Estimates spatio-temporal kernel density model

Estimates spatio-temporal kernel density model

Usage

estimateMap3DKernel(
  data,
  Longitude,
  Latitude,
  DateOne,
  DateTwo,
  center = c("Europe", "Pacific"),
  independent = NULL,
  DateType = "Interval",
  CoordType = "decimal degrees",
  Weighting = NULL,
  clusterMethod = NULL,
  nClust = 5,
  nClustRange = c(2, 10),
  kMeansAlgo = "Hartigan-Wong",
  trimRatio = 0.05,
  restr.fact = 12,
  clusterTimeRange = c(0, 1000),
  modelUnc = FALSE,
  dateUnc = "point",
  restriction = c(-90, 90, -180, 180),
  nSim = 10,
  smoothness = 1,
  kdeType = "1"
)

Arguments

data

data.frame: data

Longitude

character: name of longitude variable

Latitude

character: name of latitude variable

DateOne

character: name of date variable 1 (lower interval point / mean / single point)

DateTwo

character: name of date variable 2 (upper interval point / sd / )

center

(character) center to shift data to, either "Europe" or "Pacific"

independent

character: name of presence/absence variable (optional)

DateType

character: one of "Interval", "Mean + 1 SD uncertainty" and "Single Point"

CoordType

character: type of longitude/latitude coordinates. One of "decimal degrees", "degrees minutes seconds" and "degrees decimal minutes"

Weighting

character: name of weighting variable

clusterMethod

character: cluster method

nClust

numeric: how many clusters

nClustRange

numeric: range of potential mclust cluster

kMeansAlgo

character: kmeans algorithm as in stats:kmeans

trimRatio

numeric: proportion of observations to be trimmed by tclust

restr.fact

numeric: clustering restriction factor

clusterTimeRange

numeric vector: time range of cluster

modelUnc

boolean: Include dating uncertainty

dateUnc

character: one of "uniform", "normal", "point"

restriction

numeric vector: spatially restricts model data 4 entries for latitude (min/max) and longitude(min/max)

nSim

numeric: number of bootstrap samples

smoothness

numeric: smoothness adjustment

kdeType

character: "1" for correlated bandwidth, "2" for diagonal bandwidth, "3" for diagonal, equal long/lat bandwidth

Examples

if (FALSE) {
# load data
data <- readRDS(system.file("extData", "exampleData.Rds", package = "DSSM"))
# estimate model-map
map <- estimateMap3D(data = data, independent = "d13C", Longitude = "longitude",
Latitude = "latitude", DateOne = "dateLower", DateTwo = "dateUpper", Site = "site")
# Plot the map
plotMap3D(model = map, time = median(data$dateLower, na.rm = TRUE))
}