lathyrus: Demographic Dataset of _Lathyrus vernus_ Population

Description Usage Format Source Examples

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

1

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

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# Lathyrus example using blocksize - when repeated patterns exist in variable
# order
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)

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)

# Lathyrus example without blocksize - when no repeated patterns exist in
# variable order and all variables names are specified
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 July 22, 2021, 9:10 a.m.