clonal_line: Organize clonal line information
In lucasnell/clonewars: Clonal Evolution in Aphid Metapopulations

clonal_line

R Documentation

Organize clonal line information

Description

To smooth stage structure out over time, not all 4th instar aphids move to adulthood immediately. If adulthood starts on day t, then half of aphids at age t-2 move to adulthood, and half at age t-1 do, too. I adjusted age t-2, too, to avoid this affecting the growth rate too much.

Usage

clonal_line(
  name,
  density_0,
  resistant = FALSE,
  mumm_prop = NULL,
  surv_juv_apterous = NULL,
  surv_adult_apterous = NULL,
  repro_apterous = NULL,
  surv_juv_alates = "low",
  surv_adult_alates = "low",
  repro_alates = "low",
  surv_paras = "low",
  temp = "low",
  p_instar_smooth = 0.5
)

Arguments

`name`	String for clonal line name.
`density_0`	A single number or 2-column matrix indicating starting aphid densities for each field. Aphids are equally distributed among plants if simulating multiple plants per field. If a number, there will be no starting alates and a total apterous density equal to the number provided. Stages will be calculated based on the stable age distribution. If a matrix, it must have 5 rows (rows indicate instar) or a row per aphid age (rows indicate age in days). Matrix column indicates apterous vs alate.
`resistant`	Logical or vector of survivals of singly attacked and multiply attacked aphids. If a logical, `FALSE` is equivalent to `c(0,0)` and results in no resistance. `TRUE` results in the resistance values for a resistance line from unpublished work by Anthony Ives. Defaults to `FALSE`.
`mumm_prop`	Vector of probabilities of singly attacked and multiply attacked aphids being successfully parasitized. Defaults to `NULL`, which results in being equal to `1 - resistant`.
`surv_juv_apterous`	A single number for the juvenile survival rate for apterous aphids. Defaults to `NULL`, which results in estimates from a medium-reproduction line.
`surv_adult_apterous`	A vector of adult survival probabilities for apterous aphids. Defaults to `NULL`, which results in estimates from a medium-reproduction line.
`repro_apterous`	A vector of fecundities for for apterous aphids. Defaults to `NULL`, which results in estimates from a medium-reproduction line.
`surv_juv_alates`	A single number for the juvenile survival rate for alates aphids. Defaults to `"low"`, which results in estimates from a low-reproduction line.
`surv_adult_alates`	A vector of adult survival probabilities for alates aphids. Defaults to `"low"`, which results in estimates from a low-reproduction line.
`repro_alates`	A vector of fecundities for for alates aphids. Defaults to `"low"`, which results in estimates from a low-reproduction line.
`surv_paras`	A single number for the juvenile survival rate for parasitized aphids. Because parasitized aphids don't make it to adulthood, this is the only survival rate necessary. Defaults to `"low"`, which results in estimates from a low-reproduction line.
`temp`	Single string specifying `"low"` (20º C) or `"high"` (27º C) temperature. Defaults to `"low"`.
`p_instar_smooth`	A value greater than zero here makes not all 4th instar aphids go to the adult stage at the same time. Of the 4th instars that would've moved to adulthood, `p_instar_smooth` remain as 4th instars. To keep the growth rate approximately equal, for the aphids that would've transitioned to 4th instar, `p_instar_smooth` move to adulthood instead. Defaults to `0.5`.