[AniMov] AniMov Digest, Vol 101, Issue 5

Elodie Camprasse elodie.camprasse at gmail.com
Tue Jul 8 13:17:19 CEST 2014


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

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Subject: AniMov Digest, Vol 101, Issue 5

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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 <Nicolas.Morellet at toulouse.inra.fr>
To: animov at faunalia.it
Subject: Re: [AniMov] AniMov Digest, Vol 101, Issue 2
Message-ID: <53BBD07B.7000903 at toulouse.inra.fr>
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: 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 8:00 PM
> To: animov at faunalia.it
> Subject: AniMov Digest, Vol 101, Issue 2
>
> 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
>
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>
> 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
>
>   
>
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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
>
>
>
> _______________________________________________
> AniMov mailing list
> AniMov at faunalia.it
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