equiv_input: Create an Equivalence Vector for Each Population
In adapt3: Adaptive Dynamics and Community Matrix Model Projections
equiv_input R Documentation
Create an Equivalence Vector for Each Population
Description
Function equiv_input() creates a data frame summarizing the weighting
of individuals of different species, populations, and stages relative to one
another in terms of the overall community size or population size.
Equivalance values can be thought of as Lotka-Volterra coefficients.
Usage
equiv_input(mpm, stage2 = NA, stage1 = NA, age2 = NA, value = 1)
Arguments
mpm
The lefkoMat object to be used in projection. Can be an example
MPM if function-based projection is planned.
stage2
A vector showing the name or number of a stage in occasion
t that should be set to a positive number of individuals in the start
vector. Abbreviations for groups of stages are also usable (see Notes).
This input is required for all stage-based and age-by-stage MPMs. Defaults to
NA.
stage1
A vector showing the name or number of a stage in occasion
t-1 that should be set to a positive number of individuals in the
start vector. Abbreviations for groups of stages are also usable (see Notes).
This is only used for historical MPMs, since the rows of hMPMs correspond to
stage-pairs in times t and t-1 together. Only required for
historical MPMs, and will result in errors if otherwise used.
age2
A vector showing the age of each respective stage in occasion
t that should be set to a positive number of individuals in the start
vector. Only used for Leslie and age-by-stage MPMs. Defaults to NA.
value
A vector showing the values, in order, of the number of
individuals set for the stage or stage-pair in question. Defaults to
1.
Value
A list of class adaptEq, with four objects, which can be
used as input in function project3(). The last three include
the ahstages, hstages, and agestages objects from the
lefkoMat object supplied in mpm. The first element in the list
is a data frame with the following variables:
stage2
Stage at occasion t.
stage_id_2
The stage number associated with stage2.
stage1
Stage at occasion t-1, if historical. Otherwise NA.
stage_id_1
The stage number associated with stage1.
age2
The age of individuals in stage2 and, if applicable,
stage1. Only used in age-by-stage MPMs.
row_num
A number indicating the respective starting vector element.
value
Number of individuals in corresponding stage or stage-pair.
Notes
Users should generally consider which species, population, and / or stage to
set as the reference, which should be designated with a value of 1.
In some life histories, certain stages may not count against population size
with regards to the kind and value of density dependence decided on. An
example might be the dormant seed stage in some plant species. These
equivalence values should be set to 0.
Entries in 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 non-reproductive 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 non-propagule 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.
Examples
library(lefko3)
data(cypdata)
data(cypa_data)
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)
cycaraw_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)
cyparaw_v1 <- verticalize3(data = cypa_data, noyears = 18, firstyear = 1994,
individcol = "plant_id", blocksize = 2, sizeacol = "Inf.94",
sizebcol = "Veg.94", repstracol = "Inf.94", fecacol = "Inf.94",
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)
cyp_supp_list1 <- list(cypsupp2r, cypsupp2r)
cycamatrix2r <- rlefko2(data = cycaraw_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")
cypamatrix2r <- rlefko2(data = cyparaw_v1, stageframe = cypframe_raw,
year = "all", stages = c("stage3", "stage2", "stage1"),
size = c("size3added", "size2added"), supplement = cypsupp2r,
yearcol = "year2", patchcol = "patchid", indivcol = "individ")
cyp_mpm_list <- list(cycamatrix2r, cypamatrix2r)
cyca2_start <- start_input(cycamatrix2r, stage2 = c("SD", "P1", "P2"),
value = c(500, 100, 200))
cypa2_start <- start_input(cypamatrix2r, stage2 = c("SD", "P1", "P2"),
value = c(5000, 1000, 2000))
cyp_start_list <- list(cyca2_start, cypa2_start)
cyp2_dv <- density_input(cypamatrix2r, stage3 = c("SD", "P1"),
stage2 = c("rep", "rep"), style = c(1, 1), alpha = c(0.5, 1.2),
beta = c(1.0, 2.0), type = c(2, 1))
cyp_dv_list <- list(cyp2_dv, cyp2_dv)
cyp_eq <- equiv_input(cycamatrix2r,
stage2 = c("SD", "P1", "SL", "D", "XSm", "Sm", "Md", "Lg", "XLg"),
value = c(0, 1, 1, 1, 1, 1, 1, 1, 1))
eq_list <- list(cyp_eq, cyp_eq)
cyp_comm_proj <- project3(mpms = cyp_mpm_list, starts = cyp_start_list,
density = cyp_dv_list, times = 10)
summary(cyp_comm_proj)
adapt3 documentation built on June 7, 2026, 9:08 a.m.
