updated with dynamic calibration experiments

This release records the state of the codebase for submission of a journal paper (details to follow pending review)

v1.4.1

This release has no major changes to the previous version (v1.4.1). It's purpose is to log the state of the model before conducting a large merge consisting of the dynamic re-calibration work.

v1.4.0

This is a large release that incorporates a number of changes made including but not restricted to:

• Removal of data from git-lfs and migrated to Azure
• Removal of old quant_api code
• Updated defaults.yml

Commits

• [8cc167e]: removed proportion_asymptomatic (this is no longer used in the opencl model) (Nick Malleson) #215
• [6a9e22e]: trying to get ABC working (Nick Malleson) #215
• [eaaa428]: figured out that ABC needs a stochastic model otherwise it doest sample from the prior properly so added a new argument to run_opencl_model_multi that randomises the ids (Nick Malleson) #215
• [a7e9172]: bump version number 1.3.0 (Alex Coleman) #212
• [e5022f7]: fixing the long branch names created by the GHA issue brancher (Alex Coleman) #213
• [1893b33]: minor (Nick Malleson) #215
• [9b3ddf9]: continuing with ABC (Nick Malleson) #215
• [e43c461]: Merge branch 'master' into nm_sensitivity_testing (Nick Malleson) #215
• [02caf94]: got abc working with 1 parameter (Nick Malleson) #215
• [c33cb90]: got abc working with 1 parameter (Nick Malleson) #215
• [dce6663]: Removed junk from the test file (Nick Malleson) #215
• [ad83829]: updating github actions to fix #166 (Alex Coleman) #216
• [2fbeb37]: minor (Nick Malleson) #217
• [c5287ec]: Merge branch 'nm_sensitivity_testing' of https://github.com/Urban-Analytics/RAMP-UA into nm_sensitivity_testing (Nick Malleson) #217
• [133b53c]: Merge branch 'master' into nm_sensitivity_testing (Nick Malleson) #217
• [f8e8ab0]: minor (Nick Malleson) #217
• [5507df6]: fixed incorrect error calculation (Nick Malleson) #223
• [50445b6]: fixed problem about not comparing cumulative cases (Nick Malleson) #223
• [0f26d83]: fixed bug that meant the daily cases rather than cumulative cases were being compared to the (cumulative) observations (Nick Malleson) #223
• [7d07ef9]: got simplex method (multiple parameters) and ABC working (with one parameter) (Nick Malleson) #223
• [52e5f33]: got abc working with multiple parameters (Nick Malleson) #223
• [485d057]: fixed bug in dictionary iteration (Nick Malleson) #223
• [4d4ffd3]: Add files via upload (Fiona Spooner) #222
• [2b00ed1]: Add files via upload (Fiona Spooner) #222
• [421b88e]: Update default.yml (Fiona Spooner) #222
• working on plotting abc with multiple parameters #223 (Nick Malleson)
• [aba45fb]: Update default.yml (Nick Malleson) #223
• [6ecf4c8]: minor:working on multi-paramet abc (Nick Malleson) #227
• [3ec5451]: Merge branch 'nm_sensitivity_testing' of https://github.com/Urban-Analytics/RAMP-UA into nm_sensitivity_testing (Nick Malleson) #227
• [4848a59]: tried sampling from the posterior to make new model predictions (Nick Malleson) #227
• [8ec0021]: added pickled abc multi-param results (Nick Malleson) #227
• [24a262d]: removing proportion asymptomatic - current master gui doesn't run as this parameter no longer exists (Fiona Spooner) #224
• [cfa0c3f]: matching with the R/Python model (Fiona Spooner) #225
• [757208a]: Merge branch 'master' into symptomatic_multi (Fiona Spooner) #225
• [1def62a]: updateing gui to include the updated number of age mortality rates (Fiona Spooner) #226
• [24e11cf]: sorry keep branching from branches (Fiona Spooner) #226
• [f8f9158]: ran multi-parameter ABC for more iterations and the results improved a lot (Nick Malleson) #227
• [30568ac]: fix test by setting param explicitly (Rory) #225
• [23698f5]: finished ABC for now (Nick Malleson) #227
• [c163a1a]: Merge branch 'master' into nm_sensitivity_testing (Nick Malleson) #227
• moved calibration stuff into a dir called "calibration" and made new ipynb for abc stuff #227 (Nick Malleson)
• [bb7448b]: minor (Nick Malleson) #227
• [[3951a54](https://github.com/U...

