R: Formal class KinPairData

KinPairData-class {kindisperse}

R Documentation

Formal class KinPairData

Description

The class KinPairData is a formal (S4) class for storing kinship and lifespan dispersal information concerning kin pairs. It is the base class on which the KinPairSimulation class is built. The KinPairData class is used to store information about the spatial distribution of kin dyads for use in calculating axial sigmas of intergenerational dispersal as initially implemented in Jasper et al. 2019 (doi: 10.1111/1755-0998.13043).

Usage

## S4 method for signature 'KinPairData'
show(object)

## S4 method for signature 'KinPairData'
initialize(
  .Object,
  data = NULL,
  kinship = NULL,
  lifestage = NULL,
  cycle = NULL,
  ...
)

Arguments

`object`	an object of class KinpairData
`.Object`	the KinPairData object to be constructed
`data`	data about kinship to be used to construct object (tibble, data.frame, or numeric vector of distances)
`kinship`	character. Kinship category value for object. - one of PO, FS, HS, AV, HAV, GG, 1C, H1C, GAV, HGAV, 1C1, H1C1, GGG, 2C, and H2C.
`lifestage`	character. Lifestage value for object. - one of 'immature', 'ovipositional' or 'unknown'
`cycle`	non-negative integer or vector of two such integers - Represents the number of complete breeding cycles each simulated individual has undergone before the sampling point, where the time between birth and first reproduction is coded as '0', that between first and second reproduction '1', etc. (default 0). If the first individual was sampled as a juvenile & the second as an adult of equivalent stage, the vector c(0, 1) would be used. In most situations, defualt will be appropriate
`...`	additional argument to pass to downstream functions in future
`KinPairData`	object of class KinPairData

Details

This class is essentially wrapped around the tbl_df class but with (a) expectations around certain columns that must be present (id1, id2, kinship, & distance - three 'character' & one 'numeric' column), as well as (b) additional attributes (kinship, lifestage, & cycle) characterizing the close-kin dyads being stored.These attributes, as well as the embedded vector of distances, can be accessed with the methods kinship, lifestage, breeding_cycle and distances.

Objects from this class are returned from the df_to_kinpair and csv_to_kinpair functions (& related), and are directly constructed with the namesake KinPairData() function. They can be passed to the sample_kindist function for filtering and subsampling, and to axial functions (including axials_standard and axpermute_standard) for estimation of axial dispersal.

Value

returns object of class KinPairData

No return value, called for side effects

Returns an object of class KinPairData

Methods (by generic)

show: standard print method
initialize: initialize method

Slots

kinship: character - one of PO, FS, HS, AV, HAV, GG, 1C, H1C, GAV, HGAV, 1C1, H1C1, GGG, 2C, and H2C.
lifestage: character - lifestage at sampling - either 'immature', 'ovipositional' or a stage corresponding to a DispersalModel custom stage
cycle: non-negative integer or vector of two such integers - Represents the number of complete breeding cycles each individual has undergone before the sampling point, where the time between birth and first reproduction is coded as '0', that between first and second reproduction '1', etc. (default 0). If the first individual was sampled as a juvenile & the second as an adult of equivalent stage, the vector c(0, 1) would be used. In most situations, the default will be appropriate
tab: tbl_df. - tibble of dispersal values