# Bayesian Inference of Landscape Occupancy from Presence-Only Data

## Documentation for package ‘bayesLopod’ version 1.0.1

- DESCRIPTION file.

## Help Pages

Andropogon_shape | Number of detection of Andropogon gerardii and it's target group in several counties in the Midwest
LopodData-class | An S4 class to contain data to be input into a bayesLopod model.
LopodData_Class | An S4 class to contain data to be input into a bayesLopod model.
lopodDens | Kernel density estimates of global occupancy model parameters.
LopodModel | An S4 class containing a LopodModel.
LopodModel-class | An S4 class containing a LopodModel.
lopodRaster | Crate raster object for a parameter estimated in a LopodModel
lopodShape | Crate Shape object for a parameter estimated in a LopodModel
lopodSummary | Summary statistics for a LopodModel
lopodTrace | Plots the values of model parameters for each chain across iterations
modelLopod | Run a Bayes inference of Landscape Occupancy from Presence-Only Data on Stan
modelParams | Internal function to extract parameters from a StanModel object
rasterDistToRecords | Internal - Create a Stack with distance matrices to sampled and detected cells
rasterLopodData | Create a LopodData object from Raster data
rasterStudyArea | Internal - Create a Raster object with Study Area from Raster data
shapeLopodData | Create a LopodData object from Raster data
simSpRecords | Coordinates for detections of a simulated species
simSpSamplingEffort | Coordinates for sampling events targeting a simulated species
xyToRaster | Crate Shape object for a parameter estimated in a LopodModel