summary.lefkoElas: Summarize lefkoElas Objects

In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

Summarize lefkoElas Objects

Description

Function summary.lefkoElas() summarizes lefkoElas objects. Particularly, it breaks down elasticity values by the kind of ahistorical and, if applicable, historical transition.

Usage

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

Arguments

object	A lefkoElas object.
...	Other parameters currently not utilized.

Value

A list composed of 2 data frames. The first, hist, is a data frame showing the summed elasticities for all 16 kinds of historical transition per matrix, with each column corresponding to each elasticity matrix in order. The second, ahist, is a data frame showing the summed elasticities for all 4 kinds of ahistorical transition per matrix, with each column corresponding to each elasticity matrix in order.

Examples

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)

lathsupp3 <- supplemental(stage3 = c("Sd", "Sd", "Sdl", "Sdl", "Sd", "Sdl", "mat"),
  stage2 = c("Sd", "Sd", "Sd", "Sd", "rep", "rep", "Sdl"),
  stage1 = c("Sd", "rep", "Sd", "rep", "npr", "npr", "Sd"),
  eststage3 = c(NA, NA, NA, NA, NA, NA, "mat"),
  eststage2 = c(NA, NA, NA, NA, NA, NA, "Sdl"),
  eststage1 = c(NA, NA, NA, NA, NA, NA, "NotAlive"),
  givenrate = c(0.345, 0.345, 0.054, 0.054, NA, NA, NA),
  multiplier = c(NA, NA, NA, NA, 0.345, 0.054, NA),
  type = c(1, 1, 1, 1, 3, 3, 1), type_t12 = c(1, 2, 1, 2, 1, 1, 1),
  stageframe = lathframe, historical = TRUE)

lathsupp2 <- supplemental(stage3 = c("Sd", "Sdl", "Sd", "Sdl"), 
  stage2 = c("Sd", "Sd", "rep", "rep"),
  givenrate = c(0.345, 0.054, NA, NA),
  multiplier = c(NA, NA, 0.345, 0.054),
  type = c(1, 1, 3, 3), stageframe = lathframe, historical = FALSE)
  
ehrlen3 <- rlefko3(data = lathvert, stageframe = lathframe, year = "all", 
  stages = c("stage3", "stage2", "stage1"), supplement = lathsupp3,
  yearcol = "year2", indivcol = "individ")

ehrlen2 <- rlefko2(data = lathvert, stageframe = lathframe, year = "all",
  stages = c("stage3", "stage2"), supplement = lathsupp2,
  yearcol = "year2", indivcol = "individ")

ehrlen3elas <- elasticity3(ehrlen3)
ehrlen2elas <- elasticity3(ehrlen2)

summary(ehrlen3elas)
summary(ehrlen2elas)

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