Description Usage Arguments Value Examples
Run a Bayes inference of Landscape Occupancy from Presence-Only Data on Stan
1 2 | modelLopod(LopodData, varP = F, q = NULL, pmin = 0, CAR = F,
nChains = 4, warmup = 2000, sampling = 1000, nCores = 4)
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LopodData |
Object with the data to be used in the Model |
varP |
Boolean. If TRUE, detectability will vary across cells. If FALSE a global value for detectability will be estimated. |
q |
Number between 0 and 1 or NULL. Rate of false detections. If NULL the values will be estimated by the model. |
pmin |
Number between 0 and 1. Minimum value for detectability in a unit in which the species occurs. |
CAR |
Boolean. If TRUE, (and if a adjacency matrix is included in the LopodData object) a conditional auto-regression analysis will be performed for occupancy across units. |
nChains |
Number of Markov chains used by the Stan model. |
warmup |
Number of iterations for each chain to be discarded as warm-up. |
sampling |
Number of iterations for each chain to be sampled (after warm-up). |
nCores |
Number of cores to use when executing the chains in parallel. |
A LopodModel object.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | data("simSpRecords", package = "bayesLopod")
data("simSpSamplingEffort", package = "bayesLopod")
simSpRasters = xyToRaster(xyRecords = simSpRecords,xySamplingEffort = simSpSamplingEffort,
basemap = NULL, nrows = 10, extentExpansion = 0)
ld_Raster = rasterLopodData(rasterN = simSpRasters[["samplingEffort"]],
rasterY = simSpRasters[["spDetections"]], Adjacency = FALSE )
mLopodRaster = modelLopod(LopodData = ld_Raster, varP = TRUE, q = NULL,
pmin = 0, CAR = FALSE, nChains = 1,warmup = 10,sampling = 10,nCores = 1)
data("Andropogon_shape", package = "bayesLopod")
ld_Shape = shapeLopodData(Shapefile = Andropogon_shape, fieldN = "sampEffort",
fieldY = "detections", Adjacency = FALSE, keepFields = FALSE)
mLopodShape = modelLopod(LopodData = ld_Shape, varP = FALSE, q = NULL,
pmin = 0, CAR = FALSE, nChains = 1,warmup = 5,sampling = 5,nCores = 1)
## Not run:
data("simSpRecords", package = "bayesLopod")
data("simSpSamplingEffort", package = "bayesLopod")
simSpRasters = xyToRaster(xyRecords = simSpRecords,xySamplingEffort = simSpSamplingEffort,
basemap = NULL, nrows = 50, extentExpansion = 0)
ld_Raster_adMatrix = rasterLopodData(rasterN = simSpRasters[["samplingEffort"]],
rasterY = simSpRasters[["spDetections"]], Adjacency = TRUE )
mLopodRaster = modelLopod(LopodData = ld_Raster_adMatrix, varP = TRUE, q = NULL,
pmin = 0.1, CAR = FALSE, nChains = 4,warmup = 500,sampling = 100,nCores = 4)
data("Andropogon_shape", package = "bayesLopod")
ld_Shape = shapeLopodData(Shapefile = Andropogon_shape, fieldN = "sampEffort",
fieldY = "detections", Adjacency = TRUE, keepFields = FALSE)
mLopodShape = modelLopod(LopodData = ld_Shape, varP = TRUE, q = NULL,
pmin = 0, CAR = TRUE, nChains = 4,warmup = 500,sampling = 100,nCores =4)
## End(Not run)
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