[AniMov] AniMov Digest, Vol 101, Issue 8

Elodie Camprasse elodie.camprasse at gmail.com
Thu Jul 10 02:52:53 CEST 2014


Thanks Nicolas for the info!

Elodie Camprasse
6/187 Auburn Road
Hawthorn, VIC 3122
Australia 

Email: elodie.camprasse at gmail.com
Website: http://hors-des-sentiers-battus.e-monsite.com/
Mobile: (+61) 049 794 0793 

-----Original Message-----
From: AniMov [mailto:animov-bounces at faunalia.it] On Behalf Of
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Sent: Tuesday, 8 July 2014 9:46 PM
To: animov at faunalia.it
Subject: AniMov Digest, Vol 101, Issue 8

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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.Morellet at toulouse.inra.fr>
To: Animal Movement <animov at faunalia.it>
Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 4
Message-ID: <53BBD73D.9020203 at 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.camprasse at gmail.com
> Website: http://hors-des-sentiers-battus.e-monsite.com/
> Mobile: (+61) 049 794 0793
>
> -----Original Message-----
> From: AniMov [mailto:animov-bounces at faunalia.it] On Behalf Of
> animov-request at faunalia.it
> Sent: Tuesday, 8 July 2014 8:26 PM
> To: animov at faunalia.it
> Subject: AniMov Digest, Vol 101, Issue 4
>
> Send AniMov mailing list submissions to
> 	animov at faunalia.it
>
> To subscribe or unsubscribe via the World Wide Web, visit
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>
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>
>
> 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 <stefanoanile at yahoo.it>
> To: "animov at faunalia.it" <animov at faunalia.it>
> Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 2
> Message-ID:
> 	<1404815163.60370.YahooMailNeo at 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-request at faunalia.it"
> <animov-request at faunalia.it> ha scritto:
>   
>
>
> Send AniMov mailing list submissions to
> ??? animov at 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-request at faunalia.it
>
> You can reach the person managing the list at ??? animov-owner at 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.camprasse at gmail.com>
> To: <animov at 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$y) : - not meaningful for factors...... There
were
> 50 or more warnings.
>
> Elodie Camprasse
> 6/187 Auburn Road
> Hawthorn, VIC 3122
> Australia
>
> Email:?elodie.camprasse at gmail.com
> Website:?http://hors-des-sentiers-battus.e-monsite.com/
> Mobile:?(+61) 049 794 0793?
>
> -----Original Message-----
> From: AniMov [mailto:animov-bounces at faunalia.it] On Behalf Of
> animov-request at faunalia.it
> Sent: Tuesday, 8 July 2014 7:07 PM
> To: animov at faunalia.it
> Subject: AniMov Digest, Vol 101, Issue 1
>
> Send AniMov mailing list submissions to
> ??? animov at faunalia.it
>
> To subscribe or unsubscribe via the World Wide Web, visit ???
> http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
> or, via email, send a message with subject or body 'help' to ???
> animov-request at faunalia.it
>
> You can reach the person managing the list at ??? animov-owner at faunalia.it
>
> When replying, please edit your Subject line so it is more specific than
> "Re: Contents of AniMov digest..."
>
>
> Today's Topics:
>
> ?  1. Cannot create ltraj object (Elodie Camprasse) ?  2. Re: Cannot
create
> ltraj object (Morellet Nicolas)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 8 Jul 2014 18:21:40 +1000
> From: "Elodie Camprasse" <elodie.camprasse at gmail.com>
> To: <animov at faunalia.it>
> Subject: [AniMov] Cannot create ltraj object
> Message-ID: <019c01cf9a85$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.camprasse at gmail.com> elodie.camprasse at 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 --------------
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>
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> achment-0001.html>
>
> ------------------------------
>
> Message: 2
> Date: Tue, 08 Jul 2014 11:06:54 +0200
> From: Morellet Nicolas <Nicolas.Morellet at toulouse.inra.fr>
> To: animov at faunalia.it
> Subject: Re: [AniMov] Cannot create ltraj object
> Message-ID: <53BBB4AE.9000202 at 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.camprasse at gmail.com <mailto:elodie.camprasse at 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 at 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
**********************************************************


---
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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 <stefanoanile at yahoo.it>
To: "animov at faunalia.it" <animov at faunalia.it>
Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 7
Message-ID:
	<1404819939.32496.YahooMailNeo at 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-request at faunalia.it"
<animov-request at faunalia.it> ha scritto:
 


Send AniMov mailing list submissions to
??? animov at 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-request at faunalia.it

You can reach the person managing the list at
??? animov-owner at 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.camprasse at gmail.com>
To: <animov at 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.camprasse at gmail.com
Website:?http://hors-des-sentiers-battus.e-monsite.com/
Mobile:?(+61) 049 794 0793?

