Argument,Input,Description
start,startLocation,a data frame with x and y coordinates
timesteps,simSteps,an integer describing the length of the simulation
des_options,10,an integer describing the number of foraging destination options an animal is offered
options,12,an integer describing the number of movement options an animal is offered
shelterLocations,BADGER_shelterLocs,a data frame providing x and y coordinates of the shelter locations
shelterSize,BADGER_shelterSize,a value describing the radius around shelter sites that movement step lengths are reduced
avoidPoints,BADGER_avoidLocs,a data frame providing x and y coordinates of the avoidance locations
destinationRange,BADGER_destinationRange,a numeric vector of length two that contains the shape and scale values that describe the Gamma distribution for potential foraging destinations
destinationDirection,BADGER_destinationDirection,a numeric vector of length two that contains the mean and concentration values that describe the Von Mises distribution for potential foraging destinations
destinationTransformation,BADGER_destinationTransformation,a value to choose the type of transformation applied to the animal's attraction to a chosen destination
destinationModifier,BADGER_destinationModifier,a value modifying the animal's attraction to a chosen destination
avoidTransformation,BADGER_avoidTransformation,a value to chose the type of transformation applied to the animal's avoidance to avoidance locations
avoidModifier,BADGER_avoidModifier,a value modifying the animal's avoidance of avoidance locations
k_step,BADGER_k_step,a vector of three numbers describing the three behavioural states' Gamma distributions' shape parameter for step lengths
s_step,BADGER_s_step,a vector of three numbers describing the three behavioural states' Gamma distributions' scale parameter for step lengths
mu_angle,BADGER_mu_angle,a vector of three numbers describing the three behavioural states' Von Mises distributions' mean parameter for turn angles
k_angle,BADGER_k_angle,a vector of three numbers describing the three behavioural states' Von Mises distributions' concentration parameter for turn angles
rescale_step2cell,BADGER_rescale,a numeric value to specify the size of the environmental matrices cells
behave_Tmat,BADGER_behaveMatrix,a 3x3 numeric matrix describing the transition probabilities between the three behavioural states
rest_Cycle,BADGER_rest_Cycle,"a vector length 4 for amplitude, midline, offset and frequency to define the resting/active cycle"
additional_Cycles,BADGER_additional_Cycles,"a data.frame 4 columns wide for amplitude, midline, offset and frequency to define any additional activity cycles, where each row is another cycle"
shelteringMatrix,BADGER_shelter,three arguments for the three matrices describing the landscape the simulated animal occupies
foragingMatrix,BADGER_forage,
movementMatrix,BADGER_move,