v1.3.0

Commits

• [ab7e015]: added example dir with starting files for colab examples (Alex Coleman) #199
• [1d85d54]: added environment file (Alex Coleman) #199
• [b9b371e]: adjusted path names in sh file (Alex Coleman) #199
• [61d8c5c]: adjusted install script (Alex Coleman) #199
• [0fe14d8]: removed some packages from example colab yml (Alex Coleman) #199
• [d3794e7]: corrected yml indentation (Alex Coleman) #199
• [36bd1bb]: initial first draft of colab notebook (Alex Coleman) #199
• [2b8ac42]: attempting to resolve import errors relates to issue #182 (Alex Coleman) #199
• [ae15cb6]: initial working notebook with correct env setup (Alex Coleman) #199
• [a231895]: updated dependencies for final geopandas step (Alex Coleman) #199
• [ec331af]: updated repository to include fetching default cache file (Alex Coleman) #199
• [43819da]: updated notebook name (Alex Coleman) #199
• [1f485cc]: added in ocl-id-system to enable gpu detection (Alex Coleman) #199
• [4863b33]: updated script with working install lines (Alex Coleman) #199
• [5ddbbb2]: updated script due to git clone failure (Alex Coleman) #199
• [e6151a6]: closed if block (Alex Coleman) #199
• [3a2b0fb]: corrected quotation marks in python expression line (Alex Coleman) #199
• [ae2b472]: added import sys for python expression (Alex Coleman) #199
• [ddca703]: corrected python exp line (Alex Coleman) #199
• [493feed]: setting sys path doesn't work for colab so will move it to notebook (Alex Coleman) #199
• [0b9089f]: updated notebook for #185 that includes: (Alex Coleman) #199
• [3c4bca2]: added quiet options for installs (Alex Coleman) #199
• [1068b65]: added a second parameter to calibration (Nick Malleson) #209
• [5af6969]: TEMPOARILY commented out Inspector import to work on ubuntu headless (Nick Malleson) #209
• [6729171]: Merge branch 'nm_sensitivity_testing' of https://github.com/Urban-Analytics/RAMP-UA into nm_sensitivity_testing (Nick Malleson) #209
• [2df328e]: minor (Nick Malleson) #209
• [a85372b]: Merge branch 'nm_sensitivity_testing' of https://github.com/Urban-Analytics/RAMP-UA into nm_sensitivity_testing (Nick Malleson) #209
• [5989f71]: refactored Functions class to make it a more formal class that runs the OpenCL model rather than just a placeholder for generic functions (Nick Malleson) #209
• [7738d89]: refactored Functions class to make it a more formal class that runs the OpenCL model rather than just a placeholder for generic functions (Nick Malleson) #209
• [c299d74]: fixed tests (Nick Malleson) #209
• [301893d]: renamed test file (Nick Malleson) #209
• [6787f9e]: added tests for the new run_model_with_params function (Nick Malleson) #209
• [a399f00]: refactored Functions class to make it a more formal class that runs the OpenCL model rather than just a placeholder for generic functions (Nick Malleson) #209
• [8f8edb3]: Merge branch 'master' into nm_sensitivity_testing (Nick Malleson) #209
• [334f859]: Merge branch 'master' into nm_sensitivity_testing (Nick Malleson) #209
• [0444f0c]: remove redundant functions.py file - logic now in opencl_runner.py (Nick Malleson) #209
• [60af4a7]: bump version number (Alex Coleman) #200
• [a250baf]: moved sys path setting into different jupyter cell (Alex Coleman) #190
• [e64493c]: updating age based ifr in line with Imperial report 34 - https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/2020-10-29-COVID19-Report-34.pdf (Fiona Spooner) #201
• [6720b6b]: minor change to instructions about how to generate a snapshot (Nick Malleson) #209
• [7500887]: updated notebooks to use new seeding in opencl model (#194) (Nick Malleson) #209
• [ab9f962]: fixing param struct (Fiona Spooner) #201
• [[b61a61f](https://...

