initialise_inds: Initialise individuals
In resevol: Simulate Agricultural Production and Evolution of Pesticide Resistance

initialise_inds

R Documentation

Initialise individuals

Description

Initialise new individuals into the IBM. This function is generally not needed because it is run inside the run_farm_sim function to generate new individuals for simulations. To initialise individuals with this function, it is necessary to set the mine_output argument to output from the mine_gmatrix function. This output includes all of the information necessary to build individuals with genomes that produce traits that covary in a pre-specified way. The arguments of this function include addition information for building the individual array, which is a two-dimensional array in which each individual occupies a row, and each column specifies a character of the individual (including all genome loci). See vignettes for a more detailed explanation.

Usage

initialise_inds(
  mine_output,
  N = 1000,
  xdim = 100,
  ydim = 100,
  repro = "sexual",
  neutral_loci = 10,
  max_age = 9,
  min_age_move = 0,
  max_age_move = 9,
  min_age_reproduce = 0,
  max_age_reproduce = 9,
  min_age_feed = 0,
  max_age_feed = 9,
  food_consume = 0.25,
  pesticide_consume = 0.1,
  rand_age = FALSE,
  move_distance = 1,
  food_needed_surv = 0.25,
  pesticide_tolerated_surv = 0.1,
  food_needed_repr = 0,
  pesticide_tolerated_repr = 0,
  reproduction_type = "lambda",
  mating_distance = 1,
  lambda_value = 1,
  movement_bouts = 1,
  selfing = TRUE,
  feed_while_moving = FALSE,
  pesticide_while_moving = FALSE,
  mortality_type = 0,
  age_food_threshold = NA,
  age_pesticide_threshold = NA,
  metabolism = 0,
  baseline_metabolism = 0,
  min_age_metabolism = 1,
  max_age_metabolism = 9
)

Arguments

`mine_output`	The output from mine_gmatrix
`N`	Number of individuals to be initialised
`xdim`	Horizontal dimensions of the landscape
`ydim`	Vertical dimensions of the landscape
`repro`	Type of reproduction allowed: "asexual", "sexual", and "biparental". Note that if repro != "asexual", this causes a diploid genome.
`neutral_loci`	The number of neutral loci individuals have (must be > 0)
`max_age`	The maximum age of an individual
`min_age_move`	The minimum age at which an individual can move
`max_age_move`	The maximum age at which an individual can move
`min_age_reproduce`	The minimum age which an individual can reproduce
`max_age_reproduce`	The maximum age which an individual can reproduce
`min_age_feed`	The minimum age at which an individual feeds
`max_age_feed`	The maximum age at which an individual feeds
`food_consume`	The amount of food consumed during feeding
`pesticide_consume`	Amount of pesticide consumed while on a cell
`rand_age`	Initialise individuals with a random age (TRUE/FALSE)
`move_distance`	Maximum cells moved in one bout of movement
`food_needed_surv`	Food needed to survive (if over min_age_feed)
`pesticide_tolerated_surv`	Pesticide tolerated by individual
`food_needed_repr`	Food needed to reproduce 1 offspring
`pesticide_tolerated_repr`	Pesticide tolerated to allow reproduction
`reproduction_type`	Poisson reproduction ("lambda") vs "food_based"
`mating_distance`	Distance in cells within which mate is available
`lambda_value`	individual value for poisson reproduction
`movement_bouts`	Number of bouts of movement per time step
`selfing`	If sexual reproduction, is selfing allowed? (TRUE/FALSE)
`feed_while_moving`	Do individuals feed after each movement bout?
`pesticide_while_moving`	Individuals consume pesticide after move bout?
`mortality_type`	Type of mortality (currently only one option)
`age_food_threshold`	Age at which food threshold is enacted
`age_pesticide_threshold`	Age at which pesticide threshold is enacted
`metabolism`	The amount of consumed food lost each time step
`baseline_metabolism`	A fixed baseline rate added to 'metabolism'+
`min_age_metabolism`	The minimum age affected by metabolism
`max_age_metabolism`	The maximum age affected by metabolism

Value

A two-dimensional array of individuals for simulation

Examples

gmt       <- matrix(data = 0, nrow = 2, ncol = 2);
diag(gmt) <- 1;
mg        <- mine_gmatrix(gmatrix = gmt, loci = 4, layers = 2, indivs = 100, 
                         npsize = 100, max_gen = 4, prnt_out = FALSE);
inds      <- initialise_inds(mine_output = mg, N = 40, repro = "asexual");

resevol documentation built on July 13, 2022, 5:06 p.m.