lathyrus: Demographic Dataset of _Lathyrus vernus_ Population
In lefko3: Historical and Ahistorical Population Projection Matrix Analysis

lathyrus

R Documentation

Demographic Dataset of Lathyrus vernus Population

Description

A dataset containing the states and fates of Lathyrus vernus (spring vetch), family Fabaceae, from a population in Sweden monitored annually from 1988 to 1991 in six study plots.

Usage

data(lathyrus)

Format

A data frame with 1119 individuals and 34 variables. Each row corresponds to a unique individual, and each variable from Volume88 on refers to the state of the individual in a given year.

SUBPLOT: A variable refering to patch within the population.
GENET: A numeric variable giving a unique number to each individual.
Volume88: Aboveground volume in cubic mm in 1988.
lnVol88: Natural logarithm of Volume88.
FCODE88: Equals 1 if flowering and 0 if not flowering in 1988.
Flow88: Number of flowers in 1988.
Intactseed88: Number of intact mature seeds produced in 1988. Not always an integer, as in some cases seed number was estimated via linear modeling.
Dead1988: Marked as 1 if known to be dead in 1988.
Dormant1988: Marked as 1 if known to be alive but vegetatively dormant in 1988.
Missing1988: Marked as 1 if not found in 1988.
Seedling1988: Marked as 1, 2, or 3 if observed as a seedling in year t. Numbers refer to certainty of assignment: 1 = certain that plant is a seedling in 1988, 2 = likely that plant is a seedling in 1988, 3 = probable that plant is a seedling in 1988.
Volume89: Aboveground volume in cubic mm in 1989.
lnVol89: Natural logarithm of Volume89.
FCODE89: Equals 1 if flowering and 0 if not flowering in 1989.
Flow89: Number of flowers in 1989.
Intactseed89: NZumber of intact mature seeds produced in 1989. Not always an integer, as in some cases seed number was estimated via linear modeling.
Dead1989: Marked as 1 if known to be dead in 1989.
Dormant1989: Marked as 1 if known to be alive but vegetatively dormant in 1989.
Missing1989: Marked as 1 if not found in 1989.
Seedling1989: Marked as 1, 2, or 3 if observed as a seedling in year t. Numbers refer to certainty of assignment: 1 = certain that plant is a seedling in 1989, 2 = likely that plant is a seedling in 1989, 3 = probable that plant is a seedling in 1989.
Volume90: Aboveground volume in mm<sup>3</sup> in 1990.
lnVol90: Natural logarithm of Volume90.
FCODE90: Equals 1 if flowering and 0 if not flowering in 1990.
Flow90: Number of flowers in 1990.
Intactseed90: NZumber of intact mature seeds produced in 1990. Not always an integer, as in some cases seed number was estimated via linear modeling.
Dead1990: Marked as 1 if known to be dead in 1990.
Dormant1990: Marked as 1 if known to be alive but vegetatively dormant in 1990.
Missing1990: Marked as 1 if not found in 1990.
Seedling1990: Marked as 1, 2, or 3 if observed as a seedling in year t. Numbers refer to certainty of assignment: 1 = certain that plant is a seedling in 1990, 2 = likely that plant is a seedling in 1990, 3 = probable that plant is a seedling in 1990.
Volume91: Aboveground volume in mm<sup>3</sup> in 1991.
lnVol91: Natural logarithm of Volume91.
FCODE91: Equals 1 if flowering and 0 if not flowering in 1991.
Flow91: Number of flowers in 1991.
Intactseed91: NZumber of intact mature seeds produced in 1991. Not always an integer, as in some cases seed number was estimated via linear modeling.
Dead1991: Marked as 1 if known to be dead in 1991.
Dormant1991: Marked as 1 if known to be alive but vegetatively dormant in 1991.
Missing1991: Marked as 1 if not found in 1991.
Seedling1991: Marked as 1, 2, or 3 if observed as a seedling in year t. Numbers refer to certainty of assignment: 1 = certain that plant is a seedling in 1991, 2 = likely that plant is a seedling in 1991, 3 = probable that plant is a seedling in 1991.

Source

Ehrlen, J. 2000. The dynamics of plant populations: does the history of individuals matter? Ecology 81(6):1675-1684.

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",
  juvcol = c("Seedling1988", "Seedling1989", "Seedling1990", "Seedling1991"),
  sizeacol = c("Volume88", "Volume89", "Volume90", "Volume91"),
  repstracol = c("FCODE88", "FCODE89", "FCODE90", "FCODE91"),
  fecacol = c("Intactseed88", "Intactseed89", "Intactseed90", "Intactseed91"),
  deadacol = c("Dead1988", "Dead1989", "Dead1990", "Dead1991"),
  nonobsacol = c("Dormant1988", "Dormant1989", "Dormant1990", "Dormant1991"),
  censorcol = c("Missing1988", "Missing1989", "Missing1990", "Missing1991"), 
  stageassign = lathframe, stagesize = "sizea",
  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)

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

ehrlen3mean <- lmean(ehrlen3)
ehrlen3mean$A[[1]]

lambda3(ehrlen3mean)

lefko3 documentation built on Sept. 11, 2024, 9:35 p.m.