Simulate and Estimate Close-Kin Dispersal Kernels
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Documentation for package ‘kindisperse’ version 0.10.2
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A B C D E F G H I K L M O P R S T U V W
-- A --
| access_sigmas | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
| axials | Estimate the axial dispersal distance of a kernel |
| axials_add | Add axial distributions |
| axials_combine | Combine axial distributions to produce a mixed distribution |
| axials_decompose | Decompose an axial distribution into simple components |
| axials_standard | Calculate the intergenerational (PO) dispersal kernel from the distributions of close kin |
| axials_subtract | Subtract axial distributions |
| axpermute | Estimate the axial dispersal distance of a kernel with confidence intervals |
| axpermute_standard | Calculate the intergenerational (PO) dispersal kernel from the distributions of close kin (bootstrapped) |
| axpermute_subtract | Subtract axial distributions with confidence intervals |
-- B --
| breeding_cycle | Access breeding cycle at sampling of 'DispersalModel' object. |
| breeding_cycle-method | Access breeding cycle at sampling of 'DispersalModel' object. |
| breeding_stage | Access life stage at which breeding occurs of 'DispersalModel' object |
| breeding_stage-method | Access life stage at which breeding occurs of 'DispersalModel' object |
| breedsigma | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
| breedsigma-method | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
| breedsigma<- | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
-- C --
| check_valid_kinship | Check valid kinship |
| check_valid_lifestage | Check valid lifestage |
| csv_to_kinpair | Reads '.csv' and converts to 'KinPairData' object |
-- D --
| df_to_kinpair | Convert dataframe or tibble to 'KinPairData' class |
| DispersalModel | DispersalModel Class |
| DispersalModel-class | DispersalModel Class |
| dispersal_model | Create Dispersal Model of an Organism |
| dispersal_vector | Access dispersal vector of 'DispersalModel' object. |
| dispersal_vector-method | Access dispersal vector of 'DispersalModel' object. |
| display_appdata | Show printout of named items stored in appdata. |
| distances | Access or assign 'distances' category of 'KinPairData' class objects |
| distances-method | Access or assign 'distances' category of 'KinPairData' class objects |
-- E --
| elongate | Change the shape (aspect ratio) of a rectangle while preserving area |
-- F --
| filtertype | Access filtertype of 'KinPairSimulation' object |
| filtertype-method | Access filtertype of 'KinPairSimulation' object |
| filtertype<- | Access filtertype of 'KinPairSimulation' object |
| filter_methods | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| fs | Access FS phase split point of 'DispersalModel' object. |
| fs-method | Access FS phase split point of 'DispersalModel' object. |
-- G --
| get_dispersal_model | Access dispersal model of 'KinPairSimulation' object |
| get_dispersal_model-method | Access dispersal model of 'KinPairSimulation' object |
| gravsigma | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
| gravsigma-method | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
| gravsigma<- | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
-- H --
| hs | Access HS phase split point of 'DispersalModel' object. |
| hs-method | Access HS phase split point of 'DispersalModel' object. |
-- I --
| initialize-method | DispersalModel Class |
| initialize-method | Formal class KinPairData |
| initialize-method | KinPairSimulation Class |
| initsigma | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
| initsigma-method | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
| initsigma<- | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
| is.DispersalModel | Check if object is of class 'DispersalModel' |
| is.KinPairData | Check if object is of class KinPairData |
| is.KinPairSimulation | Check if object is of class KinPairSimulation |
-- K --
| kernelshape | Access kernel type of 'KinPairSimulation' object |
| kernelshape-method | Access kernel type of 'KinPairSimulation' object |
| kerneltype | Access or assign kerneltype of 'KinPairSimulation' object |
| kerneltype-method | Access or assign kerneltype of 'KinPairSimulation' object |
| kerneltype<- | Access or assign kerneltype of 'KinPairSimulation' object |
| KinPairData | Formal class KinPairData |
| KinPairData-class | Formal class KinPairData |
| KinPairSimulation | KinPairSimulation Class |
| KinPairSimulation-class | KinPairSimulation Class |
| KinPairSimulation_composite | Constructor for KinPairSimulation Class (composite) |
| KinPairSimulation_custom | Constructor for KinPairSimulation Class (custom) |
| KinPairSimulation_simple | Constructor for KinPairSimulation Class (simple) |
| kinpair_to_csv | Write 'KinPairData' object to '.csv' format |
| kinpair_to_tibble | Extract KinPairData class object to tibble |
| kinpair_to_tsv | Write 'KinPairData' object to '.tsv' format |
| kinship | Access or assign 'kinship' category of 'KinPairData' class objects |
| kinship-method | Access or assign 'kinship' category of 'KinPairData' class objects |
| kinship<- | Access or assign 'kinship' category of 'KinPairData' class objects |
| kinship<--method | Access or assign 'kinship' category of 'KinPairData' class objects |
| kin_pair_data | Make new KinPairData object |
