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and Environmental Modeling","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"# Supporting [automated forecasting](https://github.com/weecology/portal-forecasts) of [rodent populations](https://portal.weecology.org/)\n\n\u003cimg src=\"man/figures/portalcasting.png\" alt=\"hexagon software logo, light grey blue background, basic lettering at the top says portalcasting, main image is a drawn all black rodent standing on two feet with a fishing rod in hand and a brown fishing hat on head, standing next to a tan and green tackle box.\" width=\"200px\" align=\"right\"\u003e   \n\n[![R-CMD-check](https://github.com/weecology/portalcasting/actions/workflows/r-cmd-check.yaml/badge.svg)](https://github.com/weecology/portalcasting/actions/workflows/r-cmd-check.yaml)\n[![Docker](https://github.com/weecology/portalcasting/actions/workflows/docker-publish.yml/badge.svg)](https://github.com/weecology/portalcasting/actions/workflows/docker-publish.yml)\n[![Codecov test coverage](https://img.shields.io/codecov/c/github/weecology/portalcasting/main.svg)](https://app.codecov.io/github/weecology/portalcasting/branch/main)\n[![Lifecycle:maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![License](http://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/weecology/portal-forecasts/master/LICENSE)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3332973.svg)](https://doi.org/10.5281/zenodo.3332973)\n[![NSF-1929730](https://img.shields.io/badge/NSF-1929730-blue.svg)](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1929730)\n[![JOSS](https://joss.theoj.org/papers/10.21105/joss.03220/status.svg)](https://doi.org/10.21105/joss.03220)\n\n\n## Overview\n\nThe `portalcasting` package offers a comprehensive system for developing, deploying, and evaluating ecological models that forecast changes in ecological systems over time. It particularly focuses on the long-term study of mammal population and community dynamics, known as the [Portal Project](https://portal.weecology.org/).\n\n### Core Depedencies\n\nThe `portalcasting` package depends on the **PortalData**  and  **portalr** packages.\n\n-  [PortalData](https://github.com/weecology/PortalData) is the collection of all the Portal project data.\n-  [portalr](https://github.com/weecology/portalr) is a collection of functions to summarize the Portal data.\n\nThe `portalcasting` package integrates the [PortalData repository](https://github.com/weecology/PortalData) and the [portalr data management package](https://github.com/weecology/portalr) into a streamlined pipeline. This pipeline is used to forecast.\n\nThe functionality of `portalcasting` extends beyond its deployment, as its functions are portable. This allows users to establish a fully-functional replica repository on either a local or remote machine, facilitating the development and testing of new models within a [sandbox](https://en.wikipedia.org/wiki/Sandbox_software_development) environment.\n\n## Current deployment:\n\nThe [Portal-forecasts](https://github.com/weecology/portal-forecasts) houses tools that leverage the portalcasting pipeline to generate weekly forecasts.\nThe forecasts are then showcased on the [Portal Forecasts website](https://portal.naturecast.org).\nThis website offers users an interactive interface to explore the forecasting results.\nThe source code for this website is [hosted on GitHub](https://github.com/weecology/portal-forecast-web).\nAdditionally, the portal-forecasts repository archives the forecasts on both GitHub and Zenodo\n\n## Docker Container\n\nWe leverage a [Docker container](https://hub.docker.com/r/weecology/portalcasting) to enable reproducibility of the [Portal forecasting](https://github.com/weecology/portal-forecasts).\nPresently, we use a [Docker](https://hub.docker.com/r/weecology/portalcasting) image of the software environment to create a container for running the code.\nThe image is automatically rebuilt when there is a new `portalcasting` release, tagged with both the `latest` and version-specific (`vX.X.X`) tags, and pushed to [DockerHub](https://hub.docker.com/r/weecology/portalcasting).\n\nBecause the `latest` image is updated with releases, the current main branch code in `portalcasting` is typically, but not necessarily always, being executed within the [predictions repository](https://github.com/weecology/portalPredictions).\n\nThe API is actively developed and welcomes any contributors.\n\n## Installation\n\nYou can install the package from github:\n\n```r\ninstall.packages(\"remotes\")\nremotes::install_github(\"weecology/portalcasting\")\n```\n\nYou will need to install `rjags` and JAGS.\n\nMacOS users are recommended to install rjags after reading the instructions on the package's README file, or use the JAGS discussion forum thread for help under the [MacOS installation of JAGS](https://sourceforge.net/p/mcmc-jags/discussion/search/?q=MacOS+installation\u0026project=0).\n\n\n```r\ninstall.packages(\"rjags\", configure.args=\"--enable-rpath\")\n```\n\n## Production environment\n\nIf you wish to spin up a local container from the `latest` `portalcasting` image (to ensure that you are using a copy of the current production environment for implementation of the `portalcasting` pipeline), you can run\n\n```\nsudo docker pull weecology/portalcasting\n```\nfrom a shell on a computer with [Docker](https://www.docker.com/) installed.\n\n\n## Usage\n\nGet started with the [\"how to set up a Portal Predictions directory\" vignette](https://weecology.github.io/portalcasting/articles/getting_started.html).\n\nIf you are interested in adding a model to the preloaded [set of models](https://weecology.github.io/portalcasting/articles/current_models.html), see the [\"adding a model and data\" vignette](https://weecology.github.io/portalcasting/articles/adding_model_and_data.html). That document also details how to expand the datasets available to new and existing models.\n\n\n## Developer and Contributor notes\n\nWe welcome any contributions in form of models or pipeline changes.\n\nFor the workflow, please checkout the [contribution](.github/CONTRIBUTING.md) and [code of conduct](.github/CODE_OF_CONDUCT.md) pages. \n\n\n## Acknowledgements\n\nThis project is developed in active collaboration with [DAPPER Stats](https://www.dapperstats.com/).\n\nThe motivating study—the Portal Project—has been funded nearly continuously since 1977 by the [National Science Foundation](https://www.nsf.gov/), most recently by [DEB-1622425](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1622425) to S. K. M. Ernest.\nMuch of the computational work was supported by the [Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative](https://www.moore.org/initiative-strategy-detail?initiativeId=data-driven-discovery) through [Grant GBMF4563](https://www.moore.org/grant-detail?grantId=GBMF4563) to E. P. 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