Orphaned holes in LoCoH K

Question

I am trying to estimate the home range of wolves and would like to use LoCoH to do that. However I am running into a orphaned hole problem that I really do not know how to solve.

var <- read.csv("Varåa1708_2018.csv", sep = ";")

str(var)

IndividId   : Factor w/ 1 level "M17-08": 1 1 1 1 1 1 1 1 1 1 ...
 $ ProjectCode : int  12950000 12950000 12950000 12950000 12950000 12950000 12950000 12950000 12950000 12950000 ...
 $ SpeciesCode : int  5 5 5 5 5 5 5 5 5 5 ...
 $ SexCode     : int  1 1 1 1 1 1 1 1 1 1 ...
 $ AgeInMonths : Factor w/ 12 levels "Minst 34","Minst 35",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ DateTime    : Factor w/ 4265 levels "01.01.2019 00:00",..: 2018 2019 2020 2021 2022 2023 2121 2122 2123 2124 ...
 $ Latitude    : num  61.1 61.1 61.1 61.1 61.1 ...
 $ Longitude   : num  12.4 12.4 12.4 12.4 12.4 ...
 $ Northing    : int  6780152 6780160 6779922 6779893 6779899 6779904 6779904 6779905 6779917 6779912 ...
 $ Easting     : int  360914 360893 360426 360492 360489 360480 360491 360475 360432 360426 ...
 $ UTMZone     : int  33 33 33 33 33 33 33 33 33 33 ...
 $ UTMX        : int  360914 360893 360426 360492 360489 360480 360491 360475 360432 360426 ...
 $ UTMY        : int  6780152 6780160 6779922 6779893 6779899 6779904 6

v18data.xy = var[c("Longitude","Latitude")]

v18xysp <- SpatialPoints(v18data.xy)
proj4string(v18xysp) <- CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +towgs84=0,0,0")
                        

Create a Spatial Data Frame from relocations

spptv18<-data.frame(v18xysp)
idspv18 <- data.frame(vara18$IndividId)

Add ID

coordinates(idspv18)<-spptv18

proj4string(idspv18) <- CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +towgs84=0,0,0")

locsdf <-as.data.frame(idspv18)

head(locsdf)

  vara18.IndividId Longitude Latitude
1           M17-08  12.41730 61.13125
2           M17-08  12.41691 61.13132
3           M17-08  12.40842 61.12901
4           M17-08  12.40966 61.12877
5           M17-08  12.40960 61.12883
6           M17-08  12.40944 61.12887

LoCoH

var1 <- LoCoH.k.area(idspv18, k=c(16:25))

var2<- LoCoH.k(idspv18, k=24)

Error message I get:

Error in rgeos::createPolygonsComment(oobj) :
rgeos_PolyCreateComment: orphaned hole, cannot find containing polygon for hole at index 81

In addition: Warning messages:

1: In proj4string(xy) : CRS object has comment, which is lost in output 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") : Discarded datum Unknown based on WGS84 ellipsoid in CRS definition, but +towgs84= values preserved 3: In proj4string(xy) : CRS object has comment, which is lost in output

I have tried using UTM instead of LatLong, tried to clean the orphaned holes using cleangeo but that showed that I had no issues with my data. I am a bit of a newbie with R.

Answer 1

Consider using the newer t-locoh (https://tlocoh.r-forge.r-project.org/), which functions identically to LoCoH.k when time is ignored.