v1.2.0

Commits

• [c8d0db9]: new directory for experiments (Nick Malleson) #169
• [f321584]: moved notebook to experiments dir (Nick Malleson) #169
• [906dcc0]: read parameters in from the parameters file (Nick Malleson) #169
• [0e1ed7e]: trying to get multiprocess version workin in notebook (Nick Malleson) #169
• [b5fd4c9]: trying to implement multiprocess model running but processes still hanging, I think to do with the notebook server (Nick Malleson) #169
• [5e741c1]: still trying to get multiprocessing working (Nick Malleson) #169
• [891fa1a]: trying to get multiprocess working in the notebook (Nick Malleson) #169
• [0f1deeb]: slight changes to allow for the new infection_prob function (Fiona Spooner) #167
• [6ff451a]: updating to run new infection_prob function (Fiona Spooner) #167
• [f8c3506]: Delete covid_run.R (Fiona Spooner) #167
• [21e8510]: replace hard-coded number of diseases (7) with a count from the DiseaseStatus enum (Nick Malleson) #169
• [5352e23]: making graphs showing variability (Nick Malleson) #169
• [79e44c8]: Introduced a str representaiton of DiseaseStatus to prevent need for use of disease_status.name.lower() in dicts and also use a dictionary comprehension to cut down some code repetition (Nick Malleson) #169
• [7991453]: added error bars to plots, now will start sensitivity testing (Nick Malleson) #169
• [300043b]: added error bars to plots, now will start sensitivity testing (Nick Malleson) #169
• [ece3e8f]: updated results analysis to include error bars (Nick Malleson) #169
• [dc3ab30]: updated results analysis to include error bars (Nick Malleson) #169
• [9523a32]: recreating no lockdown issue (Fiona Spooner) #170
• [755f31f]: Merge branch 'master' of https://github.com/Urban-Analytics/RAMP-UA into charlie_probability (Fiona Spooner) #170
• [2113e6a]: removed the do_lockdown variable fro population_initialisation, it was redundant now that most of the model logic is in microsim_model.py (Nick Malleson) #170
• [e59cca9]: moved the reading of the lockdown file and creation of the time_activity_multiplier into main.py. Now it is not part of the population caches so if the lockdown file changes the old caches can still be used. (Nick Malleson) #170
• [cf5a369]: exposed store_detailed_counts so that model can run faster if required (Nick Malleson) #169
• [fd48d2d]: removed temp file (Nick Malleson) #169
• [99ea756]: updated test to read lockdown file separately from population initialisation (Nick Malleson) #170
• [df34f35]: updated test to read lockdown file separately from population initialisation (Nick Malleson) #170
• [bf45135]: Merge branch 'master' into spoonerf-issue-168-No_lockdown_not_working (Nick Malleson) #170
• [93d196c]: updated hazard kernel function (cshenton) #171
• [21caa7e]: symptomatic risk function working (Fiona Spooner) #174
• [c12a90c]: make the repetition number (reprn) an object level variable so that it can be passed to the R code (Nick Malleson) #178
• [e0d1975]: pass the repetition number to the calculate_disease_status function (Nick Malleson) #178
• [d5bd103]: moved random number generator into the microsim model (Nick Malleson) #176
• [75525a8]: updated tests now that random number generator has moved from population initialisation to microsim model (Nick Malleson) #176
• [a081b38]: adding in seed logic (Fiona Spooner) #179
• [5b3cadc]: taking in the repnr from python (Fiona Spooner) #178
• [73eda3b]: Merge branch 'nickmalleson-issue-173-Send_Python_repetition_number_to_R' of https://github.com/Urban-Analytics/RAMP-UA into set_seed (Fiona Spooner) #179
• [5e54811]: setting seed as default and printing the see (Fiona Spooner) #179
• [28a1ed5]: removing some infection_length() vars that are no longer needed (Fiona Spooner) #178
• [10d7683]: Merge branch 'master' into nickmalleson-issue-173-Send_Python_repetition_number_to_R (Fiona Spooner) #178
• [042b7da]: Merge branch 'nickmalleson-issue-173-Send_Python_repetition_number_to_R' of https://github.com/Urban-Analytics/RAMP-UA into set_seed (Fiona Spooner) #179
• [f9087c9]: adding seed to the necessary functions (Fion...

