rlefko3: Create Raw Historical Matrix Projection Model
In lefko3: Historical and Ahistorical Population Projection Matrix Analysis
View source: R/matrixcreation.R
rlefko3 R Documentation
Create Raw Historical Matrix Projection Model
Description
Function rlefko3() returns raw historical MPMs, including the
associated component transition and fecundity matrices, data frames
describing the ahistorical stages used and the historical paired stages, and
a data frame describing the population, patch, and occasion time associated
with each matrix.
Usage
rlefko3(
data,
stageframe,
year = "all",
pop = NULL,
patch = NULL,
censor = FALSE,
stages = NULL,
alive = c("alive3", "alive2", "alive1"),
obsst = NULL,
size = c("sizea3", "sizea2", "sizea1"),
sizeb = NULL,
sizec = NULL,
repst = c("repstatus3", "repstatus2", "repstatus1"),
matst = c("matstatus3", "matstatus2", "matstatus1"),
fec = c("feca3", "feca2", "feca1"),
supplement = NULL,
repmatrix = NULL,
overwrite = NULL,
yearcol = NULL,
popcol = NULL,
patchcol = NULL,
indivcol = NULL,
censorcol = NULL,
censorkeep = 0,
NRasRep = FALSE,
format = "ehrlen",
reduce = FALSE,
simple = FALSE,
err_check = FALSE,
sparse_output = FALSE
)
Arguments
data
A vertical demographic data frame, with variables corresponding
to the naming conventions in verticalize3() and
historicalize3().
stageframe
A stageframe object that includes information on the size,
observation status, propagule status, reproduction status, immaturity status,
and maturity status of each ahistorical stage.
year
A variable corresponding to observation occasion, or a set of
such values, given in values associated with the year term used in
vital rate model development. Can also equal "all", in which case
matrices will be estimated for all occasions. Defaults to "all".
pop
A variable designating which populations will have matrices
estimated. Should be set to specific population names, or to "all" if
all populations should have matrices estimated.
patch
A variable designating which patches or subpopulations will have
matrices estimated. Should be set to specific patch names, or to "all"
if matrices should be estimated for all patches. Defaults to NA, in
which case patch designations are ignored..
censor
If TRUE, then data will be removed according to the
variable set in censorcol, such that only data with censor values
equal to censorkeep will remain. Defaults to FALSE.
stages
An optional vector denoting the names of the variables within
the main vertical dataset coding for the stages of each individual in
occasions t+1, t, and t-1. The names of stages in these
variables should match those used in the stageframe exactly. If left
blank, then rlefko3() will attempt to infer stages by matching values
of alive, size, repst, and matst to
characteristics noted in the associated stageframe.
alive
A vector of names of binomial variables corresponding to status
as alive (1) or dead (0) in occasions t+1, t, and
t-1, respectively.
obsst
A vector of names of binomial variables corresponding to
observation status in occasions t+1, t, and t-1,
respectively. Defaults to NULL, in which case observation status is
not used.
size
A vector of names of variables coding the primary size variable
in occasions t+1, t, and t-1, respectively. Defaults to
c("sizea3", "sizea2", "sizea1").
sizeb
A vector of names of variables coding the secondary size
variable in occasions t+1, t, and t-1, respectively.
Defaults to NULL, in which case this variable is not used.
sizec
A vector of names of variables coding the tertiary size
variable in occasions t+1, t, and t-1, respectively.
Defaults to NULL, in which case this variable is not used.
repst
A vector of names of variables coding reproductive status in
occasions t+1, t, and t-1, respectively. Defaults to
c("repstatus3", "repstatus2", "repstatus1"). Must be supplied if
stages is not provided.
matst
A vector of names of variables coding maturity status in
occasions t+1, t, and t-1, respectively. Defaults to
c("matstatus3", "matstatus2", "matstatus1"). Must be supplied if
stages is not provided.
fec
A vector of names of variables coding fecundity in occasions
t+1, t, and t-1, respectively. Defaults to
c("feca3", "feca2", "feca1").
supplement
An optional data frame of class lefkoSD that
provides supplemental data that should be incorporated into the MPM. Three
kinds of data may be integrated this way: transitions to be estimated via the
use of proxy transitions, transition overwrites from the literature or
supplemental studies, and transition multipliers for fecundity. This data
frame should be produced using the supplemental() function.
