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Improvements for consistency #62
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Adding some updates to the proposed to-dos Change order of config sections to:
For Outcomes and Interventions sections:Proposed changes to make it easier to understand the intervention/scenario definitions. First, need to decide if it's worth having the ability to re-run the outcomes part only without re-running the full SEIR model.
For interventions section
|
Bringing here the improvements for config V3 Config Structure changesThe concept of scenario for outcomes is phased out. One config = One structure. Only modifiers can be changed. The configs sections are described below. There are four types of runs but users should only be advised to do either (seir+outcomes) or (seir+outcomes+inference).
So what is the purpose of the StackedModifier if every intervention is applied ?
Note that the config elements can be put in any order So how do the new modifiers sections work. There are two possibilities:
B. Multiple scenarios config
substructure:Outcomes
ProbabilitiesThe
is still valid but can be abbreviated
this applies to all probabilities distributions for gempyor: modifiers, outcomes, parameters, ... Nomenclature changesInterventionschanged
and removed ReduceR0 The For outcomes intervention_param_name has been changed to modifier_parameter geoid:change geoid to subpop For Outcomes
Initial ConditionsSetInitialCondition comp changed to mc_name Fitting initial conditionsinitial_conditions: Parameters:
Filestructure:we don't nest scenarios in folder (e.g TODO
from @alsnhll in #62
Useful messageshttps://iddynamicsjhu.slack.com/archives/GU0SBC2AC/p1693600672108579?thread_ts=1693399856.162839&cid=GU0SBC2AC Alison BIG TODO that needs discussionFrom Alison: |
fixed more problems with saving of both global and chimeric files
since R Studio changed it's default, so when someone runs Code -> Reindent Lines to clean things up it now does 2 instead of 4, and Git thinks this is an edited line
To agree with change in default in R Studio, to avoid indent changes being registered as tracked changes in Git
…flepiMoP into breaking-improvments # Conflicts: # flepimop/main_scripts/inference_slot.R
I had introduced a few mistakes before in the process of correcting previous problems. Now everything working as intended. Updated file names to make clear what is proposed s what is the current accepted value.
… If it does, not, return error, printing the name of the file.
… If it does, not, return error, printing the name of the file.
…flepiMoP into breaking-improvments # Conflicts: # flepimop/main_scripts/inference_slot.R
…flepiMoP into breaking-improvments
Among other changes:
Interventions
changed
and removed ReduceR0
geoid:
change geoid to subpop
affected_geoids > subpop
place > subpop
Initial Conditions
SetInitialCondition comp changed to mc_name
Fitting initial conditions
initial_conditions:
method: SetInitialConditionsFolderDraw
seeding_file_type: init
perturbation:
distribution: truncnorm
mean: 0
sd: 0.02
a: -1
b: 1
and in the initial initial condition files are csvs or parquet like
subpop,mc_name,amount,pertub
AK, R_age_01_19, .3, TRUE
AK, S_age_01_19, remain, FALSE
...
TODO
Useful messages
https://iddynamicsjhu.slack.com/archives/GU0SBC2AC/p1693600672108579?thread_ts=1693399856.162839&cid=GU0SBC2AC Alison
https://iddynamicsjhu.slack.com/archives/GU0SBC2AC/p1693223628997289 Koji