Overview
secpRod is an open source package for the analysis and calculation of secondary production for populations and communities in R. secpRod uses data from repeated sampling of population abundance and size structure in a tall data structure and a taxon information sheet as the base objects. In addition to estimating secondary production for communities with multiple methods, secpRod also provides a tools to perform data processing actions common in the workflow prior to calculation, such as length to mass conversions using length~mass relationships and visualizing population density and size structure to aid the determination of cohort structure and assess best methods for secondary production estimation.
Installation
# To install the latest version Github:
# install.packages('devtools')
devtools::install_github("jimjunker1/secpRod")Status: Active Development
The secpRod package is currently under development for deployment in conjunction with the ’Secondary Production and Quantitative Food Webs” chapter in the “Methods in Stream Ecology” 4th edition. This initial deployment will include tools to estimate secondary production and its uncertainty through bootstrapping approaches. Future work will include additional inferential frameworks (e.g., Bayesian inference) of these approaches.
Usage
The basic usage of the main function, calc_production(), is outlined in the “A few simple examples” vignette. This article showcases the calculation of secondary production of a single simulated population. For a full walkthrough showcasing some of the additional tools for data processing, see the “A full example” here.
Contributing
This is an actively developing package and we welcome any contributions.
Please note that the ‘secpRod’ project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
If you would like to contribute please see the contributing document.
These are heavily borrowed and adapted from the WEEcology lab Portal project adapted from the Contributor Covenant and portalr package, respectively.