View source: R/matrixcreation.R
arlefko2  R Documentation 
Function arlefko2()
returns raw ahistorical age x stage MPMs
corresponding to the patches and occasion times given, including the
associated component transition and fecundity matrices, data frames detailing
the characteristics of ahistorical stages and the exact agestage
combinations corresponding to rows and columns in estimated matrices, and a
data frame characterizing the patch and occasion time combinations
corresponding to these matrices.
arlefko2(
data,
stageframe,
year = "all",
pop = NULL,
patch = NULL,
censor = FALSE,
stages = NULL,
alive = c("alive3", "alive2"),
obsst = NULL,
size = c("sizea3", "sizea2"),
sizeb = NULL,
sizec = NULL,
repst = c("repstatus3", "repstatus2"),
matst = c("matstatus3", "matstatus2"),
fec = c("feca3", "feca2"),
supplement = NULL,
repmatrix = NULL,
overwrite = NULL,
agecol = "obsage",
yearcol = NULL,
popcol = NULL,
patchcol = NULL,
indivcol = NULL,
censorcol = NULL,
censorkeep = 0,
final_age = NA,
continue = TRUE,
prebreeding = TRUE,
NRasRep = FALSE,
reduce = FALSE,
simple = FALSE,
err_check = FALSE,
sparse_output = FALSE
)
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. Should also incorporate bin widths if size is continuous. 
year 
A variable corresponding to observation occasion, or a set
of such values, given in values associated with the year term used in linear
model development. Defaults to 
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 and t. 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 t1,
respectively. Defaults to 
size 
A vector of names of variables coding the primary size variable
in occasions t+1 and t, respectively. Defaults to

sizeb 
A vector of names of variables coding the secondary size
variable in occasions t+1 and t, respectively. Defaults to

sizec 
A vector of names of variables coding the tertiary size
variable in occasions t+1 and t, respectively. Defaults to

repst 
A vector of names of variables coding reproductive status in
occasions t+1 and t, respectively. Defaults to

matst 
A vector of names of variables coding maturity status in
occasions t+1 and t, respectively. Defaults to

fec 
A vector of names of variables coding fecundity in occasions
t+1 and t, respectively. Defaults to 
supplement 
An optional data frame of class 
repmatrix 
An optional reproduction matrix. This matrix is composed
mostly of 0s, with nonzero 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

agecol 
The variable name or column number coding for age in time t. 
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 
final_age 
The final age to model in the matrix. Defaults to the maximum age in the dataset. 
continue 
A logical value designating whether to allow continued
survival of individuals past the final age noted in the stageframe, using the
demographic characteristics of the final age. Defaults to 
prebreeding 
A logical value indicating whether the life history model
is a prebreeding model. Defaults to 
NRasRep 
If 
reduce 
A logical value denoting whether to remove agestages
associated with only 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 
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 patches and
occasions. All matrices output in R's 
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. Set to 
agestages 
A data frame showing the stage number and stage name
corresponding to 
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 patch and year of each matrix in order.
In 
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 nonzero elements in

modelqc 
This is the 
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 nonzero values. To use the default behavior of
setting all reproductive stages to reproduce at full fecundity into immature
and propagule stages but also incorporate given or proxy survival
transitions, input those given and proxy transitions through the
overwrite
options.
The reproduction matrix (field repmatrix
) may only be supplied as
ahistorical. If provided as historical, then rlefko2()
will fail and
produce an error.
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 and t. 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.
mpm_create()
flefko3()
flefko2()
aflefko2()
fleslie()
rlefko3()
rlefko2()
rleslie()
# 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)
minagevec < c(1, 1, 2, 3, 4, 5, 5, 5, 5, 5, 5)
maxagevec < c(rep(NA, 11))
cypframe_raw < sf_create(sizes = sizevector, stagenames = stagevector,
repstatus = repvector, obsstatus = obsvector, matstatus = matvector,
propstatus = propvector, immstatus = immvector, indataset = indataset,
binhalfwidth = binvec, minage = minagevec, maxage = maxagevec)
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, age_offset = 4)
# Here we use supplemental() to provide overwrite and reproductive info
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, agebased = TRUE)
cyp_mats < arlefko2(data = cypraw_v1, stageframe = cypframe_raw, year = "all",
patch = NA, censor = FALSE, stages = c("stage3", "stage2", "stage1"),
size = c("size3added", "size2added"), fec = c("feca3", "feca2"),
supplement = cypsupp2r, agecol = "obsage", yearcol = "year2",
patchcol = "patchid", indivcol = "individ", prebreeding = TRUE, final_age = NA,
continue = TRUE, reduce = FALSE)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.