Simulate and Estimate Close-Kin Dispersal Kernels

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Documentation for package ‘kindisperse’ version 0.9.2

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A B C D E F G I K L M O P R S T U V W

-- A --

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 Takes (at least) two vectors of kinship dispersal distances from defined kinship categories, and returns a resulting calculation of the parent-offspring (intergenerational) kinship dispersal kernel Further tests
axials_subtract Subtract axial distributions
axpermute Estimate the axial dispersal distance of a kernel with confidence intervals
axpermute_standard Takes (at least) two vectors of kinship dispersal distances from defined kinship categories, and returns a resulting calculation of the parent-offspring (intergenerational) kinship dispersal kernel with bootstrap-based confidence intervals. Further tests
axpermute_subtract Subtract axial distributions with confidence intervals

-- B --

breedsigma kindisperse - access sigmas of KinPairSimulation objects
breedsigma-method )
breedsigma<- Title

-- C --

check_valid_kinship Check if vector of kinship categories contains all valid entries
check_valid_lifestage Check if vector of lifestages contains all valid entries
csv_to_kinpair Reads .csv and converts to KinPairData object

-- D --

df_to_kinpair Convert dataframe or tibble to KinPairData class
display_appdata Show printout of named items stored in appdata.
distances Access distances (generic for KinPairData class)
distances-method Constructor method for 'KinPairData' objects.

-- E --

elongate Change the shape (aspect ratio) of a rectangle while preserving area

-- F --

filtertype Access filter type of KinPairSimulation object
filtertype-method )
filtertype<- Title

-- G --

gravsigma kindisperse - access sigmas of KinPairSimulation objects
gravsigma-method )
gravsigma<- Title

-- I --

initialize-method Constructor method for 'KinPairData' objects.
initialize-method )
initsigma kindisperse - access sigmas of KinPairSimulation objects
initsigma-method )
initsigma<- Title
is.KinPairData Check if object is of class KinPairData
is.KinPairSimulation Check if object is of class KinPairSimulation

-- K --

kernelshape kindisperse - access kerneltype of KinPairSimulation object
kernelshape-method )
kerneltype kindisperse - access kerneltype of KinPairSimulation object
kerneltype-method )
kerneltype<- Title
KinPairData Formal class "KinPairData"
KinPairSimulation KinPairSimulation Class
KinPairSimulation_composite Constructor for KinPairSimulation Class (composite)
KinPairSimulation_simple Constructor for KinPairSimulation Class (simple)
kinpair_to_csv Write KinPairData object in .csv format (strips extra data)
kinpair_to_tibble Extract KinPairData class object to tibble
kinpair_to_tsv Write KinPairData object in .tsv format (strips extra data)
kinship Access or assign kin category (generic for KinPairData class)
kinship-method Constructor method for 'KinPairData' objects.
kinship<- Access or assign kin category (generic for KinPairData class)
kinship<--method Constructor method for 'KinPairData' objects.

-- L --

lifestage Access or assign lifestage (generic for KinPairData class)
lifestage-method Constructor method for 'KinPairData' objects.
lifestage<- Access or assign lifestage (generic for KinPairData class)
lifestage<--method Constructor method for 'KinPairData' objects.
lower Access & filter by filter parameters of KinPairSimulation Object
lower-method )
lower<- Access & filter by filter parameters of KinPairSimulation Object
lower<--method )

-- M --

mentari Position & kinship information of _Aedes aegypti_ from Mentari Court, Malaysia
mount_appdata Mount KinPairData Objects for use in kindisperse app

-- O --

ovisigma kindisperse - access sigmas of KinPairSimulation objects
ovisigma-method )
ovisigma<- Title

-- P --

posigma kindisperse - access sigmas of KinPairSimulation objects
posigma-method )
posigma<- Title

-- 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 & filter by filter parameters of KinPairSimulation Object
sampledims-method )
sampledims<- Access & filter by filter parameters of KinPairSimulation Object
sampledims<--method )
samplenum Access & filter by filter parameters of KinPairSimulation Object
samplenum-method )
samplenum<- Access & filter by filter parameters of KinPairSimulation Object
samplenum<--method )
sample_kindist Subsample and filter a KinPairSimulation Object
show-method Constructor method for 'KinPairData' objects.
show-method )
simdims Access simulation dimensions of KinPairSimulation object
simdims-method )
simdims<- Title
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 kindisperse - access simtype of KinPairSimulation object
simtype-method )
simtype<- Title
simulate_kindist_composite Simulate kin dispersal distance pairs with composite sigmas
simulate_kindist_simple Simulate kin dispersal distance pairs with simple sigma
spacing Access & filter by filter parameters of KinPairSimulation Object
spacing-method )
spacing<- Access & filter by filter parameters of KinPairSimulation Object
spacing<--method )

-- 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 & filter by filter parameters of KinPairSimulation Object
upper-method )
upper<- Access & filter by filter parameters of KinPairSimulation Object
upper<--method )

-- V --

vector_to_kinpair Convert vector of kin separation distances to KinPairData class

-- W --

write_kindata Write KinPairData or KinPairSimulation object in .kindata format (no information lost)