cdcgov/wastewater-informed-covid-forecasting issues and pull requests

#208 - Issue 207: test time varying offset

Pull Request - State: open - Opened by kaitejohnson 11 days ago

#204 - 203 update scoringutils 2.0.0

Pull Request - State: closed - Opened by kaitejohnson 15 days ago - 1 comment

#202 - Hot fix full targets eval

Pull Request - State: open - Opened by kaitejohnson 17 days ago

#200 - Time varying offset eval

Pull Request - State: closed - Opened by kaitejohnson 18 days ago

#103 - add a warning message and a new file to write out missing files

Pull Request - State: closed - Opened by kaitejohnson 4 months ago

#103 - add a warning message and a new file to write out missing files

Pull Request - State: closed - Opened by kaitejohnson 4 months ago

#102 - Add a flag to check that expected scores aren't missing

Issue - State: open - Opened by kaitejohnson 4 months ago
Labels: bug

#102 - Add a flag to check that expected scores aren't missing

Issue - State: open - Opened by kaitejohnson 4 months ago
Labels: bug

#101 - add functionality to save cmdstan csvs for both models

Pull Request - State: closed - Opened by kaitejohnson 4 months ago - 1 comment

#101 - add functionality to save cmdstan csvs for both models

Pull Request - State: closed - Opened by kaitejohnson 4 months ago - 1 comment

#100 - Figure 2 rough draft components

Pull Request - State: closed - Opened by kaitejohnson 4 months ago - 5 comments

#100 - Figure 2 rough draft components

Pull Request - State: closed - Opened by kaitejohnson 4 months ago - 5 comments

#99 - Quick fix of the hospital admissions post processing

Pull Request - State: closed - Opened by kaitejohnson 4 months ago

#99 - Quick fix of the hospital admissions post processing

Pull Request - State: closed - Opened by kaitejohnson 4 months ago

#98 - Hot fix retro rt formatting

Pull Request - State: closed - Opened by kaitejohnson 4 months ago

#98 - Hot fix retro rt formatting

Pull Request - State: closed - Opened by kaitejohnson 4 months ago

#97 - change call in eval config list to refer to path not dir

Pull Request - State: closed - Opened by kaitejohnson 5 months ago

#97 - change call in eval config list to refer to path not dir

Pull Request - State: closed - Opened by kaitejohnson 5 months ago

#95 - Point workflows at action endpoints, remove custom/vendored actions

Pull Request - State: closed - Opened by dylanhmorris 5 months ago

#95 - Point workflows at action endpoints, remove custom/vendored actions

Pull Request - State: closed - Opened by dylanhmorris 5 months ago

#94 - Replace vendored github actions

Issue - State: closed - Opened by dylanhmorris 5 months ago
Labels: enterprise practices

#94 - Replace vendored github actions

Issue - State: closed - Opened by dylanhmorris 5 months ago
Labels: enterprise practices

#93 - updates to codebase to reflect recent dev

Pull Request - State: closed - Opened by kaitejohnson 5 months ago

#93 - updates to codebase to reflect recent dev

Pull Request - State: closed - Opened by kaitejohnson 5 months ago

#92 - Check packages against `goodpractice`

Issue - State: open - Opened by damonbayer 5 months ago - 1 comment

#92 - Check packages against `goodpractice`

Issue - State: open - Opened by damonbayer 5 months ago - 1 comment

#91 - Add Damon to author list

Pull Request - State: closed - Opened by damonbayer 5 months ago - 1 comment

#91 - Add Damon to author list

Pull Request - State: closed - Opened by damonbayer 5 months ago - 1 comment

#90 - update gitignore to exclude batch files for now

Pull Request - State: closed - Opened by kaitejohnson 5 months ago

#90 - update gitignore to exclude batch files for now

Pull Request - State: closed - Opened by kaitejohnson 5 months ago

#89 - WIP exp gamma implementation

Pull Request - State: open - Opened by kaitejohnson 5 months ago
Labels: help wanted, model development

#89 - WIP exp gamma implementation

Pull Request - State: open - Opened by kaitejohnson 5 months ago
Labels: help wanted, model development

#88 - NCP gamma sum approximation 2nd pass

Pull Request - State: open - Opened by kaitejohnson 5 months ago
Labels: help wanted, model development

#88 - NCP gamma sum approximation 2nd pass

Pull Request - State: open - Opened by kaitejohnson 5 months ago
Labels: help wanted, model development

#87 - Implementation of NCP with normal approximation to iid sum of gammas

Pull Request - State: open - Opened by kaitejohnson 5 months ago
Labels: help wanted, model development

#87 - Implementation of NCP with normal approximation to iid sum of gammas

Pull Request - State: open - Opened by kaitejohnson 5 months ago
Labels: help wanted, model development

#86 - Episewer take 3

Pull Request - State: closed - Opened by kaitejohnson 5 months ago
Labels: model development

#86 - Episewer take 3

Pull Request - State: closed - Opened by kaitejohnson 5 months ago
Labels: model development

#85 - Rerun evaluation model runs

Issue - State: closed - Opened by kaitejohnson 5 months ago - 1 comment
Labels: evaluation

#85 - Rerun evaluation model runs

Issue - State: closed - Opened by kaitejohnson 5 months ago - 1 comment
Labels: evaluation

