Code

Merge emcee_batch Into dev#404

Code

Merged

TimothyWillard merged 68 commits intodevHopkinsIDD/flepiMoP:devfrom feature/403/emcee_batchHopkinsIDD/flepiMoP:feature/403/emcee_batchCopy head branch name to clipboardDec 4, 2024

+2,714-18,874

Commits

Commits on Sep 16, 2024

• fixes the argument call to the plot of emcee chains

  jcblemai

  committed
  8974cc4

• finish the plot

  jcblemai

  committed
  1453303

• fix emcee rmse error spotted by Tim in #300

  jcblemai

  committed
  e4bbd8c

Commits on Sep 17, 2024

• Save seir, spar and snpi on save, + made more granullar to access a funciton that just run a simulation

  jcblemai

  committed
  311a20b

• fix

  jcblemai

  committed
  80e63b8

• change the order so it fails fast if something already exist

  jcblemai

  committed
  bf7c37a

Commits on Sep 18, 2024

• a very hacky and stupid batch hack to fight memory creep...

  jcblemai

  committed
  6725bf6

Commits on Sep 19, 2024

• trying to trigger a llik reevaluation

  jcblemai

  committed
  70bbee8

• solve #316: likelihood are discarded during resume

  jcblemai

  committed
  465d0bb

Commits on Sep 20, 2024

• upgrade plot to show the transformed data

  jcblemai

  committed
  2c54cfd

Commits on Sep 25, 2024

• plotting proections

  jcblemai

  committed
  f1ecbe6

• file structure

  jcblemai

  committed
  b5409a7

• add poisson likelihood

  twallema

  committed
  ebbf2c2

• add new distributions - retain old distributions

  twallema

  committed
  589af08

• miscopied the poisson from pySODM

  twallema

  committed
  b797cf7

• match data format gempyor --> not summed over dates --> happens after

  twallema

  committed
  3ca0c7a

Commits on Sep 26, 2024

• fix plot-fit for one outcome

  twallema

  committed
  88686cd

• tentative: propose cocktail of emcee "moves"

  twallema

  committed
  1b1ddb2

Commits on Sep 27, 2024

• compatibility with python on longleaf. To remove ?

  jcblemai

  committed
  7e2a061

• Merge branch 'emcee_batch' of https://github.com/HopkinsIDD/flepiMoP into emcee_batch

  jcblemai

  committed
  8849b24

Commits on Sep 28, 2024

• plot fix

  jcblemai

  committed
  6caa83f

• Merge branch 'emcee_batch' of https://github.com/HopkinsIDD/flepiMoP into emcee_batch

  jcblemai

  committed
  a843710

• nicer grid

  jcblemai

  committed
  ae86e52

Commits on Sep 30, 2024

• simplify my life

  jcblemai

  committed
  965ef19

Commits on Oct 3, 2024

• reload groundtruth to help with usage

  jcblemai

  committed
  33bd35c

• default to making config plots

  jcblemai

  committed
  b590d92

• new config

  jcblemai

  committed
  5ee0f2b

• cocktail change

  jcblemai

  committed
  ce59add

• energy savings :D

  jcblemai

  committed
  fabc759

Commits on Oct 4, 2024

• add a precheck for config sensitivity after what happen on Flu R1 2024

  jcblemai

  committed
  d80f213

• error

  jcblemai

  committed
  fb5618f

Commits on Oct 15, 2024

• this check is vad...

  jcblemai

  committed
  823d81f

• postprocessing script

  jcblemai

  committed
  88e305b

• gen markdown

  jcblemai

  committed
  ec12e4b

Commits on Oct 30, 2024

• draft of modifiers support of out of reach subpops, still unsafe

  jcblemai

  committed
  37f7901

Commits on Oct 31, 2024

• remove print

  jcblemai

  committed
  f186244

• temp

  jcblemai

  committed
  a18d170

• merge

  jcblemai

  committed
  b99afec

Commits on Nov 7, 2024

• very iugly code for cli that plot modifiers activation and time series

  jcblemai

  committed
  3ddc975

• add outcoems parameters

  jcblemai

  committed
  5ea3d41

• tried the outcoems NPI plot

  jcblemai

  committed
  a3541d5

• tried the outcoems NPI plot

  jcblemai

  committed
  6da7439

• fix one subpop

  jcblemai

  committed
  29de35e

Commits on Nov 8, 2024

• added postprocessing for several subpop

  jcblemai

  committed
  0439fcd

Commits on Nov 15, 2024

• Pull HPC init/build from main into emcee_batch

  Show description for ab86912
  TimothyWillard

  committed
  ab86912

Commits on Nov 19, 2024

• Pull postprocessing from emcee_batch

  TimothyWillard

  committed
  7ae2917

• Pull examples from emcee_batch

  TimothyWillard

  committed
  3977b8d

• Merge emcee_batch into feature/403/emcee_batch

  Show description for 0c67060
  TimothyWillard

  committed
  0c67060

• Apply black formatter post-merge

  TimothyWillard

  committed
  029f8c8

• Update tests for Statistics to pass

  TimothyWillard

  committed
  d58f6d9

• Missing compartments runtime error and tests

  Show description for 0055ed8
  TimothyWillard

  committed
  0055ed8

• Edits to make test_outcome_scenario pass

  Show description for fc23642
  TimothyWillard

  committed
  fc23642

Commits on Nov 21, 2024

• Update test_outcome_modifiers_scenario_with_load

  Show description for 9347849
  TimothyWillard

  committed
  9347849

• Update test_outcomes_npi test

  Show description for aeb3a77
  TimothyWillard

  committed
  aeb3a77

• Update test_outcomes_npi_custom_pname test

  Show description for b65276c
  TimothyWillard

  committed
  b65276c

• Updates to make inference tests pass

  Show description for 413690b
  TimothyWillard

  committed
  413690b

• Fix test_full_npis_read_write test

  Show description for dfc2ae3
  TimothyWillard

  committed
  dfc2ae3

• Update test_spatial_groups test config

  Show description for 0c1bb46
  TimothyWillard

  committed
  0c1bb46

• Bug fix compute_all_multioutcomes

  Show description for e3cb537
  TimothyWillard

  committed
  e3cb537

Commits on Nov 22, 2024

• Update the 'Inference with EMCEE' gitbook docs

  TimothyWillard

  committed
  05b760b

Commits on Dec 2, 2024

• Remove confusing/unneeded lines

  Show description for 6cbfa5e
  TimothyWillard

  committed
  6cbfa5e

• Use confuse as_str_seq getter for subpop

  Show description for eda84e4
  TimothyWillard

  committed
  eda84e4

Commits on Dec 3, 2024

• Add test for flepimop modifiers config-plot

  Show description for 481e63f
  TimothyWillard

  committed
  481e63f

• Add CLI docs to flepimop modifiers config-plot

  TimothyWillard

  committed
  9ae6bd3

• Merge dev into feature/403/emcee_batch

  TimothyWillard

  committed
  73d2a2f

Commits on Dec 4, 2024

• Quick fix for GH-373

  Show description for 980429e
  TimothyWillard

  committed
  980429e

• Initialize GempyorInference.static_sim_arguments

  Show description for 8a83236
  TimothyWillard

  committed
  8a83236

• Merge dev into feature/403/emcee_batch

  TimothyWillard

  committed
  9ba0c24