generate_mpm_set {mpmsim}

Generate lists of Lefkovitch matrix population models (MPMs) based on life history archetypes

Description

This function is deprecated. Use rand_lefko_set instead.

Usage

generate_mpm_set(
  n = 10,
  n_stages = 3,
  archetype = 1,
  fecundity = 1.5,
  split = TRUE,
  by_type = TRUE,
  as_compadre = TRUE,
  max_surv = 0.99,
  constraint = NULL,
  attempts = 1000
)

Arguments

n

The number of MPMs to generate. Default is 10.

n_stages

The number of stages for the MPMs. Default is 3.

archetype

The archetype of the MPMs. Default is 1.

fecundity

A vector of fecundities for the MPMs. Default is 1.5.

split

A logical indicating whether to split into submatrices. Default is TRUE.

by_type

A logical indicating whether the matrices should be returned in a list by type (A, U, F, C). If split is FALSE, then by_type must is coerced to be FALSE. Defaults to TRUE.

as_compadre

A logical indicating whether the matrices should be returned as a CompadreDB object. Default is TRUE. If FALSE, the function returns a list.

max_surv

The maximum acceptable survival value, calculated across all transitions from a stage. Defaults to 0.99. This is only used if split = TRUE.

constraint

An optional data frame with 4 columns named fun, arg, lower and upper. These columns specify (1) a function that outputs a metric derived from an A matrix and (2) an argument for the function (NA, if no argument supplied) (3) the lower acceptable bound for the metric and (4) upper acceptable bound for the metric. This could be used to specify

attempts

An integer indicating the number of attempts To be made when simulating matrix model. The default is 1000. If it takes more than 1000 attempts to make a matrix that satisfies the conditions set by the other arguments, then a warning is produced.

Details

This function generates a list of n MPMs according to the specified criteria. Criteria include the archetype, and the acceptable constraining criteria, which could include lambda, generation time or any other metric derived from an A matrix. The function attempts to find matrices that fulfil the criteria, discarding unacceptable matrices. By default, if it takes more than 1000 attempts to find a suitable matrix model, then an error is produced. However, the number of attempts can be altered with the attempts parameter.

Value

A list of MPMs that meet the specified criteria.

Author(s)

Owen Jones [e-mail]

See Also

random_mpm() which this function is essentially a wrapper for.

Other Lefkovitch matrices: rand_lefko_mpm(), rand_lefko_set(), random_mpm()

Examples

set.seed(42) # set seed for repeatability

# Basic operation, without splitting matrices and with no constraints
generate_mpm_set(
  n = 10, n_stages = 5, fecundity = c(0, 0, 4, 8, 10),
  archetype = 4, split = FALSE, by_type = FALSE, as_compadre = FALSE
)

# Constrain outputs to A matrices with lambda between 0.9 and 1.1
library(popbio)
constrain_df <- data.frame(
  fun = "lambda", arg = NA, lower = 0.9, upper =
    1.1
)
generate_mpm_set(
  n = 10, n_stages = 5, fecundity = c(0, 0, 4, 8, 10),
  archetype = 4, constraint = constrain_df, as_compadre = FALSE
)

# As above, but using popdemo::eigs function instead of popbio::lambda
# to illustrate use of argument
library(popdemo)
constrain_df <- data.frame(
  fun = "eigs", arg = "lambda", lower = 0.9, upper =
    1.1
)
generate_mpm_set(
  n = 10, n_stages = 5, fecundity = c(0, 0, 4, 8, 10),
  archetype = 4, constraint = constrain_df, as_compadre = FALSE
)

# Multiple constraints
# Constrain outputs to A matrices with lambda between 0.9 and 1.1, generation
# time between 3 and 5 and damping ratio between 1 and 7.
library(popbio)
constrain_df <- data.frame(
  fun = c("lambda", "generation.time", "damping.ratio"),
  arg = c(NA, NA, NA),
  lower = c(0.9, 3.0, 1.0),
  upper = c(1.1, 5.0, 7.0)
)
generate_mpm_set(
  n = 10, n_stages = 5, fecundity = c(0, 0, 4, 8, 10),
  archetype = 4, constraint = constrain_df, as_compadre = FALSE
)