adapt3 (version 2.0.0)

plot.adaptProj: Create Plot of Community Projection

Description

Function plot.adaptProj plots community projections.

Usage

# S3 method for adaptProj
plot(
  x,
  repl = 1,
  agg_only = FALSE,
  auto_ylim = TRUE,
  auto_col = TRUE,
  auto_lty = TRUE,
  auto_lwd = TRUE,
  auto_title = FALSE,
  ...
)

Value

A plot of the results of a project3() run.

Arguments

x

An adaptProj object.

repl

The replicate to plot. Defaults to 1, in which case the first replicate is plotted.

agg_only

A logical value indicating whether to plot only the aggregate community density. Defaults to FALSE, in which case population sizes of all constituent populations are also plotted.

auto_ylim

A logical value indicating whether the maximum of the y axis should be determined automatically. Defaults to TRUE, but reverts to FALSE if any setting for ylim is given.

auto_col

A logical value indicating whether to shift the color of lines associated with each patch automatically. Defaults to TRUE, but reverts to FALSE if any setting for col is given.

auto_lty

A logical value indicating whether to shift the line type associated with each replicate automatically. Defaults to TRUE, but reverts to FALSE if any setting for lty is given.

auto_lwd

A logical value indicating whether to shift the line width associated with each density trend automatically. Defaults to TRUE, but reverts to FALSE if any setting for lwd is given.

auto_title

A logical value indicating whether to add a title to each plot. The plot is composed of the concatenated population and patch names. Defaults to FALSE.

...

Other parameters used by functions plot.default() and lines().

Notes

Output plots are currently limited to time series of population size.

Examples

library(lefko3)
data(cypdata)

data(cypa_data)

sizevector <- c(0, 0, 0, 0, 0, 0, 1, 2.5, 4.5, 8, 17.5)
stagevector <- c("SD", "P1", "P2", "P3", "SL", "D", "XSm", "Sm", "Md", "Lg",
  "XLg")
repvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
obsvector <- c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
matvector <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
immvector <- c(0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0)
propvector <- c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
indataset <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
binvec <- c(0, 0, 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)

cycaraw_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)
  
cyparaw_v1 <- verticalize3(data = cypa_data, noyears = 18, firstyear = 1994,
  individcol = "plant_id", blocksize = 2, sizeacol = "Inf.94",
  sizebcol = "Veg.94", repstracol = "Inf.94", fecacol = "Inf.94",
  stageassign = cypframe_raw, stagesize = "sizeadded", NAas0 = TRUE,
  NRasRep = TRUE)

cypsupp2r <- supplemental(stage3 = c("SD", "P1", "P2", "P3", "SL", "D", 
    "XSm", "Sm", "SD", "P1"),
  stage2 = c("SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "rep",
    "rep"),
  eststage3 = c(NA, NA, NA, NA, NA, "D", "XSm", "Sm", NA, NA),
  eststage2 = c(NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", NA, NA),
  givenrate = c(0.10, 0.20, 0.20, 0.20, 0.25, NA, NA, NA, NA, NA),
  multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, 0.5, 0.5),
  type =c(1, 1, 1, 1, 1, 1, 1, 1, 3, 3),
  stageframe = cypframe_raw, historical = FALSE)
cyp_supp_list1 <- list(cypsupp2r, cypsupp2r)

cycamatrix2r <- rlefko2(data = cycaraw_v1, stageframe = cypframe_raw, 
  year = "all", stages = c("stage3", "stage2", "stage1"),
  size = c("size3added", "size2added"), supplement = cypsupp2r,
  yearcol = "year2", indivcol = "individ")

cypamatrix2r <- rlefko2(data = cyparaw_v1, stageframe = cypframe_raw, 
  year = "all", stages = c("stage3", "stage2", "stage1"),
  size = c("size3added", "size2added"), supplement = cypsupp2r,
  yearcol = "year2", indivcol = "individ")

cyp_mpm_list <- list(cycamatrix2r, cypamatrix2r)

cyca2_start <- start_input(cycamatrix2r, stage2 = c("SD", "P1", "P2"),
  value = c(500, 100, 200))
cypa2_start <- start_input(cypamatrix2r, stage2 = c("SD", "P1", "P2"),
  value = c(5000, 1000, 2000))
cyp_start_list <- list(cyca2_start, cypa2_start)

cyp2_dv <- density_input(cypamatrix2r, stage3 = c("SD", "P1"),
  stage2 = c("rep", "rep"), style = c(1, 1), alpha = c(0.5, 1.2),
  beta = c(1.0, 2.0), type = c(2, 1))
cyp_dv_list <- list(cyp2_dv, cyp2_dv)

cyp_comm_proj <- project3(mpms = cyp_mpm_list, starts = cyp_start_list,
  density = cyp_dv_list, times = 10)

plot(cyp_comm_proj, lwd = 2, bty = "n")