Should be used in place of or in addition to an overwrite table (see
overwrite below) and a reproduction matrix (see repmatrix
below).
repmatrix
An optional reproduction matrix. This matrix is composed
mostly of 0s, with non-zero entries acting as element identifiers and
multipliers for fecundity (with 1 equaling full fecundity). If left blank,
and no supplement is provided, then rlefko3() will assume that
all stages marked as reproductive produce offspring at 1x that of estimated
fecundity, and that offspring production will yield the first stage noted as
propagule or immature. To prevent this behavior, input just 0, which
will result in fecundity being estimated only for transitions noted in
supplement above. May be the dimensions of either a historical or an
ahistorical matrix. If the former, then the fecundity estimation of this
function may be unpredictable. If the latter, then all stages will be used in
occasion t-1 for each suggested ahistorical transition.
overwrite
An optional data frame developed with the
overwrite() function describing transitions to be overwritten
either with given values or with other estimated transitions. Note that this
function supplements overwrite data provided in supplement.
yearcol
The variable name or column number corresponding to occasion
t in the dataset.
popcol
The variable name or column number corresponding to the
identity of the population.
patchcol
The variable name or column number corresponding to patch in
the dataset.
indivcol
The variable name or column number coding individual
identity.
censorcol
The variable name or column number denoting the censor
status. Only needed if censor = TRUE.
censorkeep
The value of the censor variable denoting data elements to
keep. Defaults to 0.
NRasRep
If data does not include stage assignments, then this
option determines whether non-reproductive and reproductive individuals
should be lumped into the same stages. Defaults to FALSE.
format
A string indicating whether to estimate matrices in
ehrlen format or deVries format. The latter adds one unborn
prior stage to account for the prior state of newborns. Defaults to
ehrlen format.
reduce
A logical value denoting whether to remove historical stages
associated exclusively with zero transitions. These are removed only if the
respective row and column sums in ALL matrices estimated equal 0. Defaults to
FALSE.
simple
A logical value indicating whether to produce A,
U, and F matrices, or only the latter two. Defaults to
FALSE, in which case all three are output.
err_check
A logical value indicating whether to append extra
information used in matrix calculation within the output list. Defaults to
FALSE.
sparse_output
A logical value indicating whether to output matrices
in sparse format. Defaults to FALSE, in which case all matrices are
output in standard matrix format.
Value
If all inputs are properly formatted, then this function will return
an object of class lefkoMat, which is a list that holds the matrix
projection model and all of its metadata. Its structure is a list with the
following elements:
A
A list of full projection matrices in order of sorted populations,
patches, and occasions. All matrices output in the matrix class, or in
the dgCMatrix class from the Matrix package if sparse.
U
A list of survival transition matrices sorted as in A. All
matrices output in the matrix class, or in the dgCMatrix class
from the Matrix package if sparse.
F
A list of fecundity matrices sorted as in A. All matrices
output in the matrix class, or in the dgCMatrix class from the
Matrix package if sparse.
hstages
A data frame matrix showing the pairing of ahistorical stages
used to create historical stage pairs.
agestages
A data frame showing age-stage pairs. In this function, it
is set to NA. Only used in output to function aflefko2().
ahstages
A data frame detailing the characteristics of associated
ahistorical stages, in the form of a modified stageframe that includes
status as an entry stage through reproduction.
labels
A data frame giving the population, patch, and year of each
matrix in order.
dataqc
A vector showing the numbers of individuals and rows in the
vertical dataset used as input.
matrixqc
A short vector describing the number of non-zero elements in
U and F matrices, and the number of annual matrices.
modelqc
This is the qc portion of the modelsuite input
in function-based MPMs. Empty in this function.
