pyrola: Demographic Dataset of Pyrola japonica and Pyrola subaphylla Populations, in Horizontal Format

Description

A dataset containing the states and fates of Pyrola japonica and Pyrola subaphylla, family Ericaceae, from populations in the vicinity of Mt. Bandai, Fukushima Prefecture, Japan, resulting from monitoring that occurred annually between 2015 and 2020.

Usage

data(pyrola)

Arguments

Format

A data frame with 454 individuals and 57 variables. Each row corresponds to an unique individual, and each variable from sprouted.2015 on refers to the state of the individual in a particular year.

species: String denoting which of the two species the individual belongs to.
population: Integer denoting whcih population the individual belongs to. Synonymous with species in this dataset.
id: A numeric variable giving a unique number to each individual within each species. Note that numbers are reused among the two species.
sprouted.2015: A binomial indicating whether the individual had living aboveground tissue observable in the 2015 census.
lvs.num.2015: Number of leaves in 2015.
lvs.lng.2015: Length of largest leaf in 2015.
lvs.wdt.2015: Width of largest leaf in 2015.
inf.num.2015: Number of inflorescences in 2015.
inf.lng.tot.2015: Summed inflorescence length in 2015.
flo.tot.2015: Number of flowers in 2015.
frt.tot.2015: Number of fruits in 2015.
sprouted.2016: A binomial indicating whether the individual had living aboveground tissue observable in the 2016 census.
lvs.num.2016: Number of leaves in 2016.
lvs.lng.2016: Length of largest leaf in 2016.
lvs.wdt.2016: Width of largest leaf in 2016.
inf.num.2016: Number of inflorescences in 2016.
inf.lng.tot.2016: Summed inflorescence length in 2016.
flo.tot.2016: Number of flowers in 2016.
frt.tot.2016: Number of fruits in 2016.
sprouted.2017: A binomial indicating whether the individual had living aboveground tissue observable in the 2017 census.
lvs.num.2017: Number of leaves in 2017.
lvs.lng.2017: Length of largest leaf in 2017.
lvs.wdt.2017: Width of largest leaf in 2017.
inf.num.2017: Number of inflorescences in 2017.
inf.lng.tot.2017: Summed inflorescence length in 2017.
flo.tot.2017: Number of flowers in 2017.
frt.tot.2017: Number of fruits in 2017.
sprouted.2018: A binomial indicating whether the individual had living aboveground tissue observable in the 2018 census.
lvs.num.2018: Number of leaves in 2018.
lvs.lng.2018: Length of largest leaf in 2018.
lvs.wdt.2018: Width of largest leaf in 2018.
inf.num.2018: Number of inflorescences in 2018.
inf.lng.tot.2018: Summed inflorescence length in 2018.
flo.tot.2018: Number of flowers in 2018.
frt.tot.2018: Number of fruits in 2018.
sprouted.2019: A binomial indicating whether the individual had living aboveground tissue observable in the 2019 census.
lvs.num.2019: Number of leaves in 2019.
lvs.lng.2019: Length of largest leaf in 2019.
lvs.wdt.2019: Width of largest leaf in 2019.
inf.num.2019: Number of inflorescences in 2019.
inf.lng.tot.2019: Summed inflorescence length in 2019.
flo.tot.2019: Number of flowers in 2019.
frt.tot.2019: Number of fruits in 2019.
sprouted.2020: A binomial indicating whether the individual had living aboveground tissue observable in the 2020 census.
lvs.num.2020: Number of leaves in 2020.
lvs.lng.2020: Length of largest leaf in 2020.
lvs.wdt.2020: Width of largest leaf in 2020.
inf.num.2020: Number of inflorescences in 2020.
inf.lng.tot.2020: Summed inflorescence length in 2020.
flo.tot.2020: Number of flowers in 2020.
frt.tot.2020: Number of fruits in 2020.

Examples

Run this code

# \donttest{
data(pyrola)

pyrola$species <- as.factor(pyrola$species)
pyrola$population <- as.factor(pyrola$population)
jreg <- pyrola[which(pyrola$population == 1),]
stagevec_jp <- c("P1", "Sdl", "Dorm", "V0nr", "V1nr", "V2nr", "V3nr", "V4nr",
  "V0r", "V1r", "V2r", "V3r", "V4r")
sizeavec_jp <- c(0, 0, 0, 0, 1, 2, 3, 7, 0, 1, 2, 3, 7)
sizeahbin_jp <- c(0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 3.5, 0.5, 0.5, 0.5, 0.5,
  3.5)
repvec_jp <- c(0, 0, 0, 0, rep(0, 4), rep(1, 5))
propvec_jp <- c(1, rep(0, 12))
immvec_jp <- c(1, 1, rep(0, 11))
matvec_jp <- c(0, 0, rep(1, 11))
obsvec_jp <- c(0, 0, 0, rep(1, 10))
indata_jp <- c(0, 0, rep(1, 11))
comments_jp <- c("protocorm", "seedling", "dormant adult", "stump", "1lf nr",
  "2lf nr", "3lf nr", "4+lf nr", "0lf r", "1lf r", "2lf r", "3lf r",
  "4+lf r")
jp_frame <- sf_create(sizes = sizeavec_jp, stagenames = stagevec_jp,
  binhalfwidth = sizeahbin_jp, repstatus = repvec_jp, obsstatus = obsvec_jp,
  indataset = indata_jp, propstatus = propvec_jp, immstatus = immvec_jp,
  matstatus = matvec_jp, comments = comments_jp)
  
jhfv <- verticalize3(data = jreg, noyears = 6, firstyear = 2015,
  individcol = "id", blocksize = 8, sizeacol = "lvs.num.2015",
  obsacol = "sprouted.2015", repstracol = "flo.tot.2015",
  repstrbcol = "frt.tot.2015", fecacol = "flo.tot.2015",
  fecbcol = "frt.tot.2015", NAas0 = TRUE, stagesize = "sizea",
  stageassign = jp_frame)
  
jp_models_ah <- modelsearch(data = jhfv, stageframe = jp_frame,
  suite = "full", vitalrates = c("surv", "obs", "size", "repst", "fec"),
  fec = c("fec3added", "fec2added"), sizedist = "poisson",
  fecdist = "negbin", fec.trunc = TRUE, historical = FALSE,
  quiet = "partial")
jp_germ <- 0.90

jp_supp2 <- supplemental(stage3 = c("Sdl", "Dorm", "V0nr", "V1nr", "P1", "Sdl"), 
  stage2 = c("P1", "Sdl", "Sdl", "Sdl", "rep", "rep"),
  eststage3 = c(NA, NA, NA, NA, NA, NA),
  eststage2 = c(NA, NA, NA, NA, NA, NA),
  givenrate = c(0.25, 0.35, 0.10, 0.10, NA, NA), # 0.345, 0.054
  multiplier = c(NA, NA, NA, NA, jp_germ * 0.5, jp_germ * 0.5),
  type = c(1, 1, 1, 1, 3, 3), stageframe = jp_frame, historical = FALSE)

jp_ahmpm <- flefko2(year = "all", stageframe = jp_frame,
  supplement = jp_supp2, modelsuite = jp_models_ah, data = jhfv,
  err_check = TRUE)

lambda3(jp_ahmpm)
# }

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