v1.1.0

Commits

• [5d65517]: individual hazard logic no errors (Rory) #153
• [28eceeb]: Merge branch 'master' into individual-hazard-opencl (Rory) #153
• [d7008b5]: update snapshot params properly (Rory) #153
• [ae552fc]: pre-multiply location hazards (Rory) #153
• [e384b50]: pass asymptomatic rate (Rory) #153
• [1b2ea01]: add test for asymptomatic, currently failing (Rory) #153
• [9cb3fd0]: use update params function (Rory) #153
• [ea0762f]: change expected proportion asymptomatic (Rory) #153
• [31bc027]: hazards test pass (Rory) #153
• [c3c879d]: don't have default asympt_hazard value (Rory) #153
• [c7949ef]: remove printf statements (Rory) #153
• [f0fd7cb]: better descriptive comment (Rory) #153
• [4b0f7b8]: update snapshot params correctly in jupyter notebook (Rory) #153
• [650d211]: now always save workers cache file (Nick Malleson) #158
• [5b7b778]: set use cache to true by default (Nick Malleson)
• [83e4488]: add test for lognormal dist (Rory) #157
• [04c4f11]: removed function to cache the workplaces as cacheing is now done for the individuals and activity locations separately so it was unnecessary (Nick Malleson) #158
• add print lines #158 (Nick Malleson)
• [b46277b]: Merge branch 'master' into nickmalleson-issue-154-_minor_save_workplaces_if_no-cache_is_true (Nick Malleson) #158
• [d69e91c]: Merge branch 'master' into lognormal-dist-opencl (Rory) #157
• [0439681]: use randn not rand (Rory) #157
• [19136d5]: don't test kurtosis (Rory) #157
• [4fda929]: change default infection lognormal param values (Rory) #157
• [cce2511]: minor (Nick Malleson) #158
• [b3929df]: removed use_cache population argument from tests (Nick Malleson) #158
• [3b7e0de]: catch an error that is caused if the parameters change between snapshots and warn about it (Nick Malleson) #158
• [340dde3]: pass obesity and other health data as buffers (Rory) #161
• [d8c7543]: Merge branch 'master' into obesity-opencl (Rory) #161
• [cd764e3]: obesity kernel logic (Rory) #161
• [23c21f0]: fix errors in snapshot test (Rory) #161
• [da4efae]: all tests pass (Rory) #161
• [9ad8cc0]: tests successful (Rory) #161
• [30deabf]: update model design doc (Rory) #161
• [068da9b]: increase mode tolerance (Rory) #161
• [ae6de60]: add switch to healthier population (Rory) #161
• [2a1fb16]: check healthy population condition properly (Rory) #161
• [50542bf]: update data size calculation (Rory) #161
• [9b81f18]: logic for increasing symptomatic rate of overweight (Rory) #162
• [e698c02]: Merge branch 'master' into obesity-affects-asymp-rate (Rory) #162
• [26348ea]: add tests (Rory) #162
• [eb1238d]: fix bug in params array size (Rory) #162
• [9a06758]: deepcopy initial snapshot (Rory) #164
• [4b992f1]: update time after seeding initial infections (Rory) #164
• [018dc20]: bumping version number (Alex Coleman) #165

