lopodShape: Crate Shape object for a parameter estimated in a LopodModel

In bayesLopod: Bayesian Inference of Landscape Occupancy from Presence-Only Data

Description

Crate Shape object for a parameter estimated in a LopodModel

Usage

lopodShape(LopodModel, param, extrapolate = T, metric = NULL, quant = 0.5)

Arguments

LopodModel	A LopodModel object
param	Unit-level model parameter to be mapped. Values "psi_Sampled" can be mapped for models without CAR analyses, "psi_i" for LopodModels with CAR analysis and "pp","cellpres_i", "pCorr","sim_y","sim_true_y","sim_false_y" for both.
extrapolate	Boolean. If True, parameters are mapped for cells that have not been sampled, this can only be done in LopodModels with CAR analysis. Only plotted for "psi_i", "pp" and, "cellpres_i".
metric	"mean" or "sd". Plots the mean or standard deviation of the posterior distribution. If NULL, the value in quant is used.
quant	Returns the raster for a given quantile of the Posterior Distribution. Default is 0.5 (the median of the posterior distribution). Not used if metric is other than NULL

Value

A Raster object.

Examples

## Not run: 
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)
psiShape_95 = lopodShape(mLopodShape, "psi_i", extrapolate = FALSE,  quant = 0.95)
psiShape_05 = lopodShape(mLopodShape, "psi_i", extrapolate = TRUE, quant = 0.05)
 #Visualize results
sp::spplot(psiShape_05, zcol = "psi_i")
sp::spplot(psiShape_95, zcol = "psi_i")

## End(Not run)

bayesLopod documentation built on Jan. 4, 2018, 5:08 p.m.