[AniMov] FPT help

Adam T. Ford atford at gmail.com
Sat Feb 19 20:30:48 CET 2011


Hello Mathieu,

Following up from our previous postings, and with the new LT package
available, I am trying to add the 'infolocs' into the FPT output.
I maxed out the memory, so Im sure I did this wrong. All I was trying to do
is have a casewise listing of the infolocs metadata attached to each row of
the FPT output.
This is what I tried, using infolocs() in the way you used used burst().

i.10m <- fpt(na.10m, seq(5, 50, 5), units = "hours")
exp.10mFPT <- do.call (rbind, i.10m)
na <- unlist(lapply(na.10m, function(i) sum(!is.na(i[, 1]))))
exp.10mFPT$burst <- rep(burst(na.10m), times = na)
exp.10mFPT$info <- rep(infolocs(na.10m), times = na)

Any help is appreciated!

Thanks,

Adam









On Mon, Jan 31, 2011 at 5:12 PM, Mathieu Basille
<basille at ase-research.org>wrote:

> Sorry, there is a mistake in the code: should be 'times' instead of
> 'each' in the rep line:
>
> bla$burst <- rep(burst(puechcirc), times = na)
>
> Mathieu.
>
>
>
> Le 2011-01-31 19:04, Adam T. Ford a écrit :
> > gorgeous code Mathieu, thanks much!
> >
> > On Mon, Jan 31, 2011 at 4:13 PM, Mathieu Basille
> > <basille at ase-research.org <mailto:basille at ase-research.org>> wrote:
> >
> >     The difference comes from the NA (fpt first removes any NAs in the
> >     coordinates).
> >
> >     Something along that line should work:
> >
> >     data(puechcirc)
> >     i <- fpt(puechcirc, seq(300,1000, length=30))
> >     bla <- do.call(rbind, i)
> >
> >     na <- unlist(lapply(puechcirc, function(i) sum(!is.na
> >     <http://is.na>(i[, 1]))))
> >     bla$burst <- rep(burst(puechcirc), each = na)
> >
> >
> >     Hope this helps,
> >     Mathieu.
> >
> >
> >     Le 2011-01-31 18:04, Adam T. Ford a écrit :
> >     > Hello Mathieu and Animovers,
> >     >
> >     > Thank you for that reply and your interest.
> >     > You are quite correct, there is a text file produced!
> >     > Still,  I am not sure which rows belong to which animals/bursts.
> >     Do you
> >     > know of a way to carry this information from the ltraj object into
> the
> >     > output of a fipati object?
> >     > Since I coerced my original dataframe into a regular timeseries
> there
> >     > will be several observations that the function  sett0 ()  filled
> in,
> >     > correct? This is why I have more rows in the fpt () output then in
> my
> >     > raw data.
> >     > But Im not sure how to match the rows of the ltraj object with the
> >     > output of fpt().
> >     > In my mind, it would make sense to write.table () the ltraj
> >     object, and
> >     > match rows with the fpt() output.
> >     > But when I tried I get:
> >     >         ERROR:  arguments imply differing number of rows
> >     >
> >     >
> >     > Thanks again,
> >     >
> >     >
> >     > Adam
> >     >
> >     > On Mon, Jan 31, 2011 at 3:45 PM, Mathieu Basille
> >     > <basille at ase-research.org <mailto:basille at ase-research.org>
> >     <mailto:basille at ase-research.org <mailto:basille at ase-research.org>>>
> >     wrote:
> >     >
> >     >     Dear Adam,
> >     >
> >     >     What's wrong with the output of write.table? I can do the
> >     following
> >     >     without any error (building upon the example of fpt):
> >     >
> >     >     data(puechcirc)
> >     >     i <- fpt(puechcirc, seq(300,1000, length=30))
> >     >     bla <- do.call(rbind, i)
> >     >     write.table(bla, file = "bla.txt")
> >     >
> >     >     And the resulting text file is fine.
> >     >
> >     >     Mathieu.
> >     >
> >     >
> >     >     Le 2011-01-31 17:37, Adam T. Ford a écrit :
> >     >     > Hello Animovers,
> >     >     >
> >     >     > I am having trouble extracting the results of the fpt ()
> >     function.
> >     >     > As far as I can tell, this function is working correctly,
> >     all the
> >     >     plots
