summary.adaptInv {adapt3}R Documentation

Summarize adaptInv Objects

Description

Function summary.adaptInv() summarizes adaptInv objects.

Usage

## S3 method for class 'adaptInv'
summary(object, ...)

Arguments

object

An adaptInv object.

...

Other parameters currently not utilized.

Value

This function only produces text summarizing the numbers of variants, time steps, replicates, ESS optima, etc.

Examples

library(lefko3)
data(cypdata)

sizevector <- c(0, 0, 0, 0, 1, 2.5, 4.5, 8, 17.5)
stagevector <- c("SD", "P1", "SL", "D", "XSm", "Sm", "Md", "Lg", "XLg")
repvector <- c(0, 0, 0, 0, 1, 1, 1, 1, 1)
obsvector <- c(0, 0, 0, 0, 1, 1, 1, 1, 1)
matvector <- c(0, 0, 0, 1, 1, 1, 1, 1, 1)
immvector <- c(0, 1, 1, 0, 0, 0, 0, 0, 0)
propvector <- c(1, 0, 0, 0, 0, 0, 0, 0, 0)
indataset <- c(0, 0, 0, 1, 1, 1, 1, 1, 1)
binvec <- c(0, 0, 0, 0.5, 0.5, 1, 1, 2.5, 7)

cypframe_raw <- sf_create(sizes = sizevector, stagenames = stagevector,
  repstatus = repvector, obsstatus = obsvector, matstatus = matvector,
  propstatus = propvector, immstatus = immvector, indataset = indataset,
  binhalfwidth = binvec)

cypraw_v1 <- verticalize3(data = cypdata, noyears = 6, firstyear = 2004,
  patchidcol = "patch", individcol = "plantid", blocksize = 4,
  sizeacol = "Inf2.04", sizebcol = "Inf.04", sizeccol = "Veg.04",
  repstracol = "Inf.04", repstrbcol = "Inf2.04", fecacol = "Pod.04",
  stageassign = cypframe_raw, stagesize = "sizeadded", NAas0 = TRUE,
  NRasRep = TRUE)

cypsupp2r <- supplemental(stage3 = c("SD", "P1", "SL", "D", 
    "XSm", "Sm", "SD", "P1"),
  stage2 = c("SD", "SD", "P1", "SL", "SL", "SL", "rep",
    "rep"),
  eststage3 = c(NA, NA, NA, "D", "XSm", "Sm", NA, NA),
  eststage2 = c(NA, NA, NA, "XSm", "XSm", "XSm", NA, NA),
  givenrate = c(0.10, 0.40, 0.25, NA, NA, NA, NA, NA),
  multiplier = c(NA, NA, NA, NA, NA, NA, 1000, 1000),
  type =c(1, 1, 1, 1, 1, 1, 3, 3),
  stageframe = cypframe_raw, historical = FALSE)

cypmatrix2r <- rlefko2(data = cypraw_v1, stageframe = cypframe_raw, 
  year = "all", patch = "all", stages = c("stage3", "stage2", "stage1"),
  size = c("size3added", "size2added"), supplement = cypsupp2r,
  yearcol = "year2", patchcol = "patchid", indivcol = "individ")
cypmean <- lmean(cypmatrix2r)

cyp_start <- start_input(cypmean, stage2 = c("SD", "P1", "D"),
  value = c(1000, 200, 4))

c2d_4 <- density_input(cypmean, stage3 = c("P1", "P1"), stage2= c("SD", "rep"),
  style = 2, time_delay = 1, alpha = 0.005, beta = 0.000005, type = c(2, 2))

# A simple projection allows us to find a combination of density dependence
# and running time that produces a stable quasi-equilibrium
cyp_proj <- projection3(cypmean, times = 250, start_frame = cyp_start,
  density = c2d_4, integeronly = TRUE)
plot(cyp_proj)

cyp_ta <- trait_axis(stageframe = cypframe_raw,
  stage3 = rep("P1", 15),
  stage2 = rep("rep", 15),
  multiplier = seq(from = 0.1, to = 10.0, length.out = 15),
  type = rep(2, 15))

cyp_inv <- invade3(axis = cyp_ta, mpm = cypmean, density = c2d_4, times = 350,
  starts = cyp_start, entry_time = c(0, 250), fitness_times = 30,
  var_per_run = 2)
summary(cyp_inv)


[Package adapt3 version 1.0.1 Index]