R package for home range estimation
adehabitatHR is a collection of tools for the estimation of animals home range.
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Questions tagged [adehabitathr]
59 questions
6
votes
1 answer
Grid too small for kernelUD /getverticeshr/adehabitatHR home range estimation
The documentation for adehabitat HR recommends the following code for calculating a 95% kernel for a home range after creating the UD object:
## Calculation of the 95 percent home range
ver <- getverticeshr(ud, 95)
For some of my data, the…
Perry Helion
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3
votes
2 answers
Error : .onLoad failed in loadNamespace() for 'tcltk', details:call: fun(libname, pkgname)
Recently I have trouble librarying the package "adehabitat". I don't know what should I do to cope with the problem. Can anyone knows and offer me help? Thanks a lot.
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0…
PHE
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2
votes
1 answer
Is there an sf (or df) based alternative to kernelUD to estimate bivariate normal kernel density?
I am switching from sp to sf but have some analysis which uses kernelUD from adehabitatHR which requires my data to be SpatialPoints. Is there an equivalent which does not use sp, perhaps instead using sf or a regular dataframe, which offers similar…
TheMargatron
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2
votes
1 answer
creating kernel density estimates for multiple animals in adehabitatHR
I am trying to create kernel density estimates (KDEs) to estimate the home ranges for multiple pairs of long-tailed tits. Despite filtering out pairs ("nest_id" variable) that have less than five GPS locations, I still get the error message "At…
Tobit
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1
vote
1 answer
How can I loop a function through every combination of levels of a factor?
I have a dataset containing a set of variables and the coordinates describing their distributions in geographic space:
set.seed(123)
#example dataset:
d <- data.frame(var=as.factor(rep(LETTERS[1:5],each=6)),x=runif(30),y=runif(30))
head(d)
var…
eazyezy
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1
vote
1 answer
MCP Home range with AdehabitatHR too small
I'm new to spatial analysis using R. I'm trying to calculate daily home ranges (MCP 100, later 95 and 50 %) using mainly the adehabitatHR package in R. I used a script provided by my colleague and it worked for her all the time. Now when I'm running…
1
vote
1 answer
Error in writeOGR when trying to export spatial polygons as shapefile in R
I am trying to export polygons that i have created for home range data but when i go to export them get this error message:
Error in writeOGR(colkud95[1, ], ".", "colonyhomerange", driver = "ESRI Shapefile") :
Spatial Polygons objects should have…
Courtney
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1
vote
1 answer
"Error in kernelUD: At least 5 relocations required to fit a home range" but have many more than 5 relocations per group
I have been making kernel density home range estimations for canid groups in an area by population and per pack across various temporal scales. However, when I attempt to run kernelUD on a subset for each year I get Error in kernelUD(P17.sp[,…
Charlie_J
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1
vote
1 answer
Sub-setting a spatial point data frame in R
I am trying to subset a spatial point data frame using the function subset as follows:
data(puechabonsp)
Chou.subset <- subset(puechabonsp,puechabonsp$relocs$Name=="Chou")
I was expecting to get all rows of the individual named "Chou" but…
Idan
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1
vote
0 answers
calculate volume of intersection of utilization distributions
I am trying to calculate the volume of intersection for the utilization distribution of many animals. I have estimated their UDs using move::brownian.bridge.dyn() for each animal then used getVolumeUD() which gives me the UD as a RasterLayer.
mod1…
klk56
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1
vote
0 answers
Why does the clusthr function on my SpatialPointsDataFrame return back a script out of bounds error?
I am trying to calculate MCP and KDE on a vhf tracking data, my dataframe has three columns, Individual, Lat and Long.
I am trying following the adahabitatHR vignette to try and create a SpatialPointsDataFrame that contains vhf data on multiple…
Josh Twining
- 11
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1
vote
0 answers
Calculate centroids from a Kernel Density
I have two R-related questions:
I'm trying to calculate centroids from a kernelUD. I was able to calculated the KernelUD, and I end up with a S4 object of class estUD. However, I cannot find a way to calculate a centroid from this probabiltiy…
Riccardo
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1
vote
1 answer
Calculating 50% and 95% kde to determine core and periphery areas of home ranges
I have GPS locations of 5 animals. I am trying to calculate the 50% and 95% kernel distribution to determine size of core and periphery areas in km2 (as a table) and I also want to plot the contours (50% and 95%) for these data. Can someone help…
EleMan
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1
vote
1 answer
Is there a way to get consistent results when replacing zero values with smaller values (ie. 0001) in compana?
I'm using the compana function in Adehabitat package to determine if used habitat is selected for from available habitat.
One of the habitat classes I'm using in my available matrix has several very low values (ie. 0.000015000) or zero values.…
Chloe B
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1
vote
1 answer
R Code adehabitatHR - Grid too small for kernelUD /getverticeshr/adehabitatHR home range estimation
Sorry, for my newb question. I'm still learning how to conduct spatial analyses in R. I realize this question has been previously asked (here).
Goal: I'm unable to run this code with simulated data within the parameters specifically for my…
Hayden
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