#84 - Make first draft of evaluation manuscript figures

Issue - State: closed - Opened by kaitejohnson 5 months ago
Labels: evaluation

#84 - Make first draft of evaluation manuscript figures

Issue - State: closed - Opened by kaitejohnson 5 months ago
Labels: evaluation

#83 - Create initial model package repo in cdcgov

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: refactor

#83 - Create initial model package repo in cdcgov

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: refactor

#82 - Map out initial ideas for implementing spatial correlation in model

Issue - State: closed - Opened by kaitejohnson 5 months ago

#82 - Map out initial ideas for implementing spatial correlation in model

Issue - State: closed - Opened by kaitejohnson 5 months ago

#81 - Get vignette on current wastewater model running

Issue - State: open - Opened by kaitejohnson 5 months ago

#81 - Get vignette on current wastewater model running

Issue - State: open - Opened by kaitejohnson 5 months ago

#80 - Use individual level shedding data to estimate G, phi, + hinge function parameters

Issue - State: open - Opened by kaitejohnson 5 months ago - 1 comment
Labels: enhancement, low priority, open question

#80 - Use individual level shedding data to estimate G, phi, + hinge function parameters

Issue - State: open - Opened by kaitejohnson 5 months ago - 1 comment
Labels: enhancement, low priority, open question

#79 - Implement MVN to estimate a site-site covariance matrix

Issue - State: open - Opened by kaitejohnson 5 months ago - 5 comments
Labels: enhancement, help wanted, medium priority

#79 - Implement MVN to estimate a site-site covariance matrix

Issue - State: open - Opened by kaitejohnson 5 months ago - 5 comments
Labels: enhancement, help wanted, medium priority

#78 - Estimate the effective susceptible population

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: open question

#78 - Estimate the effective susceptible population

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: open question

#77 - Separate site and lab level observation error

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: enhancement, medium priority, refactor

#77 - Separate site and lab level observation error

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: enhancement, medium priority, refactor

#76 - Mixture model to handle outliers within model

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: low priority

#76 - Mixture model to handle outliers within model

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: low priority

#75 - Write tests for transformation/operations in stan

Issue - State: open - Opened by kaitejohnson 5 months ago

#75 - Write tests for transformation/operations in stan

Issue - State: open - Opened by kaitejohnson 5 months ago

#74 - Use native pipes throughout

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: low priority

#74 - Use native pipes throughout

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: low priority

#73 - Model definition: add diagrams

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: documentation, low priority

#73 - Model definition: add diagrams

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: documentation, low priority

#72 - Generation interval test

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: refactor

#72 - Generation interval test

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: refactor

#71 - Literal zero negative binomial mean

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: bug

#71 - Literal zero negative binomial mean

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: bug

#70 - Incorporate `pak` into standard installation workflow

Issue - State: open - Opened by kaitejohnson 5 months ago

#70 - Incorporate `pak` into standard installation workflow

Issue - State: open - Opened by kaitejohnson 5 months ago

#69 - Tweak handling of shedding distribution in code

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: enhancement

#69 - Tweak handling of shedding distribution in code

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: enhancement

#68 - Validation of forecast submissions prior to submitting to forecast hub

Issue - State: open - Opened by kaitejohnson 5 months ago

#68 - Validation of forecast submissions prior to submitting to forecast hub

Issue - State: open - Opened by kaitejohnson 5 months ago

#67 - Add a limitations section to the model definition

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: documentation

#67 - Add a limitations section to the model definition

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: documentation

#66 - Configuration should be data, not code

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: enhancement, medium priority, enterprise practices

#66 - Configuration should be data, not code

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: enhancement, medium priority, enterprise practices

#65 - Flag submitted runs in archive

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: refactor, archiving

#65 - Flag submitted runs in archive

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: refactor, archiving

#64 - Rename arguments to model fitting functions for clarity

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: documentation, low priority

#64 - Rename arguments to model fitting functions for clarity

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: documentation, low priority

#63 - EDA to determine temporal granularity on which the observation stdev should vary in time

Issue - State: open - Opened by kaitejohnson 5 months ago

#63 - EDA to determine temporal granularity on which the observation stdev should vary in time

Issue - State: open - Opened by kaitejohnson 5 months ago

#62 - Check for low ESS on a chain-by-chain basis

Issue - State: open - Opened by kaitejohnson 5 months ago

#61 - Implement time-varying observation error stdev

Issue - State: open - Opened by kaitejohnson 5 months ago

#61 - Implement time-varying observation error stdev

Issue - State: open - Opened by kaitejohnson 5 months ago

#60 - Clean up duplication of filepaths to output

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: refactor

#60 - Clean up duplication of filepaths to output

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: refactor

#59 - Remove use of `here::here`

Issue - State: open - Opened by kaitejohnson 5 months ago

#59 - Remove use of `here::here`

Issue - State: open - Opened by kaitejohnson 5 months ago

#58 - Decide whether to track archived config files in git for production pipeline

Issue - State: open - Opened by kaitejohnson 5 months ago

#58 - Decide whether to track archived config files in git for production pipeline

Issue - State: open - Opened by kaitejohnson 5 months ago

#57 - Fix nomenclature for predicted observations

Issue - State: open - Opened by kaitejohnson 5 months ago

#57 - Fix nomenclature for predicted observations

Issue - State: open - Opened by kaitejohnson 5 months ago

#56 - Add documentation to a number of components in the production pipeline package

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: documentation, good first issue, enterprise practices

#56 - Add documentation to a number of components in the production pipeline package

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: documentation, good first issue, enterprise practices

#55 - Add documentation to a number of components in modeling package

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: documentation, good first issue, refactor, enterprise practices

#55 - Add documentation to a number of components in modeling package

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: documentation, good first issue, refactor, enterprise practices

#54 - Use stan AR(1) in fake data simulation

Issue - State: open - Opened by kaitejohnson 5 months ago
Labels: enhancement

GitHub / cdcgov/wastewater-informed-covid-forecasting issues and pull requests