{"id":27172131,"url":"https://github.com/pacificcommunity/ofp-sam-jitter-develop","last_synced_at":"2025-07-09T10:39:11.948Z","repository":{"id":193200650,"uuid":"688226266","full_name":"PacificCommunity/ofp-sam-jitter-develop","owner":"PacificCommunity","description":"Development of a General Jitter Function","archived":false,"fork":false,"pushed_at":"2024-07-15T23:43:21.000Z","size":128,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":9,"default_branch":"main","last_synced_at":"2025-04-09T09:41:59.706Z","etag":null,"topics":["jitter","model","ofp","sam"],"latest_commit_sha":null,"homepage":"","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/PacificCommunity.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":"2023-09-06T23:22:19.000Z","updated_at":"2024-07-15T23:43:24.000Z","dependencies_parsed_at":null,"dependency_job_id":"e2c52711-2aea-4321-96cc-4e73f928cfcb","html_url":"https://github.com/PacificCommunity/ofp-sam-jitter-develop","commit_stats":null,"previous_names":["pacificcommunity/ofp-sam-jitter-develop"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/PacificCommunity/ofp-sam-jitter-develop","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PacificCommunity%2Fofp-sam-jitter-develop","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PacificCommunity%2Fofp-sam-jitter-develop/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PacificCommunity%2Fofp-sam-jitter-develop/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PacificCommunity%2Fofp-sam-jitter-develop/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PacificCommunity","download_url":"https://codeload.github.com/PacificCommunity/ofp-sam-jitter-develop/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PacificCommunity%2Fofp-sam-jitter-develop/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":264441549,"owners_count":23608906,"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":["jitter","model","ofp","sam"],"created_at":"2025-04-09T09:35:23.845Z","updated_at":"2025-07-09T10:39:11.917Z","avatar_url":"https://github.com/PacificCommunity.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Development of a General Jitter Function\n\n*Commentary*\n\n## 1 Palau test (2023-08-21)\n\n*Initial test and result*\n\nAt SC19, John asked Arni if the current jitter() function can be used to jitter\nALB par files. The initial test involved the jitter.R file that was used for the\nYFT 2023 assessment and a 09.par file from a single-region ALB model, provided\nby John:\n\n- [jitter.R](function/03_yft_2023_assessment/jitter.R)\n- [09.par](parfiles/01_alb_1_region_2023/09.par)\n\nThe result from the test script,\n\n- [01_yft_2023_assessment.R](tests/01_palau/01_yft_2023_assessment.R)\n\nwas an error message:\n\n```\nError in if (flagval(par, -Selsfish[1], 48)$value == 1) { :\n  argument is of length zero\n```\n\n*Small improvement while in Palau*\n\nThe error turned out to be caused by the line\n\n```\nuniqueSels \u003c- max(flagval(par,-1:-nFish,24)$value)\n```\n\nwhich assumes that some fishery selectivities are grouped, but that's not the\ncase for the single-region ALB model. Therefore, a new and slightly improved\njitter() function was developed that handles the case when no fishery\nselectivities are grouped:\n\n- [jitter.R](function/04_palau/jitter.R)\n\nThe result from the test script,\n\n- [02_palau.R](tests/01_palau/02_palau.R)\n\nwas the successful creation of 20 jittered par files. However, the jittered par\nfiles turned out to be truncated, containing too few parameters. We were of\ncourse hoping/expecting that the jittered par files would have the same number\nof parameters as the original par file with slightly different values.\n\nThat is where the development of a general jitter function was put on hold\nduring SC19 in Palau (2023-08-21) as we had to turn our attention to SC19 tasks\nrelated to the BET and YFT assessments.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpacificcommunity%2Fofp-sam-jitter-develop","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpacificcommunity%2Fofp-sam-jitter-develop","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpacificcommunity%2Fofp-sam-jitter-develop/lists"}