| kin_pair_simulation | KinPairSimulation |
-- L --
| lifestage | Access or assign 'lifestage' category of 'KinPairData' class objects |
| lifestage-method | Access or assign 'lifestage' category of 'KinPairData' class objects |
| lifestage<- | Access or assign 'lifestage' category of 'KinPairData' class objects |
| lifestage<--method | Access or assign 'lifestage' category of 'KinPairData' class objects |
| lower | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| lower-method | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| lower<- | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| lower<--method | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
-- M --
| mentari | Position & kinship information of _Aedes aegypti_ from Mentari Court, Malaysia |
| mount_appdata | Mount 'KinPairData' Objects for use in kindisperse app |
-- O --
| ovisigma | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
| ovisigma-method | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
| ovisigma<- | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
-- P --
| posigma | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
| posigma-method | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
| posigma<- | Access or assign dispersal sigmas of 'KinPairSimulation' objects |
-- R --
| read_kindata | Reads '.kindata' filetype back to 'KinPairData' or 'KinPairSimulation' object. |
| rebase_dims | Change the dimensions of a KinPairSimulation Object and shift kinpairs so at least one individual is within the area |
| reset_appdata | Reset kindisperse appdata |
| reset_tempdata | Reset app tempdata (internal mem) |
| retrieveall_appdata | Retrieve all 'KinPairData' objects from appdata (as list) |
| retrieve_appdata | Retrieve 'KinPairData' object from appdata (single) |
| retrieve_tempdata | Retrieve all tempdata (internal mem) from app (as list) |
| run_kindisperse | Run kindisperse app |
-- S --
| sampledims | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| sampledims-method | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| sampledims<- | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| sampledims<--method | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| samplenum | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| samplenum-method | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| samplenum<- | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| samplenum<--method | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| sample_kindist | Subsample and filter a 'KinPairSimulation' or 'KinPairData' Object |
| sampling_stage | Access sampling stage of 'DispersalModel' or 'KinPairSimulation' object. |
| sampling_stage-method | Access sampling stage of 'DispersalModel' or 'KinPairSimulation' object. |
| sampling_stage<- | Access sampling stage of 'DispersalModel' or 'KinPairSimulation' object. |
| sampling_stage<--method | Access sampling stage of 'DispersalModel' or 'KinPairSimulation' object. |
| show-method | DispersalModel Class |
| show-method | Formal class KinPairData |
| show-method | KinPairSimulation Class |
| simdims | Access simulation dimensions of 'KinPairSimulation' object |
| simdims-method | Access simulation dimensions of 'KinPairSimulation' object |
| simdims<- | Access simulation dimensions of 'KinPairSimulation' object |
| simgraph_data | Simple kin dispersal simulation for graphical display. (returns the data side as a tibble). |
| simgraph_graph | Simple kin dispersal simulation for graphical display. (graphs the pre-existing simulation). |
| simtype | Access or assign simulation type of 'KinPairSimulation' object |
| simtype-method | Access or assign simulation type of 'KinPairSimulation' object |
| simtype<- | Access or assign simulation type of 'KinPairSimulation' object |
| simulate_kindist_composite | Simulate kin dispersal distance pairs with composite sigmas |
| simulate_kindist_custom | Simulate kin dispersal distance pairs with custom species dispersal models. |
| simulate_kindist_simple | Simulate kin dispersal distance pairs with simple sigma |
| spacing | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| spacing-method | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| spacing<- | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| spacing<--method | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| stages | Access breeding cycle stages of 'DispersalModel' object. |
| stages-method | Access breeding cycle stages of 'DispersalModel' object. |
-- T --
| tsv_to_kinpair | Reads '.tsv' and converts to 'KinPairData' object |
-- U --
| unmount_appdata | Unmount a 'KinPairData' Object (clear slot from appdata environment) |
| upper | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| upper-method | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| upper<- | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
| upper<--method | Access or modify the 'filter' parameters of 'KinPairSimulation' objects |
-- V --
| vector_to_kinpair | Convert vector of kin separation distances to 'KinPairData' class |
| visible_stage | Access life stage at which individual is first visible to sampling (i.e. from which breeding cycles are calculated) |
| visible_stage-method | Access life stage at which individual is first visible to sampling (i.e. from which breeding cycles are calculated) |
-- W --
| write_kindata | Write 'KinPairData' or 'KinPairSimulation' object in '.kindata' format |