Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / biocore/BIRDMAn issues and pull requests

#100 - How add covariables into default model?

Issue - State: open - Opened by liucong-epi 6 months ago

#99 - Update docs

Pull Request - State: closed - Opened by gibsramen about 1 year ago

#98 - nb.to_inference() error

Issue - State: closed - Opened by akhilkommala about 1 year ago - 6 comments

#97 - Update to v0.2.0

Pull Request - State: closed - Opened by gibsramen over 1 year ago

#96 - New documentation

Pull Request - State: closed - Opened by gibsramen over 1 year ago

#95 - Update environment.yml

Issue - State: open - Opened by gibsramen over 1 year ago

#94 - Misc fixes

Pull Request - State: closed - Opened by gibsramen over 1 year ago

#93 - Fix #90

Pull Request - State: closed - Opened by gibsramen over 1 year ago

#92 - Add NB LME Single as default model

Pull Request - State: closed - Opened by gibsramen over 1 year ago

#91 - Better summary functions

Issue - State: open - Opened by mortonjt over 1 year ago

#90 - concatenate_inference method broken

Issue - State: closed - Opened by mortonjt over 1 year ago - 1 comment

#89 - More informative failure messages

Issue - State: open - Opened by mortonjt over 1 year ago - 1 comment

#87 - Add model builder

Pull Request - State: open - Opened by gibsramen over 1 year ago

#86 - Add InferenceData support to VI

Pull Request - State: closed - Opened by gibsramen over 1 year ago

#85 - Add VI inference and model building

Pull Request - State: closed - Opened by gibsramen over 1 year ago - 1 comment

#84 - Model fitting refactor

Pull Request - State: closed - Opened by gibsramen over 1 year ago - 3 comments

#83 - How to include random variables in the formula

Issue - State: open - Opened by PaulaEterovick over 1 year ago - 4 comments

#81 - No CmdStan installation found

Issue - State: open - Opened by jolespin almost 2 years ago - 9 comments

#80 - What is the recommended method for specifying enriched or depleted features?

Issue - State: open - Opened by jolespin almost 2 years ago - 1 comment

#79 - Add demo to README/docs

Issue - State: open - Opened by gibsramen over 2 years ago

#78 - Update to v0.1.0

Pull Request - State: closed - Opened by gibsramen over 2 years ago

#77 - Add docs page on Negative Binomial model

Pull Request - State: closed - Opened by gibsramen over 2 years ago

#76 - Add coords to summary docstring

Pull Request - State: closed - Opened by gibsramen over 2 years ago

#75 - Add summarize function

Pull Request - State: closed - Opened by gibsramen over 2 years ago

#74 - Update inference conversion function

Pull Request - State: closed - Opened by gibsramen over 2 years ago

#73 - Update default models & documentation

Pull Request - State: closed - Opened by gibsramen over 2 years ago

#72 - Add chunking support to ModelIterator

Pull Request - State: closed - Opened by gibsramen over 2 years ago - 1 comment

#71 - Create parallelization.rst

Pull Request - State: closed - Opened by yangchen2 over 2 years ago

#69 - Create parallelization.rst

Pull Request - State: closed - Opened by yangchen2 almost 3 years ago

#68 - Update GH actions

Pull Request - State: closed - Opened by gibsramen almost 3 years ago

#67 - updated documentation on installation

Pull Request - State: closed - Opened by yangchen2 almost 3 years ago - 1 comment

