summary.lefkoLTRE: Summarize lefkoLTRE Objects

Description Usage Arguments Value Examples

View source: R/popdyn.R

Description

Function summary.lefkoLTRE() summarizes lefkoLTRE objects. Particularly, it breaks down LTRE contributions by the kind of ahistorical and, if applicable, historical transition.

Usage

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

Arguments

object

A lefkoLTRE object.

...

Other parameters.

Value

A list composed of 2 (if deterministic) or 4 (if stochastic) data frames. If deterministic, then hist_det is a data frame showing the summed LTRE contributions for all 16 kinds of historical transition per matrix, with each column corresponding to each A matrix in order, followed by all summed positive and all summed negative contributions. Object ahist_det is a data frame showing the summed LTRE contributions for all 4 kinds of ahistorical transition per matrix, with order as before, followed by summed positive and summed negative contributions. If stochastic, then hist_mean and hist_sd are the summed LTRE contributions for the mean vital rates and variability in vital rates, respectively, according to all 16 historical transition types, followed by summed positive and negative contributions, and ahist_mean and ahist_sd are the equivalent ahistorical versions.

Examples

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# 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)

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")

ehrlen3ltre <- ltre3(ehrlen3)
summary(ehrlen3ltre)

lefko3 documentation built on Sept. 8, 2021, 9:07 a.m.