Package 'demovuln'

Title: Demographic Vulnerability Metrics for Matrix Population Models
Description: Simulates temporally structured perturbations in matrix population models and computes population reduction and integrated demographic vulnerability across perturbation regimes. Perturbations can be applied to adult survival, juvenile survival, fecundity, all demographic entries, or user-defined matrix elements. The package provides tools to simulate individual perturbation trajectories, evaluate perturbation grids, and summarize demographic vulnerability in structured populations.
Authors: Àlex Giménez-Romero [aut, cre] (ORCID: <https://orcid.org/0000-0003-2796-6801>), Meritxell Genovart [aut] (ORCID: <https://orcid.org/0000-0003-2919-1288>)
Maintainer: Àlex Giménez-Romero <[email protected]>
License: MIT + file LICENSE
Version: 0.1.0
Built: 2026-05-28 18:10:19 UTC
Source: https://github.com/cran/demovuln

Help Index

Apply a proportional perturbation to a projection matrix

Description

Apply a proportional perturbation to a projection matrix

Usage

apply_perturbation(
  model,
  target,
  magnitude,
  survival_affects_fecundity = TRUE,
  custom_mask = NULL
)

Arguments

model

A demovuln_model object or a numeric square projection matrix.
target

One of "adult_survival", "juvenile_survival", "fecundity", "all", or "custom".
magnitude

Proportional reduction applied to the selected entries. Must lie in ⁠[0, 1]⁠.
survival_affects_fecundity

Logical. If TRUE, survival perturbations scale whole source-stage columns, including fecundity entries.
custom_mask

Optional logical matrix used when target = "custom".

Value

Perturbed projection matrix.

Build a perturbation target mask

Description

Return a logical matrix selecting the entries affected by a perturbation.

Usage

build_target_mask(
  model,
  target,
  survival_affects_fecundity = TRUE,
  custom_mask = NULL
)

Arguments

model

A demovuln_model object or a numeric square projection matrix.
target

One of "adult_survival", "juvenile_survival", "fecundity", "all", or "custom".
survival_affects_fecundity

Logical. If TRUE, survival perturbations scale whole source-stage columns, including fecundity entries.
custom_mask

Optional logical matrix used when target = "custom".

Value

Logical matrix with the same dimensions as the projection matrix.

Compute integrated demographic vulnerability

Description

Compute integrated demographic vulnerability

Usage

compute_vulnerability(table, column = "population_reduction")

Arguments

table

Data frame returned by run_grid().
column

Name of the column containing percent population reduction.

Value

Mean percent population reduction, ignoring missing values.

Dominant eigenvalue of a projection matrix

Description

Dominant eigenvalue of a projection matrix

Usage

dominant_eigenvalue(A)

Arguments

A

Numeric square projection matrix.

Value

The real part of the eigenvalue with largest modulus.

Enumerate perturbation-grid scenarios

Description

Enumerate perturbation-grid scenarios

Usage

grid_scenarios(grid, skip_infeasible = TRUE)

Arguments

grid

A demovuln_grid object.
skip_infeasible

Logical. If TRUE, discard regimes where duration is greater than period.

Value

Data frame with columns magnitude, duration, period, and feasible.

Matrix population model

Description

Create a matrix population model and define the demographic targets used by perturbation functions.

Usage

matrix_population_model(
  A,
  fecundity_mask = NULL,
  fecundity_rows = 1L,
  adult_stages = NULL,
  juvenile_stages = NULL,
  name = NULL
)

Arguments

A

Numeric square projection matrix. Columns are source stages at time t and rows are destination stages at time t + 1.
fecundity_mask

Optional logical matrix with the same dimensions as A, identifying fecundity entries.
fecundity_rows

Integer vector identifying rows interpreted as newborn or reproductive-output rows. Defaults to the first row.
adult_stages

Optional integer vector with source-stage columns interpreted as adult or reproductive stages.
juvenile_stages

Optional integer vector with source-stage columns interpreted as juvenile or pre-reproductive stages.
name

Optional model or species label.

Value

An object of class demovuln_model.

Perturbation grid

Description

Perturbation grid

Usage

perturbation_grid(magnitudes, durations, periods)

Arguments

magnitudes

Numeric vector of proportional reductions.
durations

Integer vector of perturbation durations.
periods

Integer vector of perturbation periods.

Value

An object of class demovuln_grid.