Notes
The default behavior of this function is to estimate fecundity with regards
to transitions specified via associated fecundity multipliers in either
supplement or repmatrix. If both of these fields are left
empty, then fecundity will be estimated at full for all transitions leading
from reproductive stages to immature and propagule stages. However, if a
supplement is provided and a repmatrix is not, or if
repmatrix is set to 0, then only fecundity transitions noted in the
supplement will be set to non-zero values. To use the default behavior of
setting all reproductive stages to reproduce at full fecundity into immature
and propagule stages but incorporate given or proxy survival transitions,
input those given and proxy transitions through the overwrite option.
The reproduction matrix (field repmatrix) may be supplied as either
historical or ahistorical. If provided as ahistorical, then flefko3()
will assume that all historical transitions involving stages noted for
occasions t and t+1 should be set to the respective fecundity
multipliers noted.
Users may at times wish to estimate MPMs using a dataset incorporating
multiple patches or subpopulations. Should the aim of analysis be a general
MPM that does not distinguish these patches or subpopulations, the
patchcol variable should be left to NA, which is the default.
Otherwise the variable identifying patch needs to be named.
Input options including multiple variable names must be entered in the order
of variables in occasion t+1, t, and t-1. Rearranging
the order WILL lead to erroneous calculations, and may lead to
fatal errors.
Although this function is capable of assigning stages given an input
stageframe, it lacks the power of verticalize3() and
historicalize3() in this regard. Users are strongly
encouraged to use the latter two functions for stage assignment.
See Also
mpm_create()
flefko3()
flefko2()
aflefko2()
arlefko2()
fleslie()
rlefko2()
rleslie()
Examples
# 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)
cypsupp3r <- supplemental(stage3 = c("SD", "SD", "P1", "P1", "P2", "P3", "SL",
"D", "XSm", "Sm", "D", "XSm", "Sm", "mat", "mat", "mat", "SD", "P1"),
stage2 = c("SD", "SD", "SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "SL",
"SL", "SL", "D", "XSm", "Sm", "rep", "rep"),
stage1 = c("SD", "rep", "SD", "rep", "SD", "P1", "P2", "P3", "P3", "P3",
"SL", "SL", "SL", "SL", "SL", "SL", "mat", "mat"),
eststage3 = c(NA, NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm", "D", "XSm", "Sm",
"mat", "mat", "mat", NA, NA),
eststage2 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
"XSm", "D", "XSm", "Sm", NA, NA),
eststage1 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
"XSm", "XSm", "XSm", "XSm", NA, NA),
givenrate = c(0.1, 0.1, 0.2, 0.2, 0.2, 0.2, 0.25, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA),
multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, 0.5, 0.5),
type = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3),
type_t12 = c(1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
stageframe = cypframe_raw, historical = TRUE)
cypmatrix3r <- rlefko3(data = cypraw_v1, stageframe = cypframe_raw,
year = "all", patch = "all", stages = c("stage3", "stage2", "stage1"),
size = c("size3added", "size2added", "size1added"),
supplement = cypsupp3r, yearcol = "year2", patchcol = "patchid",
indivcol = "individ")
lefko3 documentation built on Oct. 14, 2023, 1:07 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
View source: R/matrixcreation.R
| rlefko3 | R Documentation |
Create Raw Historical Matrix Projection Model
Description
Function rlefko3() returns raw historical MPMs, including the
associated component transition and fecundity matrices, data frames
describing the ahistorical stages used and the historical paired stages, and
a data frame describing the population, patch, and occasion time associated
with each matrix.
