65 questions
0
votes
0
answers
17
views
Brownian bridge kernel method (BBKM) in adehabitatHR: 'subscript out of bounds' error for home range getverticeshr ()
I have a dataframe with 5-minutes relocation data recorded for several days and for 500+ cows. I created a loop to calculate the daily explored area (home range) of each cow using the minimum convex ...
- 37
1
vote
0
answers
45
views
Error in "as.ltraj" in r: "Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 1, 1206, 0"
I am trying to work out the tortuosity of echidna movement using GPS data from 10 individuals. The tags were programmed to take hourly fixes, however, since echidnas often are in burrows, the success ...
- 11
1
vote
1
answer
106
views
adehabitatHR KUD loop not overlaying mapping correctly in R
I have some code which calculates KUD at 95% from fish position data, restricted by the bounds of a shapefile, and then plots this, and overlays the shapefile on top.
########## BOUND KUD TO SHAPEFILE ...
- 491
0
votes
1
answer
54
views
Analysis of trajectories with ltraj returning odd outputs, why?
I am working with tracking data and stumbled upon the functions from the package "adehabitatLT", which I find quite handy for obtaining the descriptive parameters of my trajectories.
All ...
- 29
2
votes
1
answer
93
views
Interpreting unexpected values in kerneloverlapHR(method = "PHR") using adehabitat package in R
I am trying to calculate home range overlap for multiple groups of animals using the kerneloverlaphr() function from the adehabitatHR package in R. I am hoping to use the "PHR" method; see ...
- 51
0
votes
0
answers
127
views
Calculate the Utilization Distribution Overlap Index (UDOI) in QGIS or in R using a different package than adehabitat
I have a series of home ranges of 2 different species and I need to calculate their overlap (UDOI, specifically). I created these home ranges using the ks package specifically because I wanted to use ...
- 1
0
votes
1
answer
234
views
geom_sf missing geometry with SpatialPolygonsDataFrame
I'm working with some GPS collared animals and using LoCoH.a function in the adehabitatHR package to generate a SpatialPolygonsDataFrame.
library(tidyverse)
library(lubridate)
library(adehabitatHR)
...
- 31
0
votes
0
answers
28
views
How can I fix error longer object length is not a multiple of shorter object length
I am using the kerneloverlaphr function to estimate the overlap of 10 Home range, however I get
error longer object length is not a multiple of shorter object length.
How can I fix it?
However, I ...
0
votes
1
answer
172
views
Error from adehabitatLT::as.ltraj() because dates are not class POSIXct but str(dates) indicates they are POSIXct
The adehabitatLR::as.ltraj() function calculates animal trajectories. The function requires dates to be class POSIXct. I followed the same steps in the example section of the help document using a ...
- 143
1
vote
1
answer
78
views
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:...
- 163
2
votes
1
answer
368
views
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 ...
- 21
0
votes
0
answers
170
views
How to set a grid for kernelbb() in adehabitatHR packge
I'm trying to calculate home range size of individuals. So, I'm studying several functions in adehabitatHR package, including MCP(), KernelUD(), kernellbb() and BRB().
I'd like to use same grid of ...
0
votes
2
answers
163
views
How to use and understand rstats parallel processing with HPC Acenet Siku cluster, SLURM, futures, rslurm, and lapply() equivalents
Background: I am using the adehabitatHR package to create utilize distribution estimates (UDEs) of wildlife populations.
Problem: How to manage memory with parallel processing. A huge amount of memory ...
- 205
0
votes
1
answer
150
views
ADEHabitat Smoothing parameters Sig1and2
I am trying to build some BBMM code and although it produces the outputs I want, I am having trouble figuring out the proper smoothing parameters using Sig 1 and Sig 2. When I use the liker function ...
- 43
0
votes
1
answer
289
views
How to create an estUDm object from utilization distributions created with GIS?
I created kernel densities/utilization distributions for multiple animals in ArcGIS Pro instead of using the adehabitatHR package in R because I needed a different smoothing parameter estimator and I ...
- 1
0
votes
1
answer
255
views
Combining two or more estUDm objects into a single estUDm object
I know it is possible to combine multiple estUD objects into a single class-estUDm object using:
tot <- list(estUD1=estUD1, estUD2=estUD2, estUD3=estUD3)
class(tot) <- "estUDm"
...
- 131
0
votes
1
answer
218
views
questionable home range values with mcp() (minimum convex polygon) in R
I am trying to calculate the home range of a whole species and seperate two groups based on sex. I used mcp() and it runs but the output is questionable.
Here is my data
library(raster)
library(dismo)...
0
votes
0
answers
145
views
Trouble with kerneloverlaphr() after clipping land
I seem to experience a similar issue to the one raised here https://stat.ethz.ch/pipermail/r-sig-geo/2012-December/016858.html, but which never received an answer...
Background:
I have GPS tracking ...
- 131
0
votes
1
answer
267
views
Convert from spatialpixeldataframe to estUD
In short: I have a spatialpixeldataframe of a utilization distribution of an animal across a grid (udspdf) which I need to convert to estUD-class.
Background to how I got there: After calculating the ...
- 131
0
votes
0
answers
221
views
adehabitatHR: In proj4string(xy) : CRS object has comment, which is lost in output
I'm trying to create kernel density map from point data (available as .shp and .csv) for 5 different species,at global scale. For some individual, there is only one point locality, but for the others ...
- 3
0
votes
1
answer
58
views
Create a raster with 1 (habitat) and 0 (non-habitat) for kernel estimation
I need to create a raster that I use as a grid for kernel estimation of seabird tracking data.
