3122 > Australia > > Email: [email protected] > Website: http://hors-des-sentiers-battus.e-monsite.com/ > Mobile: (+61) 049 794 0793 > > -----Original Message----- > From: AniMov [mailto:[email protected]] On Behalf Of > [email protected] > Sent: Tuesday, 8 July 2014 8:00 PM > To: [email protected] > Subject: AniMov Digest, Vol 101, Issue 2 > > Send AniMov mailing list submissions to > [email protected] > > 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 > [email protected] > > You can reach the person managing the list at > [email protected] > > 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" <[email protected]> > To: <[email protected]> > Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 1 > Message-ID: <[email protected]> > 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:[email protected] > Website:?http://hors-des-sentiers-battus.e-monsite.com/ > Mobile:?(+61) 049 794 0793? > > -----Original Message----- > From: AniMov [mailto:[email protected]] On Behalf Of > [email protected] > Sent: Tuesday, 8 July 2014 7:07 PM > To: [email protected] > Subject: AniMov Digest, Vol 101, Issue 1 > > Send AniMov mailing list submissions to > [email protected] > > 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 > [email protected] > > You can reach the person managing the list at > [email protected] > > 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" <[email protected]> > To: <[email protected]> > Subject: [AniMov] Cannot create ltraj object > Message-ID: <[email protected]> > 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$latitude) > [1] 14444. > > > > Thanks in advance for pointing me in the right direction! > Elodie > > > > Elodie Camprasse > > 6/187 Auburn Road > > Hawthorn, VIC 3122 > > Australia > > > > Email: <mailto:[email protected]> [email protected] > > Website: <http://hors-des-sentiers-battus.e-monsite.com/> > http://hors-des-sentiers-battus.e-monsite.com/ > > Mobile: <tel:%28%2B61%29%20049%20794%200793> (+61) 049 794 0793 > > > > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://lists.faunalia.it/pipermail/animov/attachments/20140708/180cd7 > 2f/att > achment-0001.html> > > ------------------------------ > > Message: 2 > Date: Tue, 08 Jul 2014 11:06:54 +0200 > From: Morellet Nicolas <[email protected]> > To: [email protected] > Subject: Re: [AniMov] Cannot create ltraj object > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hello Elodie, > > Could you try ? > data_used = droplevels(data_used) > Maybe some individuals are present in the id variable (if this is a > factor > variable) but with missing component(s). > > Cheers, > Nicolas. > > > Le 08/07/2014 10:21, Elodie Camprasse a ?crit : >> Folks, >> >> I have been encountering a problem when using the adehabitatLT >> package and specifically the function as.ltraj and I was hoping >> someone could give me a clue on how to solve the problem! >> >> I am working with GPS data. I have got 20 different files with tracks >> that > I have merged together; it looks like I have successfully created a > POSIXct column that I added to the dataframe and I have one column > with latitude and one with longitude, as well as an ID column that has > the ID of my individual birds; however, when I use the as.ltraj function, I get the following error: > "Error in as.ltraj(xy = data_used[, c("latitude", "longitude")], date > = data_used$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: [email protected] <mailto:[email protected]> >> >> Website: http://hors-des-sentiers-battus.e-monsite.com/ >> >> Mobile: (+61) 049 794 0793 <tel:%28%2B61%29%20049%20794%200793> >> >> >> >> _______________________________________________ >> AniMov mailing list >> [email protected] >> http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov > > > > _______________________________________________ > AniMov mailing list > [email protected] > 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/e0797fa4/att achment.html> ------------------------------ Subject: Digest Footer _______________________________________________ AniMov mailing list [email protected] http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov ------------------------------ End of AniMov Digest, Vol 101, Issue 5 ************************************** _______________________________________________ AniMov mailing list [email protected] http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
