{"id":22215248,"url":"https://github.com/eggplantbren/dnest5","last_synced_at":"2025-07-17T15:37:01.779Z","repository":{"id":145812811,"uuid":"286889399","full_name":"eggplantbren/DNest5","owner":"eggplantbren","description":"Diffusive Nested Sampling like you've never seen it before","archived":false,"fork":false,"pushed_at":"2024-08-26T23:17:57.000Z","size":148,"stargazers_count":8,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-06-15T22:29:14.359Z","etag":null,"topics":["bayesian-inference","markov-chain-monte-carlo","nested-sampling","statistics"],"latest_commit_sha":null,"homepage":"","language":"C++","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/eggplantbren.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,"publiccode":null,"codemeta":null}},"created_at":"2020-08-12T01:48:12.000Z","updated_at":"2024-08-26T23:18:00.000Z","dependencies_parsed_at":"2024-12-02T21:42:44.966Z","dependency_job_id":null,"html_url":"https://github.com/eggplantbren/DNest5","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/eggplantbren/DNest5","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eggplantbren%2FDNest5","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eggplantbren%2FDNest5/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eggplantbren%2FDNest5/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eggplantbren%2FDNest5/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/eggplantbren","download_url":"https://codeload.github.com/eggplantbren/DNest5/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/eggplantbren%2FDNest5/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":265623310,"owners_count":23800139,"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":["bayesian-inference","markov-chain-monte-carlo","nested-sampling","statistics"],"created_at":"2024-12-02T21:26:45.321Z","updated_at":"2025-07-17T15:37:01.763Z","avatar_url":"https://github.com/eggplantbren.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"DNest5\n======\n\n(c) 2020--2024 Brendon J. Brewer.\n\nPlease Clone Recursively\n========================\n\n`$ git clone --recursive https://github.com/eggplantbren/DNest5`\n\nThis will pull in a submodule that I'm using.\n\nLICENCE\n=======\n\nGNU General Public License version 3.\n\nDependencies\n============\n\n* Boost\n* Python 3 with NumPy, matplotlib, apsw\n* SQLite3\n* yaml-cpp\n\nInstallation\n============\n\nTo compile `DNest5`, run the build script. This generates a `Makefile` and\nthen runs `make` to compile everything.\n\n`$ ./build.py`\n\nBy default, this compiles the StraightLine example from\n\u003ca href=\"https://www.jstatsoft.org/index.php/jss/article/view/v086i07/v86i07.pdf\" target=\"_blank\" rel=\"noopener noreferrer\"\u003eDNest4\u003c/a\u003e. The two executable\nfiles created are `main`, which does the sampling, and `postprocess`, which\ncreates posterior samples and computes the marginal likelihood.\n\nRunning and Outputs\n===================\n\nFirst run `main`, then run `showresults.py` in Python. Showresults calls\n`postprocess`, so you don't need to run `postprocess` on its own. It is safe\nto run `showresults.py` while `main` is still running.\n\nCompiling a Different Model\n===========================\n\nEdit `ModelType.hpp` and change the `#include` and `using` lines\nto point to a different model. Then run `./build.py` again.\n\nAt this time, all example models in the `Example` directory are implemented\nusing inheritance from the `UniformModel` class template.\nThese follow the convention where the exploration is done in terms of a coordinate system that makes the prior Uniform(0, 1) for every coordinate.\nThe user/model writer has to write the member functions `us_to_params` to\nconvert from the `us` (Uniform(0, 1) parameters) to the actual parameters,\nand `log_likelihood` in order to evaluate the likelihood function.\n\nSpecifying the Options\n======================\n\nThe configuration file `options.yaml` plays the role of DNest4's `OPTIONS`\nand its command line arguments.\n\nOutputs\n=======\n\nAll outputs are written to the `output` directory. The files are:\n\n* `dnest5.db`: An SQLite3 database of output, similar to DNest4's `sample.txt`,\n    `sample_info.txt`, and `levels.txt`, but combined into one binary file.\n* `figure?.pdf`: Figures exported by `showresults.py`. Note that if you run\n    `showresults.py' while the main process is running, some inconsistencies\n    can appear in Figure 3 between the particles and the levels. These\n    do not have any major consequences.\n* `posterior.db`: An SQLite3 database of posterior samples. Does not store\n    the samples themselves, but rather refers back to the appropriate rows\n    in `dnest5.db`.\n* `posterior.csv`: CSV file of posterior samples.\n* `results.yaml`: YAML file (plain text) with marginal likelihood values and\n    related things.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Feggplantbren%2Fdnest5","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Feggplantbren%2Fdnest5","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Feggplantbren%2Fdnest5/lists"}