[R] [R-pkgs] adehabitat version 1.7
Dear all, I have uploaded to CRAN the version 1.7 of the package 'adehabitat'. Significant changes are listed below: * The Brownian bridge kernel estimation algorithm has been greatly improved. It now takes more than 80% less time than the previous version. A new function "liker" has also been added, which estimates the one of the two smoothing parameters of the bridge kernel using a maximum likelihood approach (recommended in Horn et al., Ecology, in press). Examples of the help page demonstrate the use and interest of this function. Comparison between kernelbb and the Visual basic algorithm provided in the paper of Horn et al. returned consistent results. * The function kernelUD has also been improved. It now takes more than 50% less time than the previous version. In addition the "grid" argument of this function, now also allows a list of objects of class "asc" to be passed as grid where the UD should be estimated. Happy testing, Clément Calenge. -- Clément CALENGE LBBE - UMR CNRS 5558 - Université Claude Bernard Lyon 1 - FRANCE tel. (+33) 04.72.43.27.57 fax. (+33) 04.72.43.13.88 ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] adehabitat version 1.6
Dear all, I have just uploaded to CRAN the version 1.6 of the package 'adehabitat'. Significant changes are listed below: * The package has been reorganized into four parts (see ?adehabitat-package for a description): (i) management of raster maps, (ii) habitat selection / ecological niche analysis, (iii) home range analysis, and (iv) analysis of animals trajects. The package contains several demo files to allow an overview of these parts : demo(rastermaps), demo(homerange), demo(managltraj), demo(analysisltraj), demo(nichehs). * the package now contains a new function allowing the exploration of the ecological niche, which generalizes several factor analyses (ENFA, MADIFA, ...) and is closely related to several methods (Mahalanobis distances, selection ratios, etc.), named gnesfa() (see the examples of the help page for the properties of this analysis). * The class ltraj now distinguishes two types of trajects: type I (time not recorded, e.g. tracks of animals in the snow) and type II (time recorded, e.g. GPS monitoring). Trajects of type II may either be "regular" (constant time lag between relocations) or not. * Numerous example datasets have been added to the package to illustrate the analysis of animals trajects: 4 porpoises, 6 albatross, 1 hooded seal, 1 whale, 1 brown bear, two roe deer, two chamois, 4 ibex, 1 mouflon, 3 wild boar * Many functions have been added to allow the management of animals trajects within R: Some functions allow to handle the attributes or the storage of the trajects (typeII2typeI, typeI2typeII, sett0, cutltr, is.regular, is.sd, mindistkeep, offsetdate, set.limits), other allow to manage missing values and test their random distribution in the traject (setNA, summaryNAltraj, plotNAltraj, runsNAltraj), other allow a graphical exploration of the properties of the trajects (hist.ltraj, plot.ltraj, plotltr, sliwinltr). * Several functions now allow to test the independence of the descriptive parameters in the trajects (indmove and wawotest for dx, dy and dist, testang.ltraj for rel.angle and abs.angle) * Several functions allow to simulate common models of trajects: the correlated random walk (simm.crw), the brownian motion (simm.brown), the arithmetic brownian motion (simm.mba), the Ornstein Uhlenbeck process (simm.mou), the brownian bridge (simm.bb) and the Levy process (simm.levy). * The function explore.kasc() provides a Tk interface for the exploration of a multi-layer raster map of class "kasc" * A partitioning algorithm (still under research) is also available to partition a traject into segments with homogeneous properties (see the help page of modpartltraj) * The bugs in redisltraj and mcp.area have been corrected Happy testing, Clément CALENGE -- Clément CALENGE Laboratoire de Biométrie et Biologie évolutive UMR CNRS 5558 43 Bd. 11 Nov. 1918 69622 Villeurbanne Cedex - France Office national de la chasse et de la faune sauvage 95, rue Pierre Flourens 34000 Montpellier ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] adehabitat version 1.5