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| equiv_input | R Documentation |
Create an Equivalence Vector for Each Population
Description
Function equiv_input() creates a data frame summarizing the weighting
of individuals of different species, populations, and stages relative to one
another in terms of the overall community size or population size.
Equivalance values can be thought of as Lotka-Volterra coefficients.
Usage
equiv_input(mpm, stage2 = NA, stage1 = NA, age2 = NA, value = 1)
Arguments
mpm |
The lefkoMat object to be used in projection. Can be an example MPM if function-based projection is planned. |
stage2 |
A vector showing the name or number of a stage in occasion
t that should be set to a positive number of individuals in the start
vector. Abbreviations for groups of stages are also usable (see Notes).
This input is required for all stage-based and age-by-stage MPMs. Defaults to
|
stage1 |
A vector showing the name or number of a stage in occasion t-1 that should be set to a positive number of individuals in the start vector. Abbreviations for groups of stages are also usable (see Notes). This is only used for historical MPMs, since the rows of hMPMs correspond to stage-pairs in times t and t-1 together. Only required for historical MPMs, and will result in errors if otherwise used. |
age2 |
A vector showing the age of each respective stage in occasion
t that should be set to a positive number of individuals in the start
vector. Only used for Leslie and age-by-stage MPMs. Defaults to |
value |
A vector showing the values, in order, of the number of
individuals set for the stage or stage-pair in question. Defaults to
|
Value
A list of class adaptEq, with four objects, which can be
used as input in function project3(). The last three include
the ahstages, hstages, and agestages objects from the
lefkoMat object supplied in mpm. The first element in the list
is a data frame with the following variables:
stage2 |
Stage at occasion t. |
stage_id_2 |
The stage number associated with |
stage1 |
Stage at occasion t-1, if historical. Otherwise NA. |
stage_id_1 |
The stage number associated with |
age2 |
The age of individuals in |
row_num |
A number indicating the respective starting vector element. |
value |
Number of individuals in corresponding stage or stage-pair. |
Notes
Users should generally consider which species, population, and / or stage to
set as the reference, which should be designated with a value of 1.
In some life histories, certain stages may not count against population size
with regards to the kind and value of density dependence decided on. An
example might be the dormant seed stage in some plant species. These
equivalence values should be set to 0.
Entries in 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 non-reproductive 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 non-propagule 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.
Examples
library(lefko3)
data(cypdata)
data(cypa_data)
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)
cycaraw_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)
cyparaw_v1 <- verticalize3(data = cypa_data, noyears = 18, firstyear = 1994,
individcol = "plant_id", blocksize = 2, sizeacol = "Inf.94",
sizebcol = "Veg.94", repstracol = "Inf.94", fecacol = "Inf.94",
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)
cyp_supp_list1 <- list(cypsupp2r, cypsupp2r)
cycamatrix2r <- rlefko2(data = cycaraw_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")
cypamatrix2r <- rlefko2(data = cyparaw_v1, stageframe = cypframe_raw,
year = "all", stages = c("stage3", "stage2", "stage1"),
size = c("size3added", "size2added"), supplement = cypsupp2r,
yearcol = "year2", patchcol = "patchid", indivcol = "individ")
cyp_mpm_list <- list(cycamatrix2r, cypamatrix2r)
cyca2_start <- start_input(cycamatrix2r, stage2 = c("SD", "P1", "P2"),
value = c(500, 100, 200))
cypa2_start <- start_input(cypamatrix2r, stage2 = c("SD", "P1", "P2"),
value = c(5000, 1000, 2000))
cyp_start_list <- list(cyca2_start, cypa2_start)
cyp2_dv <- density_input(cypamatrix2r, stage3 = c("SD", "P1"),
stage2 = c("rep", "rep"), style = c(1, 1), alpha = c(0.5, 1.2),
beta = c(1.0, 2.0), type = c(2, 1))
cyp_dv_list <- list(cyp2_dv, cyp2_dv)
cyp_eq <- equiv_input(cycamatrix2r,
stage2 = c("SD", "P1", "SL", "D", "XSm", "Sm", "Md", "Lg", "XLg"),
value = c(0, 1, 1, 1, 1, 1, 1, 1, 1))
eq_list <- list(cyp_eq, cyp_eq)
cyp_comm_proj <- project3(mpms = cyp_mpm_list, starts = cyp_start_list,
density = cyp_dv_list, times = 10)
summary(cyp_comm_proj)
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