summary.lefkoProj: Summarize lefkoProj Objects

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Summarize lefkoProj Objects

Description

Function summary.lefkoProj() summarizes lefkoProj objects. Particularly, it breaks down the data frames provided in the projection element in ways meaningful for those running simulations.

Usage

## S3 method for class 'lefkoProj'
summary(
  object,
  threshold = 1,
  inf_alive = TRUE,
  milepost = c(0, 0.25, 0.5, 0.75, 1),
  ext_time = FALSE,
  ...
)

Arguments

object	A lefkoProj object.
threshold	A threshold population size to be searched for in projections. Defaults to 1.
inf_alive	A logical value indicating whether to treat infinitely large population size as indicating that the population is still extant. If FALSE, then the population is considered extinct. Defaults to TRUE.
milepost	A numeric vector indicating at which points in the projection to assess detailed results. Can be input as integer values, in which case each number must be between 1 and the total number of occasions projected in each projection, or decimals between 0 and 1, which would then be translated into the corresponding projection steps of the total. Defaults to c(0, 0.25, 0.50, 0.75, 1.00).
ext_time	A logical value indicating whether to output extinction times per population-patch. Defaults to FALSE.
...	Other parameters currently not utilized.

Value

Apart from a statement of the results, this function outputs a list with the following elements:

milepost_sums	A data frame showing the number of replicates at each of the milepost times that is above the threshold population/patch size.
extinction_times	A dataframe showing the numbers of replicates going extinct (ext_reps) and mean extinction time (ext_time) per population-patch. If ext_time = FALSE, then only outputs NA.

Notes

The inf_alive option assesses whether replicates have reached a value of NaN. If inf_alive = TRUE and a value of NaN is found, then the replicate is considered extant if the preceding value is above the extinction threshold. If the setting is inf_alive = FALSE, then a value of NaN is considered evidence of extinction.

Extinction time is calculated on the basis of whether the replicate ever falls below a single individual. A replicate with a positive population size below 0.0 that manages to rise above 1.0 individual is still considered to have gone extinct the first time it crossed below 1.0.

Examples

# Lathyrus example
data(lathyrus)

sizevector <- c(0, 100, 13, 127, 3730, 3800, 0)
stagevector <- c("Sd", "Sdl", "VSm", "Sm", "VLa", "Flo", "Dorm")
repvector <- c(0, 0, 0, 0, 0, 1, 0)
obsvector <- c(0, 1, 1, 1, 1, 1, 0)
matvector <- c(0, 0, 1, 1, 1, 1, 1)
immvector <- c(1, 1, 0, 0, 0, 0, 0)
propvector <- c(1, 0, 0, 0, 0, 0, 0)
indataset <- c(0, 1, 1, 1, 1, 1, 1)
binvec <- c(0, 100, 11, 103, 3500, 3800, 0.5)

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

lathvert <- verticalize3(lathyrus, noyears = 4, firstyear = 1988,
  patchidcol = "SUBPLOT", individcol = "GENET", blocksize = 9,
  juvcol = "Seedling1988", sizeacol = "Volume88", repstracol = "FCODE88",
  fecacol = "Intactseed88", deadacol = "Dead1988",
  nonobsacol = "Dormant1988", stageassign = lathframe, stagesize = "sizea",
  censorcol = "Missing1988", censorkeep = NA, censor = TRUE)

lathrepm <- matrix(0, 7, 7)
lathrepm[1, 6] <- 0.345
lathrepm[2, 6] <- 0.054

lathsupp3 <- supplemental(stage3 = c("Sd", "Sd", "Sdl", "Sdl", "Sd", "Sdl"), 
  stage2 = c("Sd", "Sd", "Sd", "Sd", "rep", "rep"),
  stage1 = c("Sd", "rep", "Sd", "rep", "all", "all"), 
  givenrate = c(0.345, 0.345, 0.054, 0.054, NA, NA),
  multiplier = c(NA, NA, NA, NA, 0.345, 0.054),
  type = c(1, 1, 1, 1, 3, 3), type_t12 = c(1, 2, 1, 2, 1, 1),
  stageframe = lathframe, historical = TRUE)

ehrlen3 <- rlefko3(data = lathvert, stageframe = lathframe,
  year = c(1989, 1990), stages = c("stage3", "stage2", "stage1"),
  repmatrix = lathrepm, supplement = lathsupp3, yearcol = "year2",
  indivcol = "individ")

lathproj <- projection3(ehrlen3, nreps = 5, stochastic = TRUE)
summary(lathproj)

# Cypripedium example
data(cypdata)
 
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)

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)

cypsupp3r <- supplemental(stage3 = c("SD", "SD", "P1", "P1", "P2", "P3", "SL",
    "D", "XSm", "Sm", "D", "XSm", "Sm", "mat", "mat", "mat", "SD", "P1"),
  stage2 = c("SD", "SD", "SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "SL",
    "SL", "SL", "D", "XSm", "Sm", "rep", "rep"),
  stage1 = c("SD", "rep", "SD", "rep", "SD", "P1", "P2", "P3", "P3", "P3",
    "SL", "SL", "SL", "SL", "SL", "SL", "mat", "mat"),
  eststage3 = c(NA, NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm", "D", "XSm", "Sm",
    "mat", "mat", "mat", NA, NA),
  eststage2 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
    "XSm", "D", "XSm", "Sm", NA, NA),
  eststage1 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
    "XSm", "XSm", "XSm", "XSm", NA, NA),
  givenrate = c(0.1, 0.1, 0.2, 0.2, 0.2, 0.2, 0.25, NA, NA, NA, NA, NA, NA,
    NA, NA, NA, NA, NA),
  multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
    NA, 0.5, 0.5),
  type = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3),
  type_t12 = c(1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
  stageframe = cypframe_raw, historical = TRUE)

cypmatrix3r <- rlefko3(data = cypraw_v1, stageframe = cypframe_raw, 
  year = "all", patch = "all", stages = c("stage3", "stage2", "stage1"),
  size = c("size3added", "size2added", "size1added"), 
  supplement = cypsupp3r, yearcol = "year2", 
  patchcol = "patchid", indivcol = "individ")

cypstoch <- projection3(cypmatrix3r, nreps = 5, stochastic = TRUE)
summary(cypstoch, ext_time = TRUE)

lefko3 documentation built on Oct. 14, 2023, 1:07 a.m.