Dear all, I have just uploaded to CRAN the version 1.5 of the package 'adehabitat'. Significant changes are listed below: * the package now contains a new function allowing a factorial decomposition of the Mahalanobis distances in habitat selection studies, named madifa(). * The ENFA can now be performed using all kinds of variables (numeric, factors, fuzzy, mixing of several types, etc.) * Several methods allowing the analysis of animals movements have been added, including the first passage time (function fpt()), a rediscretization algorithm (redisltraj()), and an interactive graphic window for dynamic analysis (trajdyn()) * A function for interactive exploration of maps of class "kasc" has been added (explore.kasc) * Scott Fortmann-Roe (Univ. Berkeley) programmed a better algorithm for Nearest neighbour Convex hull home range estimation. * The function kasc2spixdf() have been updated Happy testing, Clément CALENGE -- Clément CALENGE Laboratoire de Biométrie et Biologie évolutive UMR CNRS 5558 43 Bd. 11 Nov. 1918 69622 Villeurbanne Cedex - France ___ R-packages mailing list R-packages@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] adehabitat version 1.4
Dear all, I have just uploaded to CRAN the version 1.4 of the package 'adehabitat'. Significant changes are listed below: - The eigenanalysis of selection ratios (Calenge and Dufour, 2006, Ecology) can now be performed using the function eisera(). It can be used for the analysis of habitat selection when habitat can be considered to consist of several habitat types (e.g. vegetation types). - A new class, the class "ltraj", is now available for the analysis of trajectories of animals (e.g. for the analysis of data collected using GPS collars). This class automatically computes the turning angles between successive moves, the absolute angles for each move, the speeds and the net squared displacement for each relocation. This class is to be prefered to the class "traj". The class "traj" is now deprecated. Note that the data set "puechcirc" is now of the class ltraj. - The functions making the interface with the package "sp" have been updated: 'area2spol' converts an object of class 'area' into an object of class 'SpatialPolygons'. 'spol2area' converts an object of class 'SpatialPolygons' or 'SpatialPolygonsDataFrame' into an object of class 'area'. 'attpol2area' gets the data attribute of an object of class 'SpatialPolygonsDataFrame' and stores is into a data frame. 'traj2spdf' converts an object of class 'traj' into an object of class 'SpatialPointsDataFrame'. 'traj2sldf' converts an object of class 'traj' into an object of class 'SpatialLinesDataFrame'. - The function enfa() has been modified: The old components "co" and "l1" have been removed from objects of class "enfa", as they did not rely on solid mathematical theory. The old component "c1" is now named "co", and corresponds to the scores of habitat variables in the enfa (the squared norm of this vector is equal to 1 for the identity metric). As previously, the component "li" stores the scores of the resource units in the ENFA. - The function df2kasc now accept objects of class "kasc" with one column. - That's all, thanks for reading ! Questions, comments and suggestions are greatly appreciated. Happy testing, Clément Calenge -- Clément CALENGE LBBE - UMR CNRS 5558 - Université Claude Bernard Lyon 1 - FRANCE tel. (+33) 04.72.43.27.57 fax. (+33) 04.72.43.13.88 ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Strange behavior of atan2
Dear all, I've got a problem with the function atan2. For a couple of coordinates x and y, This function returns the angle between the vector of coordinates (x, y) and the abscissa axis, i.e. it is the same as atan(y/x) (as indicated on the help page). If we consider the vector with coordinates x = 0 and y = 0, we have the following result: > atan(0/0) [1] NaN This is expected. However: > atan2(0,0) [1] 0 Instead of a missing value, the function atan2 returns an angle equal to 0 radians. I've searched through the help pages, the FAQ and the forum, but I did'nt find any explanation to this result. Does anyone know if this behavior is expected, and why ? Thank you for any clues. Regards, Clément Calenge -- Clément CALENGE LBBE - UMR CNRS 5558 - Université Claude Bernard Lyon 1 - FRANCE tel. (+33) 04.72.43.27.57 fax. (+33) 04.72.43.13.88 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] [R-pkgs] adehabitat version 1.2
Dear all, I have just uploaded to CRAN the version 1.2 of the package 'adehabitat'. This package now contains new functions for the estimation of home ranges (Nearest neighbour convex hull, brownian bridge approach for kernel estimation), estimation of schoener's ratio. This package now allows a better management of objects of class "area" (see plot.area, perarea, ararea). Some arguments of the graphical functions have also been changed (kernel, image.kasc, scatter.enfa). Finally, some minor bugs have been corrected. Note that the package now need that the packages ade4 and gpclib are installed. Questions, comments and suggestions are greatly appreciated. Happy testing, Clément Calenge. ========== Clément CALENGE LBBE - UMR CNRS 5558 - Université Claude Bernard Lyon 1 - FRANCE tel. (+33) 04.72.43.27.57 fax. (+33) 04.72.43.13.88 ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] png problem
Hello,
Thanks for the fast reply.
