R: Simulate and Estimate Close-Kin Dispersal Kernels

# Simulate and Estimate Close-Kin Dispersal Kernels

## Documentation for package ‘kindisperse’ version 0.10.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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