Description Usage Arguments Value Notes Examples
View source: R/matrixcreation.R
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 year associated with each matrix.
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  rlefko3(
data,
stageframe,
year = "all",
pop = NA,
patch = NA,
censor = FALSE,
stages = NA,
alive = c("alive3", "alive2", "alive1"),
size = c("sizea3", "sizea2", "sizea1"),
repst = c("repstatus3", "repstatus2", "repstatus1"),
matst = c("matstatus3", "matstatus2", "matstatus1"),
fec = c("feca3", "feca2", "feca1"),
supplement = NA,
repmatrix = NA,
overwrite = NA,
yearcol = NA,
popcol = NA,
patchcol = NA,
indivcol = NA,
censorcol = NA,
censorkeep = 0,
format = "ehrlen",
reduce = FALSE,
err_check = 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, immaturity status, and maturity status of each ahistorical stage. Should also incorporate bin widths if size is continuous. 
year 
A variable corresponding to year or observation time, or a set of
such values, given in values associated with the year term used in linear
model development. Can also equal 
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 TRUE, then data will be removed according to the variable
set in 
stages 
An optional vector denoting the names of the variables within
the main vertical dataset coding for the stages of each individual in times
t+1, t, and t1. 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 (1) or dead (0) in times t+1, t, and t1, respectively. 
size 
A vector of names of variables coding size in times t+1,
t, and t1, respectively. Defaults to

repst 
A vector of names of variables coding reproductive status in
times t+1, t, and t1, respectively. Defaults to

matst 
A vector of names of variables coding maturity status in times
t+1, t, and t1, respectively. Defaults to

fec 
A vector of names of variables coding fecundity in times
t+1, t, and t1, respectively. Defaults to

supplement 
An optional data frame of class 
repmatrix 
A reproduction matrix, which is an optional matrix composed
mostly of 0s, with nonzero values for each potentially new individual (row)
born to each reproductive stage (column). Entries act as multipliers on
fecundity, with 1 equaling full fecundity. Fecundity multipliers provided
this way supplement rather than replace those provided in 
overwrite 
An optional data frame developed with the

yearcol 
The variable name or column number corresponding to time in time 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 0. 
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 all row and column sums in ALL matrices estimated equal 0. Defaults to FALSE. 
err_check 
A logical value indicating whether to append extra information used in matrix calculation within the output list. Used for development debugging purposes. 
If all inputs are properly formatted, then this function will return
either an object of class lefkoMat
. Output includes:
A 
A list of full projection matrices in order of sorted populations,
patches, and years. 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 
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. 
matrixqc 
A short vector describing the number of nonzero elements in

dataqc 
A vector showing the numbers of individuals and rows in the vertical dataset used as input. 
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 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 times
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.
Input options including multiple variable names must be entered in the order of variables in time t+1, t, and t1. Rearranging the order WILL lead to erroneous calculations, and will probably also lead to fatal errors.
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
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")
summary(ehrlen3)
# Cypripedium example
rm(list=ls(all=TRUE))
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", "SL", "SL", "D", "XSm", "Sm", "D", "XSm", "Sm", "SD", "P1"),
stage2 = c("SD", "SD", "SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL",
"SL", "SL", "SL", "SL", "SL", "rep", "rep"),
stage1 = c("SD", "rep", "SD", "rep", "SD", "P1", "P2", "P3", "SL", "P3",
"P3", "P3", "SL", "SL", "SL", "all", "all"),
eststage3 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm", "D",
"XSm", "Sm", NA, NA),
eststage2 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm",
"XSm", "XSm", "XSm", NA, NA),
eststage1 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm",
"XSm", "XSm", "XSm", NA, NA),
givenrate = c(0.1, 0.1, 0.2, 0.2, 0.2, 0.2, 0.25, 0.4, 0.4, 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,
0.5, 0.5),
type = c(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),
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")
summary(cypmatrix3r)

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