historicalize3  R Documentation 
Function historicalize3()
returns a vertically formatted demographic
data frame organized to create historical projection matrices, given a
vertically but ahistorically formatted data frame. This data frame is in
standard hfvdata
format and can be used in all functions in the
package.
historicalize3(
data,
popidcol = 0,
patchidcol = 0,
individcol,
year2col = 0,
year3col = 0,
xcol = 0,
ycol = 0,
sizea2col = 0,
sizea3col = 0,
sizeb2col = 0,
sizeb3col = 0,
sizec2col = 0,
sizec3col = 0,
repstra2col = 0,
repstra3col = 0,
repstrb2col = 0,
repstrb3col = 0,
feca2col = 0,
feca3col = 0,
fecb2col = 0,
fecb3col = 0,
indcova2col = 0,
indcova3col = 0,
indcovb2col = 0,
indcovb3col = 0,
indcovc2col = 0,
indcovc3col = 0,
alive2col = 0,
alive3col = 0,
dead2col = 0,
dead3col = 0,
obs2col = 0,
obs3col = 0,
nonobs2col = 0,
nonobs3col = 0,
repstrrel = 1,
fecrel = 1,
stage2col = 0,
stage3col = 0,
juv2col = 0,
juv3col = 0,
stageassign = NA,
stagesize = NA,
censor = FALSE,
censorcol = 0,
censorkeep = 0,
spacing = NA,
NAas0 = FALSE,
NRasRep = FALSE,
NOasObs = FALSE,
prebreeding = TRUE,
age_offset = 0,
reduce = TRUE,
a2check = FALSE,
quiet = FALSE
)
data 
The horizontal data file. 
popidcol 
A variable name or column number corresponding to the identity of the population for each individual. 
patchidcol 
A variable name or column number corresponding to the identity of the patch or subpopulation for each individual, if patches have been designated within populations. 
individcol 
A variable name or column number corresponding to the unique identity of each individual. 
year2col 
A variable name or column number corresponding to occasion t (year or time). 
year3col 
A variable name or column number corresponding to occasion t+1 (year or time). 
xcol 
A variable name or column number corresponding to the X coordinate of each individual in Cartesian space. 
ycol 
A variable name or column number corresponding to the Y coordinate of each individual in Cartesian space. 
sizea2col 
A variable name or column number corresponding to the primary size entry in occasion t. 
sizea3col 
A variable name or column number corresponding to the primary size entry in occasion t+1. 
sizeb2col 
A variable name or column number corresponding to the secondary size entry in occasion t. 
sizeb3col 
A variable name or column number corresponding to the secondary size entry in occasion t+1. 
sizec2col 
A variable name or column number corresponding to the tertiary size entry in occasion t. 
sizec3col 
A variable name or column number corresponding to the tertiary size entry in occasion t+1. 
repstra2col 
A variable name or column number corresponding to the production of reproductive structures, such as flowers, in occasion t. This can be binomial or count data, and is used to in analysis of the probability of reproduction. 
repstra3col 
A variable name or column number corresponding to the production of reproductive structures, such as flowers, in occasion t+1. This can be binomial or count data, and is used to in analysis of the probability of reproduction. 
repstrb2col 
A second variable name or column number corresponding to the production of reproductive structures, such as flowers, in occasion t. This can be binomial or count data. 
repstrb3col 
A second variable name or column number corresponding to the production of reproductive structures, such as flowers, in occasion t+1. This can be binomial or count data. 
feca2col 
A variable name or column number corresponding to fecundity in occasion t. This may represent egg counts, fruit counts, seed production, etc. 
feca3col 
A variable name or column number corresponding to fecundity in occasion t+1. This may represent egg counts, fruit counts, seed production, etc. 
fecb2col 
A second variable name or column number corresponding to fecundity in occasion t. This may represent egg counts, fruit counts, seed production, etc. 
fecb3col 
A second variable name or column number corresponding to fecundity in occasion t+1. This may represent egg counts, fruit counts, seed production, etc. 
indcova2col 
A variable name or column number corresponding to an individual covariate to be used in analysis, in occasion t. 
indcova3col 
A variable name or column number corresponding to an individual covariate to be used in analysis, in occasion t+1. 
indcovb2col 
A variable name or column number corresponding to a second individual covariate to be used in analysis, in occasion t. 
indcovb3col 
A variable name or column number corresponding to a second individual covariate to be used in analysis, in occasion t+1. 
indcovc2col 
A variable name or column number corresponding to a third individual covariate to be used in analysis, in occasion t. 
indcovc3col 
A variable name or column number corresponding to a third individual covariate to be used in analysis, in occasion t+1. 
