Expanded the DispersalModel
object & functions to include optional breeding_stage
& visible_stage
parameters to further define dispersal.
Altered simulate_kindist_custom()
& axials_standard()
etc. functions to explicitly take into account new aspects of the dispersal model, especially -1
cycle
numbers (which allow sampling before the 'official' beginning of a lifespan (often defined as first dispersal).
Added cycle
& override
parameters to axials_standard
& axpermute_standard
functions.
Altered simulation functions & KinPairSimulation
object to pass a model to the simulation object.
Added new tutorials to readme & vignettes for applying results to other species.
Vastly improved documentation of almost all functions
Implemented the 'DispersalModel' class and 'dispersal_model()' constructor function to enable descriptions of non-mosquito breeding & dispersal cycles. Implemented the 'simulate_kindist_custom()' function to enable simulation of custom breeding, dispersal & sampling cycled defined by 'DispersalModel' objects. Implemented the 'cycle' parameter in the above model object & simulation functions as well as 'axials_standard()' and 'axpermute_standard()' functions to enable the treatment of individuals collected at different (phased) stages of maturity. Adjusted various class & function definitions to make compatible with custom dispersal model objects & simulations (e.g. KinPairData, KinPairSimulation, df_to_kinpair()) Added generics & methods for accessing DispersalModel class objects (& the 'breeding_cycle' method for the KinPairData class)
Changed all occurrences of the 'gamma' kernelshape/method parameter value to 'vgamma' to make it clear we are using a variance-gamma distribution, not a gamma distribution. (effects simulation functions) Removed unused dispersal kernels (simulation functions) Changed simulation shape parameter default from 1 to 0.5.
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