Usage
rlefko3(
data,
stageframe,
year = "all",
pop = NULL,
patch = NULL,
censor = FALSE,
stages = NULL,
alive = c("alive3", "alive2", "alive1"),
obsst = NULL,
size = c("sizea3", "sizea2", "sizea1"),
sizeb = NULL,
sizec = NULL,
repst = c("repstatus3", "repstatus2", "repstatus1"),
matst = c("matstatus3", "matstatus2", "matstatus1"),
fec = c("feca3", "feca2", "feca1"),
supplement = NULL,
repmatrix = NULL,
overwrite = NULL,
yearcol = NULL,
popcol = NULL,
patchcol = NULL,
indivcol = NULL,
censorcol = NULL,
censorkeep = 0,
NRasRep = FALSE,
format = "ehrlen",
reduce = FALSE,
simple = FALSE,
err_check = FALSE,
sparse_output = FALSE
)
Arguments
data |
A vertical demographic data frame, with variables corresponding
to the naming conventions in |
stageframe |
A stageframe object that includes information on the size, observation status, propagule status, reproduction status, immaturity status, and maturity status of each ahistorical stage. |
year |
A variable corresponding to observation occasion, or a set of
such values, given in values associated with the |
pop |
A variable designating which populations will have matrices
estimated. Should be set to specific population names, or to |
patch |
A variable designating which patches or subpopulations will have
matrices estimated. Should be set to specific patch names, or to |
censor |
If |
stages |
An optional vector denoting the names of the variables within
the main vertical dataset coding for the stages of each individual in
occasions t+1, t, and t-1. The names of stages in these
variables should match those used in the |
alive |
A vector of names of binomial variables corresponding to status
as alive ( |
obsst |
A vector of names of binomial variables corresponding to
observation status in occasions t+1, t, and t-1,
respectively. Defaults to |
size |
A vector of names of variables coding the primary size variable
in occasions t+1, t, and t-1, respectively. Defaults to
|
sizeb |
A vector of names of variables coding the secondary size
variable in occasions t+1, t, and t-1, respectively.
Defaults to |
sizec |
A vector of names of variables coding the tertiary size
variable in occasions t+1, t, and t-1, respectively.
Defaults to |
repst |
A vector of names of variables coding reproductive status in
occasions t+1, t, and t-1, respectively. Defaults to
|
matst |
A vector of names of variables coding maturity status in
occasions t+1, t, and t-1, respectively. Defaults to
|
fec |
A vector of names of variables coding fecundity in occasions
t+1, t, and t-1, respectively. Defaults to
|
supplement |
An optional data frame of class |
repmatrix |
An optional reproduction matrix. This matrix is composed
mostly of 0s, with non-zero entries acting as element identifiers and
multipliers for fecundity (with 1 equaling full fecundity). If left blank,
and no |
overwrite |
An optional data frame developed with the
|
yearcol |
The variable name or column number corresponding to occasion t in the dataset. |
popcol |
The variable name or column number corresponding to the identity of the population. |
patchcol |
The variable name or column number corresponding to patch in the dataset. |
indivcol |
The variable name or column number coding individual identity. |
censorcol |
The variable name or column number denoting the censor
status. Only needed if |
censorkeep |
The value of the censor variable denoting data elements to
keep. Defaults to |
NRasRep |
If |
format |
A string indicating whether to estimate matrices in
|
reduce |
A logical value denoting whether to remove historical stages
associated exclusively with zero transitions. These are removed only if the
respective row and column sums in ALL matrices estimated equal 0. Defaults to
|
simple |
A logical value indicating whether to produce |
err_check |
A logical value indicating whether to append extra
information used in matrix calculation within the output list. Defaults to
|
sparse_output |
A logical value indicating whether to output matrices
in sparse format. Defaults to |
Value
If all inputs are properly formatted, then this function will return
an object of class lefkoMat, which is a list that holds the matrix
projection model and all of its metadata. Its structure is a list with the
following elements:
A |
A list of full projection matrices in order of sorted populations,