alive2col 
A variable name or column number that provides information
on whether an individual is alive in occasion t. If used, living
status must be designated as binomial (living = 
alive3col 
A variable name or column number that provides information
on whether an individual is alive in occasion t+1. If used, living
status must be designated as binomial (living = 
dead2col 
A variable name or column number that provides information on
whether an individual is dead in occasion t. If used, dead status
must be designated as binomial (living = 
dead3col 
A variable name or column number that provides information on
whether an individual is dead in occasion t+1. If used, dead status
must be designated as binomial (living = 
obs2col 
A variable name or column number providing information on
whether an individual is in an observable stage in occasion t. If
used, observation status must be designated as binomial (observed = 
obs3col 
A variable name or column number providing information on
whether an individual is in an observable stage in occasion t+1. If
used, observation status must be designated as binomial (observed = 
nonobs2col 
A variable name or column number providing information on
whether an individual is in an unobservable stage in occasion t. If
used, observation status must be designated as binomial (observed = 
nonobs3col 
A variable name or column number providing information on
whether an individual is in an unobservable stage in occasion t+1. If
used, observation status must be designated as binomial (observed = 
repstrrel 
This is a scalar multiplier making the variable represented
by 
fecrel 
This is a scalar multiplier making the variable represented by

stage2col 
Optional variable name or column number corresponding to life history stage in occasion t. 
stage3col 
Optional variable name or column number corresponding to life history stage in occasion t+1. 
juv2col 
A variable name or column number that marks individuals in
immature stages in occasion t. Function 
juv3col 
A variable name or column number that marks individuals in
immature stages in occasion t+1. Function 
stageassign 
The stageframe object identifying the life history model
being operationalized. Note that if 
stagesize 
A variable name or column number describing which size
variable to use in stage estimation. Defaults to 
censor 
A logical variable determining whether the output data should
be censored using the variable defined in 
censorcol 
A variable name or column number corresponding to a censor variable within the dataset, used to distinguish between entries to use and those to discard from analysis, or to designate entries with special issues that require further attention. 
censorkeep 
The value of the censoring variable identifying data that
should be included in analysis. Defaults to 
spacing 
The spacing at which density should be estimated, if density
estimation is desired and X and Y coordinates are supplied. Given in the same
units as those used in the X and Y coordinates given in 
NAas0 
If TRUE, then all 
NRasRep 
If set to 
NOasObs 
If 
prebreeding 
A logical term indicating whether the life history model
is prebreeding. If so, then 
age_offset 
A number to add automatically to all values of age at time
t. Defaults to 
reduce 
A logical variable determining whether unused variables and
some invariant state variables should be removed from the output dataset.
Defaults to 
a2check 
A logical variable indicating whether to retain all data with
living status at occasion t. Defaults to 
quiet 
A logical variable indicating whether to silence warnings.
Defaults to 
If all inputs are properly formatted, then this function will output
a historical vertical data frame (class hfvdata
), meaning that the
output data frame will have three consecutive years of size and reproductive
data per individual per row. This data frame is in standard format for all
functions used in lefko3
, and so can be used without further
modification. Note that determination of state in occasions t1 and
t+1 gives preference to condition in occasion t within the
input dataset. Conflicts in condition in input datasets that have both
occasions t and t+1 listed per row are resolved by using
condition in occasion t.
Variables in this data frame include the following:
rowid 
Unique identifier for the row of the data frame. 
popid 
Unique identifier for the population, if given. 
patchid 
Unique identifier for patch within population, if given. 
individ 
Unique identifier for the individual. 
year2 
Year or time in occasion t. 
firstseen 
Occasion of first observation. 
lastseen 
Occasion of last observation. 
obsage 
Observed age in occasion t, assuming first observation corresponds to age = 0. 
obslifespan 
Observed lifespan, given as 
xpos1 , xpos2 , xpos3 
X position in Cartesian space in occasions t1, t, and t+1, respectively, if provided. 
ypos1 , ypos2 , ypos3 
Y position in Cartesian space in occasions t1, t, and t+1, respectively, if provided. 
sizea1 , sizea2 , sizea3 
Main size measurement in occasions t1, t, and t+1, respectively. 
sizeb1 , sizeb2 , sizeb3 
Secondary size measurement in occasions t1, t, and t+1, respectively. 
sizec1 , sizec2 , sizec3 
Tertiary size measurement in occasions t1, t, and t+1, respectively. 
size1added , size2added , size3added 
Sum of primary, secondary, and tertiary size measurements in occasions t1, t, and t+1, respectively. 
