{"id":26592022,"url":"https://github.com/damian-oswald/pre","last_synced_at":"2025-03-23T14:32:41.127Z","repository":{"id":215656586,"uuid":"739449695","full_name":"Damian-Oswald/PRE","owner":"Damian-Oswald","description":"A repository for the R package containing the code for the process rate estimator (PRE).","archived":false,"fork":false,"pushed_at":"2024-08-11T16:10:35.000Z","size":237,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-08-11T17:28:41.944Z","etag":null,"topics":["agriculture","biogeochemistry","modelling","nitrate","nitrogen"],"latest_commit_sha":null,"homepage":"https://github.com/Damian-Oswald/process-rate-estimator","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","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":"LICENSE","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}},"created_at":"2024-01-05T15:40:51.000Z","updated_at":"2024-08-11T16:10:38.000Z","dependencies_parsed_at":"2024-01-20T23:23:47.826Z","dependency_job_id":"42dbd536-5b4a-4549-9166-f6b65edde63f","html_url":"https://github.com/Damian-Oswald/PRE","commit_stats":{"total_commits":20,"total_committers":2,"mean_commits":10.0,"dds":0.09999999999999998,"last_synced_commit":"548208979c152c6157274effb1b49da0e5be77c0"},"previous_names":["damian-oswald/pre"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Damian-Oswald%2FPRE","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Damian-Oswald%2FPRE/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Damian-Oswald%2FPRE/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Damian-Oswald%2FPRE/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Damian-Oswald","download_url":"https://codeload.github.com/Damian-Oswald/PRE/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":["agriculture","biogeochemistry","modelling","nitrate","nitrogen"],"created_at":"2025-03-23T14:32:40.381Z","updated_at":"2025-03-23T14:32:41.112Z","avatar_url":"https://github.com/Damian-Oswald.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"The R package PRE\n=================\n\nA repository for the R package containing the code for the process rate estimator (PRE). Note that this README file contains only a very brief documentation. For a more comprehensive overview, please visit the [documentation site](https://damian-oswald.github.io/process-rate-estimator/).\n\n# Installation\n\nYou can install this R package directly from GitHub using the following R command.\n\n```r\ninstall.packages(\"remotes\")\nremotes::install_github(\"https://github.com/Damian-Oswald/PRE\")\n```\n\nNext, attach the library to your search path and your good to go!\n\n```r\nlibrary(PRE)\n```\n\n# Loading the data\n\nFirst, load the prepared hyperparameters.\n\n```r\nhyperparameters \u003c- PRE::hyperparameters\n```\n\nNext, load the measurements used for the modelling.\n\n```r\nmeasurements \u003c- PRE::measurements\n```\n\nFinally, load the parameters for this session.\n\n```r\nparameters \u003c- getParameters()\n```\n\nYou may also load the parameters with some (or any number of) alternative parameter value.\n\n```r\nparameters \u003c- getParameters(BD = 1.7)\n```\n\n# Impute the missing dependent data\n\nCalculate N2O-N:\n\n```r\ndata \u003c- getN2ON(data = measurements, parameters = parameters)\n```\n\nInterpolate the missing values based on the bandwidths in `hyperparameters` (This function interpolates all values over time; and it also computes and adds the derivatives):\n\n```r\ndata \u003c- getMissing(data = data, hyperparameters = hyperparameters)\n```\n\nCalculate fluxes from measurement data (This function calculates all necessary parameters from the data)\n\n```r\ndata \u003c- calculateFluxes(data = data, parameters = parameters)\n```\n\nRead some details on a function.\n\n```r\nhelp(calculateFluxes)\n```\n\n# Run the solver once\n\nRun the solver for some column, depth and date combination.\n\n```r\nx \u003c- PRE(data = data, column = 1, depth = 7.5, date = \"2016-01-01\", n = 200, parameters = parameters)\n```\n\nPrint out information.\n\n```r\nprint(x)\n```\n\nGenerate a plot.\n\n```r\nplot(x)\n```\n\nProduce a pairwise panel plot.\n\n```r\npairs(x)\n```\n\n# Run the solver over time\n\nRun the solver for all the dates.\n\n```r\nx \u003c- longPRE(data, column = 6, depth = 90, n = 10)\n```\n\nPrint information about the PRE results.\n\n```\nprint(x)\n```\n\nPlot the results to get an overview.\n\n```r\nplot(x)\n```\n\nPlot the results for a specific process.\n\n```r\nplot(x, which = \"Nitrification\")\n```\n\nPlot the overview with fixed y-axis limits.\n\n```r\nplot(x, ylim.processes = list(Nitrification = c(-50,50), Denitrification = NA, Reduction = NA))\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdamian-oswald%2Fpre","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdamian-oswald%2Fpre","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdamian-oswald%2Fpre/lists"}