supplemental  R Documentation 
Function supplemental()
provides all necessary supplemental data for
matrix estimation, particularly bringing together data on proxy rates, data
to overwrite existing rates, identified reproductive transitions complete,
and fecundity multipliers. The function should be used to incorporate data
that affects all matrices to be created. To edit MPMs after creation, use
edit_lM()
instead.
supplemental(
historical = TRUE,
stagebased = TRUE,
agebased = FALSE,
stageframe = NULL,
stage3 = NULL,
stage2 = NULL,
stage1 = NULL,
age2 = NULL,
eststage3 = NULL,
eststage2 = NULL,
eststage1 = NULL,
estage2 = NULL,
givenrate = NULL,
multiplier = NULL,
type = NULL,
type_t12 = NULL
)
historical 
A logical value indicating whether the MPMs intended will
be historical or ahistorical. Defaults to 
stagebased 
A logical value indicating whether the MPM will be stage
based or agebystage. Defaults to 
agebased 
A logical value indicating whether the MPM will be agebased
or agebystage. Defaults to 
stageframe 
The stageframe used to produce the MPM. Required if producing any stagebased or agebystage MPM. Must be omitted for purely agebased MPMs. 
stage3 
The name of the stage in occasion t+1 in the transition
to be replaced. Abbreviations for groups of stages are also usable (see

stage2 
The name of the stage in occasion t in the transition
to be replaced. Abbreviations for groups of stages are also usable (see

stage1 
The name of the stage in occasion t1 in the transition
to be replaced. Only needed if a historical matrix is to be produced.
Abbreviations for groups of stages are also usable (see 
age2 
An integer vector of the ages in occasion t to use in transitions to be changed or replaced. Required for all age and agebystage MPMs. 
eststage3 
The name of the stage to replace 
eststage2 
The name of the stage to replace 
eststage1 
The name of the stage to replace 
estage2 
The age at time t to replace 
givenrate 
A fixed rate or probability to replace for the transition
described by 
multiplier 
A vector of numeric multipliers for fecundity or for proxy
transitions. Defaults to 
type 
A vector denoting the kind of transition between occasions
t and t+1 to be replaced. This should be entered as 
type_t12 
An optional vector denoting the kind of transition between
occasions t1 and t. Only necessary if a historical MPM in
deVries format is desired. This should be entered as 
A data frame of class lefkoSD
. This object can be used as
input in flefko3()
, flefko2()
,
rlefko3()
, rlefko2()
, and
aflefko2()
.
Variables in this object include the following:
stage3 
Stage at occasion t+1 in the transition to be replaced. 
stage2 
Stage at occasion t in the transition to be replaced. 
stage1 
Stage at occasion t1 in the transition to be replaced. 
age2 
Age at occasion t in the transition to be replaced. 
eststage3 
Stage at occasion t+1 in the transition to replace
the transition designated by 
eststage2 
Stage at occasion t in the transition to replace the
transition designated by 
eststage1 
Stage at occasion t1 in the transition to replace
the transition designated by 
estage2 
Age at occasion t in the transition to replace the
transition designated by 
givenrate 
A constant to be used as the value of the transition. 
multiplier 
A multiplier for proxy transitions or for fecundity. 
convtype 
Designates whether the transition from occasion t to occasion t+1 is a survival transition probability (1), a fecundity rate (2), or a fecundity multiplier (3). 
convtype_t12 
Designates whether the transition from occasion t1 to occasion t is a survival transition probability (1), a fecundity rate (2). 
Negative values are not allowed in givenrate
and multiplier
input. Stage entries should not be used for purely agebased MPMs, and age
entries should not be used for purely stagebased MPMs.
Fecundity multiplier data supplied via the supplemental()
function
acts in the same way as nonzero entries supplied via a reproductive matrix,
but gets priority in all matrix creations. Thus, in cases where fecundity
multipliers are provided for the same function via the reproductive matrix
and function supplemental()
, the latter is used.
Entries in stage3
, stage2
, and stage1
can include
abbreviations for groups of stages. Use rep
if all reproductive
stages are to be used, nrep
if all mature but nonreproductive stages
are to be used, mat
if all mature stages are to be used, immat
if all immature stages are to be used, prop
if all propagule stages
are to be used, npr
if all nonpropagule stages are to be used,
obs
if all observable stages are to be used, nobs
if all
unobservable stages are to be used, and leave empty or use all
if all
stages in stageframe are to be used. Also use groupX
to denote all
stages in group X (e.g. group1
will use all stages in the respective
stageframe's group 1).
Type 3 conversions are referred to as fecundity set values, or general
fecundity multipliers. These set the transitions to be used as fecundity
transitions. Transitions set here will be interpreted as being generally
reproductive, meaning that the from and to stages will be used to determine
the general fecundity transitions to incorporate into stagebased MPMs,
while the age portion of the input will be used to incorporate the actual
multiplier(s) specified. If only stage transitions at certain ages are
expected to be the sole contributors to fecundity, then type 2 conversions
should also be included in the supplement (Type 1 and 2 conversions can be
purely agespecific, and do not set reproductive transitions in MPM
creation). For example, if all stage 2 to stage 3 transitions above age 2
yield fecundity, then stage 2 to stage 3 can be set to
multiplier = 1.0
with convtype = 3
, and the same transition
for age2 = c(1, 2)
can be set to multiplier = c(0, 0)
.
edit_lM()
# Lathyrus example
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")
# Cypripedium example
data(cypdata)
sizevector < c(0, 0, 0, 0, 0, 0, 1, 2.5, 4.5, 8, 17.5)
stagevector < c("SD", "P1", "P2", "P3", "SL", "D", "XSm", "Sm", "Md", "Lg",
"XLg")
repvector < c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
obsvector < c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1)
matvector < c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
immvector < c(0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0)
propvector < c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0)
indataset < c(0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1)
binvec < c(0, 0, 0, 0, 0, 0.5, 0.5, 1, 1, 2.5, 7)
cypframe_raw < sf_create(sizes = sizevector, stagenames = stagevector,
repstatus = repvector, obsstatus = obsvector, matstatus = matvector,
propstatus = propvector, immstatus = immvector, indataset = indataset,
binhalfwidth = binvec)
cypraw_v1 < verticalize3(data = cypdata, noyears = 6, firstyear = 2004,
patchidcol = "patch", individcol = "plantid", blocksize = 4,
sizeacol = "Inf2.04", sizebcol = "Inf.04", sizeccol = "Veg.04",
repstracol = "Inf.04", repstrbcol = "Inf2.04", fecacol = "Pod.04",
stageassign = cypframe_raw, stagesize = "sizeadded", NAas0 = TRUE,
NRasRep = TRUE)
cypsupp2r < supplemental(stage3 = c("SD", "P1", "P2", "P3", "SL", "D",
"XSm", "Sm", "SD", "P1"),
stage2 = c("SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "rep",
"rep"),
eststage3 = c(NA, NA, NA, NA, NA, "D", "XSm", "Sm", NA, NA),
eststage2 = c(NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", NA, NA),
givenrate = c(0.10, 0.20, 0.20, 0.20, 0.25, NA, NA, NA, NA, NA),
multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, 0.5, 0.5),
type =c(1, 1, 1, 1, 1, 1, 1, 1, 3, 3),
stageframe = cypframe_raw, historical = FALSE)
cypmatrix2r < rlefko2(data = cypraw_v1, stageframe = cypframe_raw,
year = "all", patch = "all", stages = c("stage3", "stage2", "stage1"),
size = c("size3added", "size2added"), supplement = cypsupp2r,
yearcol = "year2", patchcol = "patchid", indivcol = "individ")
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