Description Usage Format Source Examples

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.

1 |

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.

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

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 | ```
# 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)
``` |

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