tdsa: An R package to perform time-dependent sensitivity analysis

Wee Hao Ng

September 10, 2023

Introduction

This package automates the steps required to perform time-dependent sensitivity analysis (TDSA), for both continuous- and discrete-time models. Refer to the bibliography for the theory behind TDSA, and the vignette for a simple demonstration of how to use the package.

Installation

The package requires R version (>= 3.5.0).

CRAN

To install the ranger R package from CRAN, use the R command

    install.packages("tdsa")

This should also install any dependencies that are missing.

Github

To install from GitHub, the easiest way is to use devtools, using the R command

    devtools::install_github("weehaong/tdsa")

To install from GitHub without using devtools:

1. Install the dependencies deSolve, mathjaxr and numDeriv.

2. Download and unpack the repository from GitHub.

3. Build the package using the OS terminal command

    R CMD build path_to_folder
   

   The argument path_to_folder in the command should point to the folder containing the unpacked repository. This will create a tarball (.tar.gz file), e.g. tdsa_1.0-1.tar.gz. Note that for Windows users, RTools will need to be installed, and both R and RTools added to the system or user path.

4. Install the tarball. This can be done using the R command

    install.packages(path_to_tarball, repos=NULL, type="source")
   

   where path_to_tarball should point to the tarball file created in the previous step.

Bibliography

Ng, W. H., Myers, C. R., McArt, S., & Ellner, S. P. (in press). A time for every purpose: using time-dependent sensitivity analysis to help understand and manage dynamic ecological systems. American Naturalist. doi: 10.1086/726143. eprint doi: 10.1101/2023.04.13.536769.

Ng, W. H., Myers, C. R., McArt, S., & Ellner, S. P. (in review). tdsa: An R package to perform time-dependent sensitivity analysis. Methods in Ecology and Evolution.