summary.lefkoLTRE {lefko3} | R Documentation |
Summarize lefkoLTRE Objects
Description
Function summary.lefkoLTRE()
summarizes lefkoLTRE
objects.
Particularly, it breaks down LTRE contributions by the kind of ahistorical
and, if applicable, historical transition.
Usage
## S3 method for class 'lefkoLTRE'
summary(object, ...)
Arguments
object |
A |
... |
Other parameters currently not utilized. |
Value
A list of data frames. In all cases, the first data frame is one
showing the positive, negative, and total contributions of elements in
each LTRE contribution matrix. If not a SNA-LTRE, then there are an
additional two (if deterministic) or four (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 four 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. The output for the SNA-LTRE also includes the
logs of the deterministic lambda estimated through function ltre3()
.
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", 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)