{"id":26592024,"url":"https://github.com/damian-oswald/process-rate-estimator","last_synced_at":"2025-10-18T18:19:15.507Z","repository":{"id":215147476,"uuid":"697847369","full_name":"Damian-Oswald/process-rate-estimator","owner":"Damian-Oswald","description":"A GitHub repository for the process rate estimator developed for the Sustainable Agroecosystems Group at ETH.","archived":false,"fork":false,"pushed_at":"2024-08-12T15:49:02.000Z","size":234766,"stargazers_count":3,"open_issues_count":2,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-08-13T16:05:44.070Z","etag":null,"topics":["agroecology","biochemistry","ethz","nitrogen","nitrous-oxide"],"latest_commit_sha":null,"homepage":"https://damian-oswald.github.io/process-rate-estimator/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Damian-Oswald.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-09-28T15:39:34.000Z","updated_at":"2024-08-13T16:05:44.071Z","dependencies_parsed_at":"2024-08-11T15:58:34.726Z","dependency_job_id":null,"html_url":"https://github.com/Damian-Oswald/process-rate-estimator","commit_stats":{"total_commits":100,"total_committers":4,"mean_commits":25.0,"dds":"0.030000000000000027","last_synced_commit":"541dc71e9486a24ee603d023ba4502e9fc4cf9f4"},"previous_names":["damian-oswald/process-rate-estimator"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Damian-Oswald%2Fprocess-rate-estimator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Damian-Oswald%2Fprocess-rate-estimator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Damian-Oswald%2Fprocess-rate-estimator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Damian-Oswald%2Fprocess-rate-estimator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Damian-Oswald","download_url":"https://codeload.github.com/Damian-Oswald/process-rate-estimator/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245116216,"owners_count":20563306,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["agroecology","biochemistry","ethz","nitrogen","nitrous-oxide"],"created_at":"2025-03-23T14:32:44.591Z","updated_at":"2025-10-18T18:19:10.463Z","avatar_url":"https://github.com/Damian-Oswald.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# :test_tube: Process Rate Estimator\n\nThis repository contains the source code and documentation for the process rate estimator. For a detailed (scientific) description of the process rate estimator, see Decock et al. ([2022](https://doi.org/10.5194/bg-2022-221)).\n\nThe project was done for the [sustainable agro-ecosystems group at ETH Zurich](https://sae.ethz.ch/). While the project documentation is presented on [this website](https://damian-oswald.github.io/process-rate-estimator/), the source code for the process rate estimator in contained in an R package called `PRE`. You can explore said package in [this GitHub repository](https://github.com/damian-oswald/PRE/). Meanwhile, this repository contains the scripts for running the process rate estimator on some collected data as well as the source code for reproducing the documentation page.\n\n# :file_folder: The repository structure\n\nThis repository contains:\n\n1. **The source code for the documentation page:** This repository contains the quarto documents necessary to render the documentation page (i.e., a bunch of `.qmd` and `.yml` files). Images, GIFs, bibliography etc. is in the `/resources` folder.\n2. **The R scripts for running the process rate estimator:** The R scripts in the folder `/scripts` run some part of the process rate estimator. Specifically, they (1) prepare the collected data appropriately (`scripts/data-preparation`), (2) find the best hyper-parameters (`scripts/hypertuning`), (3) run the process rate estimator itself (`scripts/run-process-rate-estimator`), (4) run the sensitivity and uncertainty analyses (`scripts/sensitivity-analysis`).\n\nNote that the latter two are subdivided into scripts that perform the calculation and scripts that generate visualizations based on the output.\n\n# :question: How can I run the process rate estimator?\n\nTo run the process rate estimator, first install the R package `PRE`.[^readme-1]\n\n[^readme-1]: This R package contains all functions that are repeatedly used throughout the workflow of this project. It's stored [on its own GitHub repository](https://github.com/Damian-Oswald/PRE/).\n\n``` r\nremotes::install_github(\"https://github.com/Damian-Oswald/PRE\")\n```\n\nAfter successful installation, you can clone this GitHub repository.\n\n``` bash\ngit clone https://github.com/Damian-Oswald/process-rate-estimator\ncd process-rate-estimator\n```\n\n## :globe_with_meridians: Reproducing the documentation site\n\nThe [documentation site](https://damian-oswald.github.io/process-rate-estimator/) was built using the [scientific publishing system Quarto](https://quarto.org). To reproduce the documentation, first install Quarto, then run `quarto render` to render the entire site.\n\n## :microbe: Running the main script\n\nAfter successful installation of the R package `PRE` and cloning of this repository, you can run the main script, which will reproduce the results for the process rate estimations.\n\n``` bash\nRscript scripts/run-process-rate-estimator/run-PRE.R\n```\n\nThese results are also documented [here](https://damian-oswald.github.io/process-rate-estimator/results.html).\n\n## :abacus: Running the sensitivity analysis\n\nTo reproduce the sensitivity analysis (which is documented [here](https://damian-oswald.github.io/process-rate-estimator/sensitivity-analysis.html)), enter the following command:\n\n``` bash\nRscript scripts/sensitivity-analysis/sensitivitiy-analysis.R\n```\n\n\u003e [!IMPORTANT]  \n\u003e Running the sensitivity analysis R script is very compute intensive and may take a few days on an ordinary computer.\n\nYou can open the corresponding R script to change parameters such as `SAMPLESIZE` and `SAMPLEREPEAT`; however, doing this will change the exact numerical results.[^readme-2]\n\n[^readme-2]: Although the *expected* results will not change.\n\nThe results written by the sensitivity analysis are also used by the uncertainty analysis.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdamian-oswald%2Fprocess-rate-estimator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdamian-oswald%2Fprocess-rate-estimator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdamian-oswald%2Fprocess-rate-estimator/lists"}