patches, and occasions. All matrices output in the |
U |
A list of survival transition matrices sorted as in |
F |
A list of fecundity matrices sorted as in |
hstages |
A data frame matrix showing the pairing of ahistorical stages used to create historical stage pairs. |
agestages |
A data frame showing age-stage pairs. In this function, it
is set to NA. Only used in output to function |
ahstages |
A data frame detailing the characteristics of associated ahistorical stages, in the form of a modified stageframe that includes status as an entry stage through reproduction. |
labels |
A data frame giving the population, patch, and year of each matrix in order. |
dataqc |
A vector showing the numbers of individuals and rows in the vertical dataset used as input. |
matrixqc |
A short vector describing the number of non-zero elements in
|
modelqc |
This is the |
Notes
The default behavior of this function is to estimate fecundity with regards
to transitions specified via associated fecundity multipliers in either
supplement or repmatrix. If both of these fields are left
empty, then fecundity will be estimated at full for all transitions leading
from reproductive stages to immature and propagule stages. However, if a
supplement is provided and a repmatrix is not, or if
repmatrix is set to 0, then only fecundity transitions noted in the
supplement will be set to non-zero values. To use the default behavior of
setting all reproductive stages to reproduce at full fecundity into immature
and propagule stages but incorporate given or proxy survival transitions,
input those given and proxy transitions through the overwrite option.
The reproduction matrix (field repmatrix) may be supplied as either
historical or ahistorical. If provided as ahistorical, then flefko3()
will assume that all historical transitions involving stages noted for
occasions t and t+1 should be set to the respective fecundity
multipliers noted.
Users may at times wish to estimate MPMs using a dataset incorporating
multiple patches or subpopulations. Should the aim of analysis be a general
MPM that does not distinguish these patches or subpopulations, the
patchcol variable should be left to NA, which is the default.
Otherwise the variable identifying patch needs to be named.
Input options including multiple variable names must be entered in the order of variables in occasion t+1, t, and t-1. Rearranging the order WILL lead to erroneous calculations, and may lead to fatal errors.
Although this function is capable of assigning stages given an input
stageframe, it lacks the power of verticalize3() and
historicalize3() in this regard. Users are strongly
encouraged to use the latter two functions for stage assignment.
See Also
mpm_create()
flefko3()
flefko2()
aflefko2()
arlefko2()
fleslie()
rlefko2()
rleslie()
Examples
# 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)
cypsupp3r <- supplemental(stage3 = c("SD", "SD", "P1", "P1", "P2", "P3", "SL",
"D", "XSm", "Sm", "D", "XSm", "Sm", "mat", "mat", "mat", "SD", "P1"),
stage2 = c("SD", "SD", "SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "SL",
"SL", "SL", "D", "XSm", "Sm", "rep", "rep"),
stage1 = c("SD", "rep", "SD", "rep", "SD", "P1", "P2", "P3", "P3", "P3",
"SL", "SL", "SL", "SL", "SL", "SL", "mat", "mat"),
eststage3 = c(NA, NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm", "D", "XSm", "Sm",
"mat", "mat", "mat", NA, NA),
eststage2 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
"XSm", "D", "XSm", "Sm", NA, NA),
eststage1 = c(NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm", "XSm", "XSm",
"XSm", "XSm", "XSm", "XSm", NA, NA),
givenrate = c(0.1, 0.1, 0.2, 0.2, 0.2, 0.2, 0.25, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA),
multiplier = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, 0.5, 0.5),
type = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3),
type_t12 = c(1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
stageframe = cypframe_raw, historical = TRUE)
cypmatrix3r <- rlefko3(data = cypraw_v1, stageframe = cypframe_raw,
year = "all", patch = "all", stages = c("stage3", "stage2", "stage1"),
size = c("size3added", "size2added", "size1added"),
supplement = cypsupp3r, yearcol = "year2", patchcol = "patchid",
indivcol = "individ")
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.