NEWS.md

In moshejasper/kindisperse: Simulate and Estimate Close-Kin Dispersal Kernels

kindisperse 0.10.1

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

kindisperse 0.10.0

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)

kindisperse 0.9.2

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.

kindisperse 0.9.1

• Added a NEWS.md file to track changes to the package.
• Fixed several display and layout issues in Shiny app
• Changed parameter of 'elongate' function from 'shape' to 'aspect' to make clear we are manipulating aspect ratios of a rectangular area.

kindisperse 0.9.0

• Permutation functions now output mean instead of median
• Changed all 'dsigma' parameters & references to 'posigma'
• Changed simulation 'method' parameter input from 'Gamma' to 'gamma'
• Changed 'lifestage' parameter values from 'larva' to 'immature' and from 'oviposition' to 'ovipositional'
• Enable package function messages to be suppressed
• Updated app tutorial and documentation (including vignettes)
• Updated KinPairSimulation '<-sampledim' method
• Added Table of Contents to README

kindisperse 0.8.0

• Added Mentari Court field data for example calculations
• Added 2d rectangular dimensions to simulate & sample functions
• Changed the way 'sample_kindist' deals with dimensions
• Added helper function 'elongate' for dimension handling
• Changed 'composite' default parameter value from 2 to 1 in function 'axpermute'
• Changed 'juvsigma' parameter & references to 'initsigma' in line with usage in paper
• included rgamma function
• Improved simgraph commands (simgraph_data, simgraph_graph)
• Cleaned up app
• Removed unneeded class methods (to_tibble). Fixed kernelshape method
• Improved package load
• Updated app interface
• Updated documentation (CRAN compatibility)

kindisperse 0.7.0

• Added options to import data from files within app
• Updated readme, package startup & vignettes
• Added gamma kernel with shape parameter to simulations

kindisperse 0.6.0

• Changed 'category' parameter in all functions and classed to 'kinship' parameter
• Added file writing and reading functions (write_kindata, read_kindata, kinpair_to_tsv, tsv_to_kinpair, kinpair_to_csv, csv_to_kinpair, kinpair_to_tibble)
• Added appdata interface environment & functions to access it (mount_appdata, unmount_appdata, display_appdata, reset_appdata, retrive_appdata)
• Enable loading of appdata into app (functions and interface)
• Improved KinPairSimulation object print function

kindisperse 0.5.0

• Replaced file-based memory storage with environment storage in app
• Added 'distances' method for KinPairData & KinPairSimulation classes
• Added functions to test class membership
• Updated axial functions to take KinPairData &c classes as input
• Limit sample size in axial permuation functions under 'std' option
• Updated class definitions
• Added class constructor functions
• Added class import functions
• Updated dependencies

kindisperse 0.4.0

• Introduced KinPairData & KinpairSimulation classes
• Added and updated class methods & documentation
• Updated app with axial functions
• Fixed bug in 'axials_decompose' function

kindisperse 0.3.0

• improved NAMESPACE
• add axial function
• document many functions

kindisperse 0.2.0

• added temp folder & contents to fix app bug
• removed broken dependencies

kindisperse 0.1.0 & prior

• initial commit

moshejasper/kindisperse documentation built on Oct. 25, 2024, 2:57 a.m.