Paul Murrell wrote:
Hi
Clément Calenge wrote:
Dear R-users,
I have a small problem with the function png(), when used with the
argument colortype="pseudo.cube".
> png("toto.png", colortype="pseudo.cube")
> image(matrix(rnorm(1), 100, 100))
> dev.off()
R is blocked at the last command (R does not
print any prompt after the last command). Nothing is
written in the file (Gimp indicates that the file is corrupted).
Did you wait long enough? This example took a little while to complete
for me (may need someone more familiar with the code to tell us why it is
so slow).
You're right, it took 45 minutes for me.
However, since I need to use this code to build a Sweave vignette,
I cannot use it too often (I have about thirty files to create, this
would take about 20 hours to build the vignette !).
I also need the colortype argument (some graphics cards
do not allow the compilation of the vignette without).
Does anyone knows how to speed up the process ?
Clément.
Paul
However,
> png("toto.png")
> image(matrix(rnorm(1), 100, 100))
> dev.off()
works fine.
I tried:
> options(X11colortype = "pseudo.cube")
> png("toto.png")
> image(matrix(rnorm(1), 100, 100))
> dev.off()
But, here again, R is blocked. I tried to replace dev.off() by
graphics.off(), but this does not resolve the problem.
The problem does not occurs when the function X11() is used
instead of the function png().
I searched through the mail archive, the FAQ, on google,
but I did not found any solution to this problem.
On the help page on the function png(),
it is indicated that "The colour handling will be that of the 'X11'
device in use".
I never used these functions before, but maybe png()
is not suitable with colortype="pseudo.cube" ?
Can you tell me where I have missed something ?
Thanks in Advance,
Clément Calenge.
>version
_
platform sparc-sun-solaris2.9
arch sparc
os solaris2.9
system sparc, solaris2.9
status
major1
minor9.1
year 2004
month06
day 21
language R
[[alternative HTML version deleted]]
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--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
[EMAIL PROTECTED]
http://www.stat.auckland.ac.nz/~paul/
==
UMR CNRS 5558 - Equipe "Ecologie Statistique"
Laboratoire de Biométrie et Biologie Evolutive
Université Claude Bernard Lyon 1
43, Boulevard du 11 novembre 1918
69622 Villeurbanne Cedex
FRANCE
tel. (+33) 04.72.43.27.57
fax. (+33) 04.72.43.13.88
__
[EMAIL PROTECTED] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] png problem
Dear R-users,
I have a small problem with the function png(), when used with the
argument colortype="pseudo.cube".
> png("toto.png", colortype="pseudo.cube")
> image(matrix(rnorm(1), 100, 100))
> dev.off()
R is blocked at the last command (R does not
print any prompt after the last command). Nothing is
written in the file (Gimp indicates that the file is corrupted).
However,
> png("toto.png")
> image(matrix(rnorm(1), 100, 100))
> dev.off()
works fine.
I tried:
> options(X11colortype = "pseudo.cube")
> png("toto.png")
> image(matrix(rnorm(1), 100, 100))
> dev.off()
But, here again, R is blocked. I tried to replace dev.off() by
graphics.off(), but this does not resolve the problem.
The problem does not occurs when the function X11() is used
instead of the function png().
I searched through the mail archive, the FAQ, on google,
but I did not found any solution to this problem.
On the help page on the function png(),
it is indicated that "The colour handling will be that of the 'X11'
device in use".
I never used these functions before, but maybe png()
is not suitable with colortype="pseudo.cube" ?
Can you tell me where I have missed something ?
Thanks in Advance,
Clément Calenge.
>version
_
platform sparc-sun-solaris2.9
arch sparc
os solaris2.9
system sparc, solaris2.9
status
major1
minor9.1
year 2004
month06
day 21
language R
[[alternative HTML version deleted]]
__
[EMAIL PROTECTED] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] polygon border
see ?chull hope this helps, Clément. At 12:34 09/10/2003 +0200, Marta Rufino wrote: Hello, Does anyone know how a function to find automaticly the border (polygon) of a cloud of points? It is for a PCA kind of analysis, where I wanted to present as the limits for each group, instead of all points... thank you in advance Marta __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