repstra1 , repstra2 , repstra3 
Main numbers of reproductive structures in occasions t1, t, and t+1, respectively. 
repstrb1 , repstrb2 , repstrb3 
Secondary numbers of reproductive structures in occasions t1, t, and t+1, respectively. 
repstr1added , repstr2added , repstr3added 
Sum of primary and secondary reproductive structures in occasions t1, t, and t+1, respectively. 
feca1 , feca2 , feca3 
Main numbers of offspring in occasions t1, t, and t+1, respectively. 
fecb1 , fecb2 , fecb3 
Secondary numbers of offspring in occasions t1, t, and t+1, respectively. 
fec1added , fec2added , fec3added 
Sum of primary and secondary fecundity in occasions t1, t, and t+1, respectively. 
censor1 , censor2 , censor3 
Censor status values in occasions t1, t, and t+1, respectively. 
juvgiven1 , juvgiven2 , juvgiven3 
Binomial variable indicating whether
individual is juvenile in occasions t1, t, and t+1.
Only given if 
obsstatus1 , obsstatus2 , obsstatus3 
Binomial observation status in occasions t1, t, and t+1, respectively. 
repstatus1 , repstatus2 , repstatus3 
Binomial reproductive status in occasions t1, t, and t+1, respectively. 
fecstatus1 , fecstatus2 , fecstatus3 
Binomial offspring production status in occasions t1, t, and t+1, respectively. 
matstatus1 , matstatus2 , matstatus3 
Binomial maturity status in occasions t1, t, and t+1, respectively. 
alive1 , alive2 , alive3 
Binomial status as alive in occasions t1, t, and t+1, respectively. 
density 
Density of individuals per unit designated in 
Warnings that some individuals occur in state combinations that do not match
any stages in the stageframe used to assign stages, and that some individuals
match characteristics of several stages in the stageframe, are common when
first working with a dataset. Typically, these situations can be identified as
NoMatch
entries in stage3
, although such entries may crop up in
stage1
and stage2
, as well. In some cases, these warnings will
arise with no concurrent NoMatch
entries. These are important warnings
and suggest that there is likely a problem with the stageframe. The most
common such problems are: 1) stages have significant overlap in
characteristics, with the most common being overlapping size bins caused by
erroneous definitions of size bin halfwidths; and 2) some individuals exist
in states not defined within the stageframe.
In some datasets with unobservable stages, observation status
(obsstatus
) might not be inferred properly if a single size variable
is used that does not yield sizes greater than 0 in all cases in which
individuals were observed. Such situations may arise, for example, in plants
when leaf number is the dominant size variable used, but individuals
occasionally occur with inflorescences but no leaves. In this instances,
it helps to mark related variables as sizeb
and sizec
, because
observation status will be interpreted in relation to all 3 size variables.
Alternatively, observation status may be input via obs2col
and
obs3col
to force computation with given values (although this requires
all instances of observation and nonobservation to be known and coded ahead
of time). Further analysis can then utilize only a single size variable, of
the user's choosing. Similar issues can arise in reproductive status
(repstatus
).
Juvenile designation should only be used when juveniles fall outside of the size classification scheme used in determining stages. If juveniles are to be size classified along the size spectrum that adults also fall on, then it is best to treat juveniles as mature but not reproductive.
Care should be taken to avoid variables with negative values indicating size, fecundity, or reproductive or observation status. Negative values can be interpreted in different ways, typically reflecting estimation through other algorithms rather than actual measured data. Variables holding negative values can conflict with data management algorithms in ways that are difficult to predict.
Unusual errors (e.g. "Error in pjf..."
) may occur in cases where the
variables are improperly passed, or where seemingly numeric variables include
text and so get automatically converted to string variables.
Density estimation is performed as a count of individuals alive and within
the radius specified in spacing
of the respective individual at some
point in time.
data(cypvert)
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_v2 < historicalize3(data = cypvert, patchidcol = "patch",
individcol = "plantid", year2col = "year2", sizea2col = "Inf2.2",
sizea3col = "Inf2.3", sizeb2col = "Inf.2", sizeb3col = "Inf.3",
sizec2col = "Veg.2", sizec3col = "Veg.3", repstra2col = "Inf2.2",
repstra3col = "Inf2.3", repstrb2col = "Inf.2", repstrb3col = "Inf.3",
feca2col = "Pod.2", feca3col = "Pod.3", repstrrel = 2,
stageassign = cypframe_raw, stagesize = "sizeadded", censorcol = "censor",
censor = FALSE, NAas0 = TRUE, NRasRep = TRUE, reduce = TRUE)
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