hopkinsidd/flepimop issues and pull requests

#96 - Outcomes: allow `param_from_file` to be omitted

Issue - State: closed - Opened by jcblemai over 1 year ago - 1 comment
Labels: gempyor, medium priority, quick issue

#95 - Make `dayofyear` and `dayofweek` accessible to compartment formula parser

Issue - State: open - Opened by jcblemai over 1 year ago - 2 comments
Labels: gempyor, medium priority

#95 - Make `dayofyear` and `dayofweek` accessible to compartment formula parser

Issue - State: open - Opened by jcblemai over 1 year ago - 2 comments
Labels: gempyor, medium priority

#94 - Creates commands for local runs from resumes

Issue - State: closed - Opened by jcblemai over 1 year ago - 1 comment
Labels: enhancement, batch, medium priority

#94 - Creates commands for local runs from resumes

Issue - State: closed - Opened by jcblemai over 1 year ago - 1 comment
Labels: enhancement, batch, medium priority

#93 - Consistent structure for filenames for non-inference runs

Issue - State: open - Opened by jcblemai over 1 year ago
Labels: good first issue, gempyor, medium priority

#93 - Consistent structure for filenames for non-inference runs

Issue - State: open - Opened by jcblemai over 1 year ago
Labels: good first issue, gempyor, medium priority

#92 - set `--upload-to-s3 False` for `--local` runs for the submission script

Issue - State: open - Opened by jcblemai over 1 year ago - 2 comments
Labels: batch, medium priority, cli

#92 - set `--upload-to-s3 False` for `--local` runs for the submission script

Issue - State: open - Opened by jcblemai over 1 year ago - 2 comments
Labels: batch, medium priority, cli

#91 - Phase out `subpop_setup: geodata.csv`

Issue - State: closed - Opened by jcblemai over 1 year ago - 2 comments
Labels: gempyor, medium priority

#91 - Phase out `subpop_setup: geodata.csv`

Issue - State: closed - Opened by jcblemai over 1 year ago - 2 comments
Labels: gempyor, medium priority

#90 - Major inference rewrite

Issue - State: closed - Opened by jcblemai over 1 year ago - 2 comments
Labels: enhancement, r-inference, medium priority

#90 - Major inference rewrite

Issue - State: closed - Opened by jcblemai over 1 year ago - 2 comments
Labels: enhancement, r-inference, medium priority

#89 - Allow seir and outcomes modifier sections to work without scenarios

Issue - State: open - Opened by alsnhll over 1 year ago - 2 comments
Labels: gempyor, config, medium priority

#89 - Allow seir and outcomes modifier sections to work without scenarios

Issue - State: open - Opened by alsnhll over 1 year ago - 2 comments
Labels: gempyor, config, medium priority

#88 - General inference improvements

Issue - State: open - Opened by saraloo over 1 year ago
Labels: enhancement, low priority, inference

#88 - General inference improvements

Issue - State: open - Opened by saraloo over 1 year ago
Labels: enhancement, low priority, inference

#87 - Inference: Adding in ability to fit timing of interventions

Issue - State: open - Opened by alsnhll over 1 year ago
Labels: enhancement, low priority, inference

#87 - Inference: Adding in ability to fit timing of interventions

Issue - State: open - Opened by alsnhll over 1 year ago
Labels: enhancement, low priority, inference

#86 - Inference: Add ability to fit the standard deviation or other parameter of the likelihood distribution

Issue - State: open - Opened by alsnhll over 1 year ago
Labels: enhancement, low priority, inference

#86 - Inference: Add ability to fit the standard deviation or other parameter of the likelihood distribution

Issue - State: open - Opened by alsnhll over 1 year ago
Labels: enhancement, low priority, inference

#85 - Include non-symmetric proposal distributions to inference algorithm

Issue - State: open - Opened by saraloo over 1 year ago
Labels: enhancement, low priority, inference

#85 - Include non-symmetric proposal distributions to inference algorithm

Issue - State: open - Opened by saraloo over 1 year ago
Labels: enhancement, low priority, inference

#84 - Make a single parameter perturbation file in inference

Issue - State: open - Opened by alsnhll over 1 year ago - 1 comment
Labels: r-inference, low priority, inference

#84 - Make a single parameter perturbation file in inference

Issue - State: open - Opened by alsnhll over 1 year ago - 1 comment
Labels: r-inference, low priority, inference

#83 - Timezone conversion messing up discrete days for model output?

Issue - State: open - Opened by alsnhll over 1 year ago
Labels: bug, low priority

#83 - Timezone conversion messing up discrete days for model output?

Issue - State: open - Opened by alsnhll over 1 year ago
Labels: bug, low priority

#82 - Update initial condition specifications and use of geodata file

Issue - State: open - Opened by shauntruelove over 1 year ago - 11 comments
Labels: bug, enhancement, high priority, medium priority

#82 - Update initial condition specifications and use of geodata file

Issue - State: open - Opened by shauntruelove over 1 year ago - 11 comments
Labels: bug, enhancement, high priority, medium priority

#81 - Revise mobility to be a rate instead of absolute numbers

Issue - State: open - Opened by shauntruelove over 1 year ago - 1 comment
Labels: enhancement, low priority

#81 - Revise mobility to be a rate instead of absolute numbers

Issue - State: open - Opened by shauntruelove over 1 year ago - 1 comment
Labels: enhancement, low priority

#80 - Remove or Restructucture "data_path" option and use in config

Issue - State: closed - Opened by shauntruelove over 1 year ago - 3 comments
Labels: bug, medium priority

#80 - Remove or Restructucture "data_path" option and use in config

Issue - State: closed - Opened by shauntruelove over 1 year ago - 3 comments
Labels: bug, medium priority

