Wildlife ecology: home range, distance sampling, occupancy, abundance and connectivity
Source:R/Wildlife.R
McpHomeRange.RdMcpHomeRange: minimum convex polygon of the relocations within the
percent quantile of distance to the centroid (adehabitatHR::mcp).
DistanceSampling: half-normal or hazard-rate detection function by
maximum likelihood (mrds parameterisation), effective strip width /
detection radius, detection probability, density and abundance (Buckland et
al. 2001). OccupancyModel: single-season occupancy (MacKenzie et al.
2002, as unmarked::occu). NmixtureModel: Poisson binomial
N-mixture (Royle 2004, as unmarked::pcount, K = max(y) + 100).
CircuitResistance: effective resistance between grid cells
(isolation by resistance, McRae 2006). LeastCostPath: Dijkstra least
cost path, cost surfaces and corridor. ResistanceFromSuitability:
Keeley et al. (2016) transform. HabitatSuitabilityIndex: geometric,
arithmetic or limiting-factor HSI. PartialMantel: partial Mantel
test (Smouse et al. 1986). GeneFlowNm: Wright's island-model
\(Nm\). HanskiConnectivity: Hanski's (1994) connectivity.
Maximum likelihood uses BFGS followed by Newton steps; standard errors come
from the inverse Hessian. Identical to the Python arm
morie.fn.wildlife; grid cells and nodes are 1-based.
Usage
McpHomeRange(xy, percent = 95)
DistanceSampling(
distances,
width,
key = "hn",
transect = "line",
effort = NULL,
area = NULL
)
OccupancyModel(y, psi_covariates = NULL, p_covariates = NULL)
NmixtureModel(y, lambda_covariates = NULL, p_covariates = NULL, K = NULL)
CircuitResistance(resistance, nodes, directions = 4)
LeastCostPath(cost, start, end, directions = 8, corridor_slack = NULL)
ResistanceFromSuitability(suitability, c = 8)
HabitatSuitabilityIndex(indices, method = "geometric", weights = NULL)
PartialMantel(A, B, C, nsim = 999L, seed = 1L)
GeneFlowNm(fst)
HanskiConnectivity(coords, occupied, areas, alpha = 1, b = 0.5)Arguments
- xy
Two-column relocations.
- percent
Percentage of relocations kept.
- distances
Perpendicular or radial distances.
- width
Truncation distance.
- key
"hn"(half-normal) or"hr"(hazard rate).- transect
"line"or"point".- effort
Total line length or number of points.
- area
Area for abundance.
- y
Detection (0/1) or count matrix, sites by visits (
NAallowed).- psi_covariates, p_covariates, lambda_covariates
Site design matrices (default intercept only).
- K
Upper summation bound for abundance.
- resistance, cost
Resistance or cost grid.
- nodes
Two-column matrix of (row, col) cells.
- directions
4 or 8 neighbours.
- start, end
Cells
c(row, col).- corridor_slack
Corridor tolerance (default 10 percent of the least cost).
- suitability
Habitat suitability in the unit interval.
- c
Transform shape.
- indices
List of suitability index variables.
- method
HSI aggregation.
- weights
Variable weights.
- A, B, C
Distance matrices.
- nsim
Permutations.
- seed
Philox seed.
- fst
Fixation index.
- coords
Patch coordinates.
- occupied
Occupancy (0/1 or probability).
- areas
Patch areas.
- alpha
Inverse mean dispersal distance.
- b
Area scaling exponent.
References
Buckland, S. T. et al. (2001). Introduction to Distance Sampling. Oxford University Press.
MacKenzie, D. I. et al. (2002). Estimating site occupancy rates when detection probabilities are less than one. Ecology 83, 2248-2255.
Royle, J. A. (2004). N-mixture models for estimating population size from spatially replicated counts. Biometrics 60, 108-115.
McRae, B. H. (2006). Isolation by resistance. Evolution 60, 1551-1561.
Keeley, A. T. H., Beier, P. and Gagnon, J. W. (2016). Estimating landscape resistance from habitat suitability. Landscape Ecology 31, 2151-2162.
Smouse, P. E., Long, J. C. and Sokal, R. R. (1986). Multiple regression and correlation extensions of the Mantel test. Systematic Zoology 35, 627-632.
Hanski, I. (1994). A practical model of metapopulation dynamics. Journal of Animal Ecology 63, 151-162.