Build a perturbation grid from frequencies

Description

Build a perturbation grid from frequencies

Usage

perturbation_grid_from_frequencies(
  magnitudes,
  durations,
  frequencies,
  generation_time = 1,
  rounding = c("nearest", "floor", "ceil")
)

Arguments

magnitudes

Numeric vector of proportional reductions.
durations

Integer vector of perturbation durations.
frequencies

Numeric vector of event frequencies, interpreted as events per generation_time projection intervals.
generation_time

Number of projection intervals corresponding to one reference generation or time unit.
rounding

One of "nearest", "floor", or "ceil".

Value

An object of class demovuln_grid.

Compute percent population reduction

Description

Compute percent population reduction

Usage

population_reduction(final_population, baseline_final_population)

Arguments

final_population

Final population size under perturbed dynamics.
baseline_final_population

Final population size under unperturbed baseline dynamics.

Value

Percent population reduction relative to the baseline.

Simulate a perturbation grid

Description

Simulate a perturbation grid

Usage

run_grid(
  model,
  target,
  grid,
  t_max,
  recovery_steps = 0L,
  start = 0L,
  initial_state = NULL,
  normalize_by_lambda = TRUE,
  survival_affects_fecundity = TRUE,
  custom_mask = NULL,
  return_trajectories = FALSE,
  skip_infeasible = TRUE,
  force_during_recovery = FALSE
)

Arguments

model

A demovuln_model object or a numeric square projection matrix.
target

One of "adult_survival", "juvenile_survival", "fecundity", "all", or "custom".
grid

A demovuln_grid object.
t_max

Number of projection intervals in the perturbation-forcing window.
recovery_steps

Number of additional unperturbed projection intervals.
start

Projection interval at which the first perturbation event starts.
initial_state

Optional initial population vector.
normalize_by_lambda

Logical. If TRUE, normalize matrices by the dominant eigenvalue of the unperturbed projection matrix.
survival_affects_fecundity

Logical. If TRUE, survival perturbations scale whole source-stage columns, including fecundity entries.
custom_mask

Optional logical matrix used when target = "custom".
return_trajectories

Logical. If TRUE, store individual simulation outputs for all feasible scenarios.
skip_infeasible

Logical. If TRUE, skip regimes where duration is greater than period. If FALSE, keep them in the output table with missing population reduction.
force_during_recovery

Logical. If TRUE, scheduled perturbations continue during the recovery window.

Value

An object of class demovuln_grid_result.

Simulate dynamics under a temporally structured perturbation

Description

Simulate dynamics under a temporally structured perturbation

Usage

simulate_dynamics(
  model,
  target = "adult_survival",
  magnitude,
  duration,
  period,
  t_max,
  recovery_steps = 0L,
  start = 0L,
  initial_state = NULL,
  normalize_by_lambda = TRUE,
  survival_affects_fecundity = TRUE,
  custom_mask = NULL,
  return_stage_vectors = FALSE,
  force_during_recovery = FALSE
)

Arguments

model

A demovuln_model object or a numeric square projection matrix.
target

One of "adult_survival", "juvenile_survival", "fecundity", "all", or "custom".
magnitude

Proportional reduction applied to the selected entries.
duration

Number of consecutive projection intervals during which each perturbation event is active.
period

Number of projection intervals between perturbation onsets.
t_max

Number of projection intervals in the perturbation-forcing window.
recovery_steps

Number of additional unperturbed projection intervals after the forcing window.
start

Projection interval at which the first perturbation event starts. The default 0 means that forcing can begin at the first projection step.
initial_state

Optional initial population vector. If omitted, the stable stage distribution of the unperturbed model is used.
normalize_by_lambda

Logical. If TRUE, baseline and perturbed matrices are divided by the dominant eigenvalue of the unperturbed projection matrix.
survival_affects_fecundity

Logical. If TRUE, survival perturbations scale whole source-stage columns, including fecundity entries.
custom_mask

Optional logical matrix used when target = "custom".
return_stage_vectors

Logical. If TRUE, return the full stage-vector trajectories.
force_during_recovery

Logical. If TRUE, scheduled perturbations continue during the recovery window. The default is FALSE.

Value

An object of class demovuln_simulation.

Stable stage distribution

Description

Stable stage distribution

Usage

stable_stage_distribution(model)

Arguments

model

A demovuln_model object or a numeric square projection matrix.

Value

Numeric vector normalized to sum to one.