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 |
repl |
The replicate to plot. Defaults to |
auto_ylim |
A logical value indicating whether the maximum of the y axis
should be determined automatically. Defaults to |
auto_col |
A logical value indicating whether to shift the color of
lines associated with each patch automatically. Defaults to |
auto_lty |
A logical value indicating whether to shift the line type
associated with each replicate automatically. Defaults to |
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 |
... |
Other parameters used by functions |
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")