> >     >     > appear in order etc.
> >     >     >
> >     >     > I have 7 animals with different sampling periods representing
> a
> >     >     total of
> >     >     > 48 'bursts'. So I have 48 dataframes assembled as a "fipati"
> >     object.
> >     >     > My problem is that I  am not sure how to compile a list of
> >     multiple
> >     >     > dataframes in way that I can analyze it statistically, or
> >     look at it
> >     >     > completely.
> >     >     >
> >     >     > I have tried (for example):
> >     >     >
> >     >     >    i <- fpt(puechcirc, seq(5, 100, 5), units = "hours")
> >     >     >    do.call(rbind, i)
> >     >     >
> >     >     > and then I tried write.table() to export to a text file but
> >     got a
> >     >     series
> >     >     > of errors, for example:
> >     >     >
> >     >     >     23] WARNING: Warning: \U used without hex digits
> >     >     >     Warning: '\A' is an unrecognized escape in a character
> >     string
> >     >     >     Warning: '\D' is an unrecognized escape in a character
> >     string
> >     >     >     Warning: '\D' is an unrecognized escape in a character
> >     string
> >     >     >     Warning: '\S' is an unrecognized escape in a character
> >     string
> >     >     >    Warning: '\J' is an unrecognized escape in a character
> string
> >     >     >
> >     >     > Has anyone else worked had success extracting information
> from a
> >     >     fipati
> >     >     > class object?
> >     >     >
> >     >     > I realize this is porbably a simple "r-rookie" question, but
> >     i cannot
> >     >     > find what I am looking for in other forums, my r book etc
> >     >     >
> >     >     > Great work on this package by the way, very helpful and much
> >     needed in
> >     >     > the ecological community.
> >     >     >
> >     >     > Adam T. Ford
> >     >     > Ph.D. Candidate
> >     >     > Department of Zoology
> >     >     > University of British Columbia
> >     >     > Vancouver, B.C
> >     >     >
> >     >     > Canada
> >     >     >
> >     >     >
> >     >     >
> >     >     >
> >     >     > _______________________________________________
> >     >     > AniMov mailing list
> >     >     > AniMov at faunalia.it <mailto:AniMov at faunalia.it>
> >     <mailto:AniMov at faunalia.it <mailto:AniMov at faunalia.it>>
> >     >     > http://lists.faunalia.it/cgi-bin/mailman/listinfo/animov
> >     >
> >     >     --
> >     >
> >     >     ~$ whoami
> >     >     Mathieu Basille, Post-Doc
> >     >
> >     >     ~$ locate
> >     >     Laboratoire d'Écologie Comportementale et de Conservation de
> >     la Faune
> >     >     + Centre d'Étude de la Forêt
> >     >     Département de Biologie
> >     >     Université Laval, Québec
> >     >
> >     >     ~$ info
> >     >     http://ase-research.org/basille
> >     >
> >     >     ~$ fortune
> >     >     ``If you can't win by reason, go for volume.''
> >     >     Calvin, by Bill Watterson.
> >     >
> >     >
> >
> >     --
> >
> >     ~$ whoami
> >     Mathieu Basille, Post-Doc
> >
> >     ~$ locate
> >     Laboratoire d'Écologie Comportementale et de Conservation de la Faune
> >     + Centre d'Étude de la Forêt
> >     Département de Biologie
> >     Université Laval, Québec
> >
> >     ~$ info
> >     http://ase-research.org/basille
> >
> >     ~$ fortune
> >     ``If you can't win by reason, go for volume.''
> >     Calvin, by Bill Watterson.
> >
> >
>
> --
>
> ~$ whoami
> Mathieu Basille, Post-Doc
>
> ~$ locate
> Laboratoire d'Écologie Comportementale et de Conservation de la Faune
> + Centre d'Étude de la Forêt
> Département de Biologie
> Université Laval, Québec
>
> ~$ info
> http://ase-research.org/basille
>
> ~$ fortune
> ``If you can't win by reason, go for volume.''
> Calvin, by Bill Watterson.
>
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