This repository contains data and code for the manuscript “Context-dependent consequences of including lagged effects on the projections of structured population models” by ——-. We investigated the consequences of including lagged effects, such as those modeled by distributed lag non-linear models, into integral projection models (i.e., IPMs). We compared population growth rates projected with deterministic IPMs, stochastic IPMs (using ‘matrix-shuffling’), and stochastic IPMs with lagged effects.

Reproducibility

This research compendium has been developed using the statistical programming language R. To work with the compendium, you will need installed on your computer the R software (v4.3 for best compatibility) itself and RStudio Desktop.

You can download the compendium as a zip file from from this URL: master.zip.

To run the compendium and reproduce all outputs:

• Open the project in RStudio by double-clicking the .Rproj file.
• This project uses renv for package management, which should be installed automatically when opening the project. Run renv::restore() to install all required packages (this will have the highest likelihood of succeeding if run on R v4.3.0).
• You can run renv::deactivate() if you want to turn of renv but keep the lockfile as a record of package versions used.
• This project uses targets for workflow management. The functions used in the project are defined in R/ and the steps are defined in _targets.R and summarized in the schematic below. Run targets::tar_make() or targets::tar_make_clustermq() from the R console to run all code and produce all outputs.

tar_source() only sources R scripts. Ignoring non-R files: R/.gitkeep + lambda_bt_det_cf declared [5 branches] + lambda_bt_dlnm_cf declared [500 branches] + lambda_bt_stoch_cf declared [5 branches] + lambda_bt_det_ff declared [5 branches] + lambda_bt_stoch_ff declared [5 branches] + lambda_bt_dlnm_ff declared [500 branches]

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Loading

NOTES:

• The targets lambda_bt_dlnm_ff and lambda_bt_dlnm_cf will take a very long time to run (days), so you may want to comment those out before attempting to reproduce results.
• If you want to make use of HPC, follow instructions here to customize templates and options.