#66 - Support for Variational Inference

Issue - State: open - Opened by mortonjt almost 3 years ago

#64 - Update docs with correct alr_to_clr params

Pull Request - State: closed - Opened by gibsramen over 3 years ago

#63 - An error in documentation

Issue - State: closed - Opened by jindongmin over 3 years ago - 1 comment

#62 - Update installation instructions for new ArviZ release

Pull Request - State: closed - Opened by gibsramen over 3 years ago

#61 - Address #56

Pull Request - State: closed - Opened by gibsramen over 3 years ago

#59 - Bad draw error when running chunks

Issue - State: open - Opened by gibsramen over 3 years ago

#58 - Initial commit of dev branch

Pull Request - State: closed - Opened by gibsramen over 3 years ago

#57 - concatenate_inferences is slow

Issue - State: open - Opened by mortonjt over 3 years ago

#56 - Allow passing in CmdStanModel compilation arguments

Issue - State: closed - Opened by gibsramen over 3 years ago

#55 - Update to version 0.0.4

Pull Request - State: closed - Opened by gibsramen over 3 years ago

#54 - Misc fixes

Pull Request - State: closed - Opened by gibsramen over 3 years ago

#53 - Update inference conversion to be transform agnostic

Pull Request - State: closed - Opened by gibsramen over 3 years ago

#52 - Refactor model API for abstract parallelization

Pull Request - State: closed - Opened by gibsramen over 3 years ago - 8 comments

#51 - Abstracting out parallelism

Issue - State: closed - Opened by mortonjt over 3 years ago - 1 comment

#50 - Add Zenodo link

Pull Request - State: closed - Opened by gibsramen over 3 years ago - 1 comment

#49 - Add tests for parameter capture

Issue - State: open - Opened by gibsramen over 3 years ago

#48 - Remove Dask integration

Pull Request - State: closed - Opened by gibsramen over 3 years ago - 1 comment

#47 - Remove metadata requirement for BaseModel

Issue - State: closed - Opened by gibsramen over 3 years ago

#46 - ENH : Adding support for chunking

Pull Request - State: closed - Opened by mortonjt over 3 years ago - 6 comments

#45 - Overflows can occur with generated quantities

Issue - State: closed - Opened by mortonjt over 3 years ago - 6 comments

#44 - Refactor conversion to InferenceData

Pull Request - State: closed - Opened by gibsramen over 3 years ago - 8 comments

#43 - Move _fit_single to directly under BaseModel

Pull Request - State: closed - Opened by gibsramen over 3 years ago

#42 - Add Zenodo link

Issue - State: closed - Opened by gibsramen over 3 years ago

#41 - Fix download links in custom LME documentation

Issue - State: closed - Opened by gibsramen almost 4 years ago

#40 - Expose _fit_single in BaseModel class

Issue - State: closed - Opened by gibsramen almost 4 years ago

#39 - posterior_predictive and log_likelihood could have sample names

Issue - State: closed - Opened by mortonjt almost 4 years ago - 2 comments

#38 - Abstract Model API further

Pull Request - State: closed - Opened by gibsramen almost 4 years ago - 1 comment

#37 - Fix bug where num_warmup isn't properly saved to a Model object

Issue - State: closed - Opened by gibsramen almost 4 years ago

#36 - Temporary files usage

Issue - State: closed - Opened by mortonjt almost 4 years ago - 3 comments

#35 - Cluster support isn't properly load balanced

Issue - State: closed - Opened by mortonjt almost 4 years ago - 3 comments

#34 - Model base class is a little too restrictive

Issue - State: closed - Opened by mortonjt almost 4 years ago - 2 comments

#33 - Write docs page on formulas

Issue - State: open - Opened by gibsramen almost 4 years ago

#32 - h5py version failing on GH Actions

Issue - State: closed - Opened by gibsramen almost 4 years ago - 1 comment

#31 - Add option to specify number of warmup draws

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#30 - Add HPC support

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#29 - Installation issues

Issue - State: closed - Opened by gibsramen almost 4 years ago - 1 comment

#28 - Proof-of-concept Slurm Cluster deployment

Pull Request - State: closed - Opened by mortonjt almost 4 years ago - 1 comment

#27 - Parallelize combining multiple fits

Issue - State: closed - Opened by gibsramen almost 4 years ago

#26 - Add QIIME 2 plugin

Issue - State: open - Opened by gibsramen almost 4 years ago - 5 comments

#25 - Initial release - big documentation upgrades

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#24 - Update multinomial model

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#23 - Update log-likelihood & posterior predictive import to inference

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#22 - Restructure log-likelihood import

Issue - State: closed - Opened by gibsramen almost 4 years ago

#21 - Fix single_fit_to_inference return type hint

Issue - State: closed - Opened by gibsramen almost 4 years ago

#20 - Add NegativeBinomial LME model

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#19 - Add option to specify number of warmup draws separately

Issue - State: closed - Opened by gibsramen almost 4 years ago

#18 - Add R^2 score and LOO functions

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#17 - Update posterior predictive & log likelihood import (+ misc changes)

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#16 - Add ESS & Rhat

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#14 - Add visualization functions for rank plot and PPC plot

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#13 - Add Hotelling T-squared test

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#12 - Enable Mypy type checking

Issue - State: closed - Opened by gibsramen almost 4 years ago - 1 comment

#11 - Enabling cluster support

Issue - State: closed - Opened by mortonjt almost 4 years ago - 1 comment

#10 - Consider sklearn way of fitting

Issue - State: open - Opened by gibsramen almost 4 years ago - 5 comments

#9 - Add attribute to ArviZ objects about model type

Issue - State: open - Opened by gibsramen almost 4 years ago

#8 - Add to_inference_object specific for default models.

Issue - State: closed - Opened by gibsramen almost 4 years ago

#7 - Refactor conversion of BIRDMAn model to ArviZ InferenceData

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#6 - Move table input away from BIOM

Issue - State: closed - Opened by gibsramen almost 4 years ago - 2 comments

#5 - Add ArviZ integration

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#4 - Add Sphinx documentation

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#3 - Switch from PyStan to cmstanpy

Pull Request - State: closed - Opened by gibsramen almost 4 years ago

#2 - Add Poisson Lognormal model

Issue - State: closed - Opened by gibsramen about 4 years ago - 1 comment

#1 - Refactor model code to OOP

Pull Request - State: closed - Opened by gibsramen about 4 years ago