plot.adaptProj {adapt3}R Documentation

Create Plot of Community Projection

Description

Function plot.adaptProj plots community projections.

Usage

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

Arguments

x

An adaptProj object.

repl

The replicate to plot. Defaults to 1, in which case the first replicate is 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_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().

Value

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

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")


[Package adapt3 version 1.0.1 Index]