#79 - Postprocessing updates with new config structure

Issue - State: open - Opened by saraloo over 1 year ago - 2 comments
Labels: post-processing, medium priority

#77 - outcome_modifier description format

Issue - State: open - Opened by kjsato over 1 year ago
Labels: enhancement, config, low priority

#77 - outcome_modifier description format

Issue - State: open - Opened by kjsato over 1 year ago
Labels: enhancement, config, low priority

#76 - Unittest on breaking improvments

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

#76 - Unittest on breaking improvments

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

#75 - Submit RSV SMH Round 1 - Due Nov 14

Issue - State: closed - Opened by shauntruelove over 1 year ago - 3 comments
Labels: submission

#75 - Submit RSV SMH Round 1 - Due Nov 14

Issue - State: closed - Opened by shauntruelove over 1 year ago - 3 comments
Labels: submission

#74 - move slurm file path fix: file_paths.create_file_names

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

#74 - move slurm file path fix: file_paths.create_file_names

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

#73 - Unittest breaking improvments

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

#73 - Unittest breaking improvments

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

#72 - New simplified config format

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

#72 - New simplified config format

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

#71 - Breaking improvments (deeper changes)

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

#71 - Breaking improvments (deeper changes)

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

#70 - Initial conditions fit in the R code

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

#70 - Initial conditions fit in the R code

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

#69 - Unittest

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

#69 - Unittest

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

#68 - Configwriter fix

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

#68 - Configwriter fix

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

#67 - config_version lookups and v4

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

#67 - config_version lookups and v4

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

#66 - Initial conditions can be fitted

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

#66 - Initial conditions can be fitted

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

#65 - Improvements to usability

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

#65 - Improvements to usability

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

#64 - Rename `geoid`and `nodename` to subpopulation

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

#64 - Rename `geoid`and `nodename` to subpopulation

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

#63 - config.writer SEIR chunk incorrectly printing rates

Issue - State: closed - Opened by saraloo over 1 year ago - 1 comment
Labels: bug, config

#63 - config.writer SEIR chunk incorrectly printing rates

Issue - State: closed - Opened by saraloo over 1 year ago - 1 comment
Labels: bug, config

#62 - Improvements for consistency

Pull Request - State: closed - Opened by jcblemai over 1 year ago - 2 comments

#62 - Improvements for consistency

Pull Request - State: closed - Opened by jcblemai over 1 year ago - 2 comments

#61 - Config.writer update

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

#61 - Config.writer update

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

#60 - fix pull of covid deaths data

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

#60 - fix pull of covid deaths data

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

#59 - Main fixvarerr

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

#59 - Main fixvarerr

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

#58 - Init files

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

#58 - Init files

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

#57 - Backup tools

Pull Request - State: closed - Opened by jcblemai over 1 year ago - 2 comments

#57 - Backup tools

Pull Request - State: closed - Opened by jcblemai over 1 year ago - 2 comments

#56 - Seeding fix

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

#56 - Seeding fix

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

#55 - Improve syntax of single initial condition file.

Issue - State: open - Opened by jcblemai over 1 year ago - 1 comment
Labels: enhancement, low priority

#55 - Improve syntax of single initial condition file.

Issue - State: open - Opened by jcblemai over 1 year ago - 1 comment
Labels: enhancement, low priority

#54 - Init files

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

#54 - Init files

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

#53 - Docker does not work on Macs with Apple chips

Issue - State: closed - Opened by alsnhll over 1 year ago - 2 comments

#52 - conda environment does not build on Mac

Issue - State: closed - Opened by alsnhll over 1 year ago - 8 comments
Labels: bug, high priority

#52 - conda environment does not build on Mac

Issue - State: closed - Opened by alsnhll over 1 year ago - 8 comments
Labels: bug, high priority

#51 - change code to read parquet or csv for any input files

Issue - State: open - Opened by shauntruelove almost 2 years ago - 1 comment
Labels: enhancement, low priority

#51 - change code to read parquet or csv for any input files

Issue - State: open - Opened by shauntruelove almost 2 years ago - 1 comment
Labels: enhancement, low priority

#50 - local_install.R fails in conda flepimop-env

Issue - State: closed - Opened by alsnhll almost 2 years ago - 1 comment

#50 - local_install.R fails in conda flepimop-env

Issue - State: closed - Opened by alsnhll almost 2 years ago - 1 comment

#49 - model_output is hardcoded in the "create_file_name" function of the flepicommon package

Issue - State: closed - Opened by shauntruelove almost 2 years ago - 3 comments

#49 - model_output is hardcoded in the "create_file_name" function of the flepicommon package

Issue - State: closed - Opened by shauntruelove almost 2 years ago - 3 comments

#48 - fix typo in select_outputs variable

Pull Request - State: closed - Opened by saraloo almost 2 years ago

#48 - fix typo in select_outputs variable

Pull Request - State: closed - Opened by saraloo almost 2 years ago

#47 - Postprocess snapshot dev

Pull Request - State: closed - Opened by saraloo almost 2 years ago

#47 - Postprocess snapshot dev

Pull Request - State: closed - Opened by saraloo almost 2 years ago

#46 - Better error handling in the script to clean old AWS S3 intermediate files

Pull Request - State: closed - Opened by jcblemai almost 2 years ago

#46 - Better error handling in the script to clean old AWS S3 intermediate files

Pull Request - State: closed - Opened by jcblemai almost 2 years ago

#45 - Config phase3

Pull Request - State: closed - Opened by shauntruelove almost 2 years ago

#45 - Config phase3

Pull Request - State: closed - Opened by shauntruelove almost 2 years ago

#44 - fix bug where the build folder was not sent

Pull Request - State: closed - Opened by jcblemai almost 2 years ago

GitHub / hopkinsidd/flepimop issues and pull requests