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demovuln for R

demovuln is a lightweight R implementation of the demographic vulnerability framework for matrix population models.

The main Python package is available at:

• PyPI: https://pypi.org/project/demovuln/
• Documentation: https://demovuln.readthedocs.io/en/latest/
• GitHub: https://github.com/agimenezromero/demovuln

This R package is intended as a companion implementation that can be installed directly from GitHub.

Installation

Install the development version from GitHub with:

install.packages("remotes")
remotes::install_github("agimenezromero/demovuln-r")

Basic usage

library(demovuln)

A <- matrix(
  c(0.0, 0.4,
    2.0, 0.7),
  nrow = 2,
  byrow = FALSE
)

model <- matrix_population_model(A)

sim <- simulate_dynamics(
  model,
  target = "adult_survival",
  magnitude = 0.25,
  duration = 1,
  period = 3,
  t_max = 50,
  recovery_steps = 10
)

sim$reduction
sim$abundance

The projection matrix follows the standard matrix-population-model convention: columns are source stages at time t, and rows are destination stages at time t + 1.

The example above produces the matrix:

     [,1] [,2]
[1,]  0.0  2.0
[2,]  0.4  0.7

Perturbation-grid analysis

grid <- perturbation_grid(
  magnitudes = seq(0, 1, length.out = 11),
  durations = c(0, 1, 2, 3),
  periods = c(1, 2, 3, 5, 10)
)

out <- run_grid(
  model,
  target = "adult_survival",
  grid = grid,
  t_max = 50,
  recovery_steps = 10
)

out$vulnerability
head(out$table)

Demographic targets

The package supports perturbations to:

• adult_survival
• juvenile_survival
• fecundity
• all
• custom

By default, adult stages are inferred as source-stage columns with at least one fecundity entry, and juvenile stages are inferred as the remaining source-stage columns. These definitions can be specified explicitly:

model <- matrix_population_model(
  A,
  adult_stages = 2,
  juvenile_stages = 1
)

Custom perturbation targets can be defined with logical masks:

custom_mask <- matrix(
  c(FALSE, TRUE,
    FALSE, FALSE),
  nrow = 2,
  byrow = FALSE
)

sim <- simulate_dynamics(
  model,
  target = "custom",
  custom_mask = custom_mask,
  magnitude = 0.5,
  duration = 1,
  period = 3,
  t_max = 50
)

Conceptual summary

For a given perturbation regime, population reduction is computed as:

rho = 100 * (1 - N_perturbed(T) / N_baseline(T))

where N_perturbed(T) is the final population size under perturbed dynamics and N_baseline(T) is the final population size under the unperturbed baseline.

Integrated vulnerability is the mean population reduction across the simulated perturbation space:

Phi = mean(rho)

Example vignettes

Example vignettes are available in the vignettes/ directory.

A complete user tutorial is included in two formats:

• inst/tutorials/demovuln-tutorial.R: executable RStudio script with theory, code, and figures.
• inst/tutorials/demovuln-tutorial-notebook.Rmd: RStudio Notebook with the same content.
• vignettes/demovuln-tutorial.Rmd: package vignette version for browseVignettes("demovuln").

To install the package and build the vignettes locally:

remotes::install_github(
  "agimenezromero/demovuln-r",
  build_vignettes = TRUE
)

browseVignettes("demovuln")

## Development checks

After cloning the repository, run:

```r
devtools::test()
devtools::check()

License

This package is distributed under the MIT License.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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