The raster needs to hold values of "1" for habitat (points at sea), and "0" for non-...
- 131
0
votes
0
answers
100
views
How to speed up creating equal distance spatial grid in R
I am using adehabitatHR to calculate the home ranges of several eagles. I would like to create a grid of 1 km x 1 km to input into the kernelUD function.
I tried to use the method as provided here: ...
- 101
2
votes
1
answer
750
views
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 ...
0
votes
1
answer
368
views
adehabitatHR home range estimation is too small
I have lat/long data of two animals tracked in Western Australia and I'd like to find their home ranges using adehabitatHR.
library(sp)
library(rgdal)
library(raster)
library(adehabitatHR)
library(sf)
...
- 25
0
votes
1
answer
313
views
AdehabitatHR::kernelUD error, geographical CRS given to non-conformant data
I am trying to perform the simple task of estimating a kernel density utilisation distribution across the foraging tracks of all females in my data set (just a visualisation exercise), and have opted ...
- 17
1
vote
1
answer
2k
views
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", ...
- 47
0
votes
1
answer
446
views
How to calculate KUD for home range analysis using the package adehabitatHR?
i am trying to calculate KUD 50% and 95% for my penguin tracking data but have run into an error. My aim is to calculate the home range densities and then export the data as a polygon.
library(...
- 47
2
votes
2
answers
801
views
"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 ...
- 99
0
votes
0
answers
145
views
How to run multiple dataframes in a list through a block of code using for loops in R?
I have a dataframe full of bird sightings, and I need to take that data and create .KMV files for each known, named bird territory (territory.name). I have a block of code that will take location data ...
- 33
0
votes
1
answer
957
views
Computing HR using Kernel Density. Grid issues?
My dataset includes animal locations and id. What I am trying to do is that I am trying to compute Home Range using kernel density function. As my dataset was huge, I tried it splitting the dataset ...
1
vote
1
answer
144
views
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 ...
- 53
1
vote
0
answers
225
views
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(...
- 11
0
votes
1
answer
62
views
Why is SpatialPointsDataFrame rounding my Y coordinates? (rounds UTM 5252636 to 5262640)
I am trying to estimate home range size using telemetry data using adehabitatHR. Every time I create a SpatialPointsDataFrame, it rounds the y-coordinate for my UTM locations. I have tried having the ...
0
votes
1
answer
1k
views
Exporting a contoured Kernel density estimation plot to raster or shapefile format
I'm trying to perform Kernel density estimation in R using some GPS data that I have. My aim is to create a contoured output with each line representing 10% of the KDE. From here i want to import the ...
- 85
1
vote
0
answers
38
views
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 ...
- 11
0
votes
1
answer
163
views
First Passage Time analysis in adehabitatLT returns only NA
Background: I try to do a First Passage Time Analysis in R using adehabitatLT. I found a good tutorial here and I can follow all the steps using my own data set up to the section with First passage ...
- 221
1
vote
0
answers
353
views
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 ...
- 23
0
votes
1
answer
290
views
How do I calculate the area of a Brownian bridge movement model?
In the adehabitatHR package there is some sample code to calculate Brownian bridge movement model for a wild boar using the kernelbb function. I would like to calculate the area of the object that ...
- 1,441
1
vote
1
answer
2k
views
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 (...
- 43
1
vote
1
answer
135
views
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 ...
- 11
2
votes
1
answer
1k
views
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 ...
- 41
1
vote
1
answer
814
views
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 ...
- 21
-2
votes
1
answer
415
views
adehabitatHR locoh.k orphan holes
I am trying to optimise the k parameter using AdehabitatHR LoCoH.k.area and it stops running when the topology is such that it can't produce a polygon. Message is:
rgeos_PolyCreateComment: ...
- 11
0
votes
1
answer
116
views
Vector addition (subtraction) in R for movement paths
I have a data frame which includes the movement path of an animal in lat/lon coordinates.
From this I have derived speed and bearing over ground. The data frame also contains the wind vector ...
- 5,181
0
votes
2
answers
616
views
export khrud object from kernelUD to raster
In R, how can I export a khrud object from function kernelUD in package adehabitat to a raster file (geoTiff)?
I tried following this thread (R: how to create raster layer from an estUDm object) ...
- 225
-1
votes
1
answer
1k
views
Plot individuals home-range with Adehabitat
I am trying to put the name from the individuals of my research in a polygons home-range plot, but after many attempts I still can not achieve it.
Here and example of my data: X and Y are coordinates ...
1
vote
1
answer
129
views
Viewing design II individual selection ratios
I've been using the R package adehabitat to calculate selection ratios for a project I'm working on involving preferences in animal foraging habitat.
When using the function widesII I can see the ...
- 11
1
vote
0
answers
110
views
AdehabitatLT and ltraj object: how to extract mean distance between relocations?
I have an ltraj object , I would like to extract the mean distance for day and the mean time for day. The date is stored as "("%d/%m/%Y %H.%M.%S"), anyway I just need the relocations that occured ...
- 11
0
votes
1
answer
254
views
Subsetting for a minimum number of locations for MCP in R, dropping individual names
I have a very similar question to that posted here: Subsetting for a minimum number of locations for MCP in R
And here Subset data frame based on number of rows per group
Where I'm trying to subset ...
- 47
0
votes
1
answer
42
views
How to create a single data set that contains two data frames using an excel file
I need to create a single data set from an excel file that looks likes the following picture 1. When I export the file to mimic it in excel, the format does not work correctly. This is what the file ...