-----Original Message-----
From: AniMov [mailto:animov-bounces at faunalia.it] On Behalf Of
animov-request at faunalia.it
Sent: Tuesday, 8 July 2014 8:26 PM
To: animov at faunalia.it
Subject: AniMov Digest, Vol 101, Issue 4

Send AniMov mailing list submissions to
??? animov at 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-request at faunalia.it

You can reach the person managing the list at
??? animov-owner at 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 <stefanoanile at yahoo.it>
To: "animov at faunalia.it" <animov at faunalia.it>
Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 2
Message-ID:
??? <1404815163.60370.YahooMailNeo at 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-request at faunalia.it"
<animov-request at faunalia.it> ha scritto:



Send AniMov mailing list submissions to
??? animov at 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-request at faunalia.it

You can reach the person managing the list at ??? animov-owner at 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.camprasse at gmail.com>
To: <animov at 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.camprasse at gmail.com
Website:?http://hors-des-sentiers-battus.e-monsite.com/
Mobile:?(+61) 049 794 0793?

-----Original Message-----
From: AniMov [mailto:animov-bounces at faunalia.it] On Behalf Of
animov-request at faunalia.it
Sent: Tuesday, 8 July 2014 7:07 PM
To: animov at faunalia.it
Subject: AniMov Digest, Vol 101, Issue 1

Send AniMov mailing list submissions to
??? animov at faunalia.it

To subscribe or unsubscribe via the World Wide Web, visit ???
http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
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You can reach the person managing the list at ??? animov-owner at 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.camprasse at gmail.com>
To: <animov at 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.camprasse at gmail.com> elodie.camprasse at 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 



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Message: 2
Date: Tue, 08 Jul 2014 11:06:54 +0200
From: Morellet Nicolas <Nicolas.Morellet at toulouse.inra.fr>
To: animov at faunalia.it
Subject: Re: [AniMov] Cannot create ltraj object
Message-ID: <53BBB4AE.9000202 at 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.camprasse at gmail.com <mailto:elodie.camprasse at 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 at 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
**********************************************************



---
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------------------------------

Message: 2
Date: Tue, 08 Jul 2014 11:43:59 +0200
From: Morellet Nicolas <Nicolas.Morellet at toulouse.inra.fr>
To: Animal Movement <animov at faunalia.it>
Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 1
Message-ID: <53BBBD5F.3000408 at 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$y) : - not meaningful for factors...... 
> There were
> 50 or more warnings.
>
> Elodie Camprasse
> 6/187 Auburn Road
> Hawthorn, VIC 3122
> Australia
>
> Email: elodie.camprasse at gmail.com
> Website: http://hors-des-sentiers-battus.e-monsite.com/
> Mobile: (+61) 049 794 0793
>
> -----Original Message-----
> From: AniMov [mailto:animov-bounces at faunalia.it] On Behalf Of 
> animov-request at faunalia.it
> Sent: Tuesday, 8 July 2014 7:07 PM
> To: animov at faunalia.it
> Subject: AniMov Digest, Vol 101, Issue 1
>
> Send AniMov mailing list submissions to ??? animov at faunalia.it
>
> To subscribe or unsubscribe via the World Wide Web, visit ??? 
> http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
> or, via email, send a message with subject or body 'help' to ??? 
> animov-request at faunalia.it
>
> You can reach the person managing the list at ??? 
> animov-owner at faunalia.it
>
> When replying, please edit your Subject line so it is more specific 
> than
> "Re: Contents of AniMov digest..."
>
>
> Today's Topics:
>
>? ?? 1. Cannot create ltraj object (Elodie Camprasse) ? ?? 2. Re: 
>Cannot create ltraj object (Morellet Nicolas)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 8 Jul 2014 18:21:40 +1000
> From: "Elodie Camprasse" <elodie.camprasse at gmail.com>
> To: <animov at faunalia.it>
> Subject: [AniMov] Cannot create ltraj object
> Message-ID: <019c01cf9a85$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.camprasse at gmail.com> elodie.camprasse at 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.Morellet at toulouse.inra.fr>
> To: animov at faunalia.it
> Subject: Re: [AniMov] Cannot create ltraj object
> Message-ID: <53BBB4AE.9000202 at 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.camprasse at gmail.com <mailto:elodie.camprasse at gmail.com>
>>
>> Website: http://hors-des-sentiers-battus.e-monsite.com/
>>
>> Mobile: (+61) 049 794 0793 <tel:%28%2B61%29%20049%20794%200793>
>>
>>
>>
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>


-- 


**********************************************************
? ? ? ? ? ? ? ? ? ? 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
**********************************************************


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