hopkinsidd/flepimop issues and pull requests

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

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

#43 - stochastic option in config

Issue - State: open - Opened by alsnhll almost 2 years ago - 1 comment
Labels: enhancement, config, medium priority

#43 - stochastic option in config

Issue - State: open - Opened by alsnhll almost 2 years ago - 1 comment
Labels: enhancement, config, medium priority

#42 - R17 dev

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

#42 - R17 dev

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

#41 - Course on how to check a run on slurm

Issue - State: closed - Opened by jcblemai almost 2 years ago - 2 comments
Labels: documentation, medium priority

#41 - Course on how to check a run on slurm

Issue - State: closed - Opened by jcblemai almost 2 years ago - 2 comments
Labels: documentation, medium priority

#40 - Harmonize SLURM logs

Issue - State: closed - Opened by jcblemai almost 2 years ago - 1 comment
Labels: batch

#40 - Harmonize SLURM logs

Issue - State: closed - Opened by jcblemai almost 2 years ago - 1 comment
Labels: batch

#39 - Better error passing between R and python

Issue - State: closed - Opened by jcblemai almost 2 years ago - 1 comment
Labels: gempyor

#39 - Better error passing between R and python

Issue - State: closed - Opened by jcblemai almost 2 years ago - 1 comment
Labels: gempyor

#38 - Build validation script thats run at beginning of model run to check input data and gt data

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

#38 - Build validation script thats run at beginning of model run to check input data and gt data

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

#37 - Build CI validation to check config/input data on commit in project repos

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

#37 - Build CI validation to check config/input data on commit in project repos

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

#36 - Simple & robust post-processing

Issue - State: closed - Opened by jcblemai almost 2 years ago - 1 comment
Labels: post-processing

#36 - Simple & robust post-processing

Issue - State: closed - Opened by jcblemai almost 2 years ago - 1 comment
Labels: post-processing

#35 - gempyor should support configs without transmission NPIs

Issue - State: closed - Opened by jcblemai almost 2 years ago - 1 comment
Labels: gempyor

#35 - gempyor should support configs without transmission NPIs

Issue - State: closed - Opened by jcblemai almost 2 years ago - 1 comment
Labels: gempyor

#34 - Inference on global spar parameters

Issue - State: open - Opened by jcblemai almost 2 years ago - 2 comments
Labels: documentation, enhancement, r-inference, medium priority

#34 - Inference on global spar parameters

Issue - State: open - Opened by jcblemai almost 2 years ago - 2 comments
Labels: documentation, enhancement, r-inference, medium priority

#33 - Unify scenario run in a simple interface

Issue - State: closed - Opened by jcblemai almost 2 years ago - 1 comment
Labels: gempyor

#33 - Unify scenario run in a simple interface

Issue - State: closed - Opened by jcblemai almost 2 years ago - 1 comment
Labels: gempyor

#32 - Add check that the input data all align.

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

#32 - Add check that the input data all align.

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

#31 - Little fixes

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

#31 - Little fixes

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

#30 - Fixing ground truth covid data:

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

#30 - Fixing ground truth covid data:

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

#29 - Saving model_output to abitrary folders

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

#29 - Saving model_output to abitrary folders

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

#28 - Spatial groups of NPI with the same values

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

#28 - Spatial groups of NPI with the same values

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

#27 - config.writer: hardcoded capitalization and param_from_file

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

#27 - config.writer: hardcoded capitalization and param_from_file

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

#26 - InferenceTest.R in Inference package contains now-defunct config options for hospitalization

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

#26 - InferenceTest.R in Inference package contains now-defunct config options for hospitalization

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

#25 - renamed "deathrates" to "outcome_scenarios" and "scenarios" to "npi_scenarios"

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

#25 - renamed "deathrates" to "outcome_scenarios" and "scenarios" to "npi_scenarios"

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

#24 - Docker issues with directory flepimop vs flepiMoP vs flepiMoP/flepimop

Issue - State: closed - Opened by alsnhll almost 2 years ago - 6 comments

#24 - Docker issues with directory flepimop vs flepiMoP vs flepiMoP/flepimop

Issue - State: closed - Opened by alsnhll almost 2 years ago - 6 comments

#23 - hardcoded requirement for US-specific geoids in geodata file

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

#23 - hardcoded requirement for US-specific geoids in geodata file

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

#22 - catching missing outcome scenarios

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

#22 - catching missing outcome scenarios

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

#21 - Coviddata fix

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

#21 - Coviddata fix

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

#20 - Gempyor: remove dependencies on config when creating setup

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

#20 - Gempyor: remove dependencies on config when creating setup

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

#19 - Error messages and gracefull failures

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

#19 - Error messages and gracefull failures

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

#18 - Fix some installation things

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

#18 - Fix some installation things

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

#17 - force `local_install.R` to install `flepicommon` package first (since it's a dependency of the others).

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

#17 - force `local_install.R` to install `flepicommon` package first (since it's a dependency of the others).

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

#16 - fix hard-coded path to `flepiMoP`

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

#16 - fix hard-coded path to `flepiMoP`

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

#15 - replace hard-coded s3 buckets with inputted ones (e.g., "idd-inference-runs")

Issue - State: closed - Opened by shauntruelove almost 2 years ago - 7 comments

#14 - Replace all hard-coded `model_output` calls with `$model_output_path` to use config-specified path

Issue - State: open - Opened by shauntruelove almost 2 years ago - 2 comments
Labels: bug, medium priority

#13 - add `gc()` garbage collection to the R loops to reduce memory creep

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

#12 - post-processing: provide full analysis

Issue - State: closed - Opened by jcblemai almost 2 years ago

#11 - gempyor optimize health outcomes computation

Issue - State: open - Opened by jcblemai almost 2 years ago - 1 comment
Labels: enhancement, medium priority, performance

#10 - SLURM: use /tmp for low latency disk usage on JHU's RockFish

Issue - State: open - Opened by jcblemai almost 2 years ago

#9 - SLURM: save some intermediate simulations

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

#8 - Add a feature to switch betwen projections and inference runs

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

#7 - Postprocessing: provide options

Issue - State: closed - Opened by jcblemai almost 2 years ago
Labels: post-processing

#6 - error handling: fail gracefully when no geoid matches an interventions "affected_geoid"

Issue - State: open - Opened by jcblemai almost 2 years ago - 1 comment
Labels: bug, medium priority

#5 - Allow initial conditions from specific files instead of seeding

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

#4 - script: duplicate failed slots from past runs

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

#3 - gempyor: flag to skip writing the seir file / inference: take advantage of that.

Issue - State: open - Opened by jcblemai almost 2 years ago - 1 comment
Labels: enhancement, gempyor, r-inference, medium priority

#2 - Harmonize runs logs on SLURM

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

#1 - Improve error management on SLURM

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

GitHub / hopkinsidd/flepimop issues and pull requests