v1.0.0

Commits

• [00b9682]: ignore R project files (rory-improbable) #149
• [f9be7bf]: copy of microsim_model file (rory-improbable) #149
• [bb3cebb]: store age snapshot (rory-improbable) #149
• [da87a44]: separate snapshotter class (rory-improbable) #149
• [3716b11]: cache each location dataframe (rory-improbable) #149
• [0b4042f]: cache activity names (rory-improbable) #149
• [bc23dc7]: loading from cache works (rory-improbable) #149
• [6a6f3b9]: code to get place ids and flows (rory-improbable) #149
• [82f3ffc]: calculate flows with correct datatypes (rory-improbable) #149
• [5d7daac]: add progress bar for processing people (rory-improbable) #149
• [eb8a7c9]: store place types and coordinates (rory-improbable) #149
• [b0473ee]: uncomment people snapshot code (rory-improbable) #149
• [f0f7e9d]: add comments (rory-improbable) #149
• [0e73d6b]: add snapshotter test (rory-improbable) #149
• [d77a4e6]: correct indices for adding to array (rory-improbable) #149
• [307a636]: add truncation and separation of big array (rory-improbable) #149
• [2bc4780]: correct sorting of 3D array (rory-improbable) #149
• [b5b3182]: add extra person to test data (rory-improbable) #149
• [ab37763]: tests pass (rory-improbable) #149
• [cfa2bf5]: process place ids and place flows arrays separately (rory-improbable) #149
• [8a6c482]: correct length for activity location arrays (rory-improbable) #149
• [267ab28]: speed up people processing (rory-improbable) #149
• [ae11562]: speed up processing place data (rory-improbable) #149
• [8832b3b]: add test for getting place data (rory-improbable) #149
• [bbc5c5b]: change snapshot filenames (rory-improbable) #149
• [45956b7]: test writing snapshot files (rory-improbable) #149
• [4366668]: load activity_names enum (rory-improbable) #149
• [8b21165]: use sentinel value instead of zero (rory-improbable) #149
• [b472fd7]: get msoa coordinates for homes (rory-improbable) #149
• [e36bb4a]: add jitter to home coordinates (rory-improbable) #149
• [76f5512]: merge from master (rory-improbable) #149
• [fe2cbd3]: fix sentinel value (rory-improbable) #149
• [eaf3d78]: remove unused import (rory-improbable) #149
• [03ed3ba]: fix sentinel value in tests (rory-improbable) #149
• [3151cdd]: initial pipeline for loading buildings and msoa shapes (rory-improbable) #149
• [1a1fcef]: correct coordinate projection code (rory-improbable) #149
• [ed92574]: add todo (rory-improbable) #149
• [59230b5]: fix point within geometry check (rory-improbable) #149
• [eab1f37]: write points to JSON file (rory-improbable) #149
• [3524e4f]: select home locations from buildings (rory-improbable) #149
• [d9ce027]: remove commented line (rory-improbable) #149
• [1bfd438]: use osm shapefile and geopandas (rory-improbable) #149
• [42b24b4]: remove commented code (rory-improbable) #149
• [777adb7]: add correct total (rory-improbable) #149
• [94ba119]: add explanatory comment (rory-improbable) #149
• [14a891d]: store area codes and not home probs (rory-improbable) #149
• [88a9d3a]: add area codes and pnothome to test snapsho...

v0.4.0

Commits

• [ac428b8]: updated gitignore to remove build and dist folders (Alex Coleman) #136
• [a26dc6f]: fix #130 (Alex Coleman) #138
• [9208337]: adding commuting flows for #139 (Nick Malleson) #141
• [b52ee6c]: added new commuting flows for work venues (for #139). I think it works now I need to write tests (Nick Malleson) #141
• [74190cd]: Update covid_run.R (Fiona Spooner) #140
• [6459659]: Merge branch 'master' into nm-commuting (Nick Malleson) #141
• [13ffd22]: fixed assigmnent of work flows - previously were pointing to the MSOA but needed to point to the actual (virtual) work location. (For #139) (Nick Malleson) #141
• [d9d463a]: added a threshold to limit number of possible work flows (For #139) (Nick Malleson) #141
• [ba91547]: added tests for new work flows (For #139) (Nick Malleson) #141
• halved number of cpus for work flows, made no different to time taken (due to hyperthreading?) #141 (Nick Malleson)
• [76155c1]: added new dummy file for commuting #139 (Nick Malleson) #141
• [fb4cdbb]: turned local outbreak off (Nick Malleson)
• [f058f2b]: create branch on issue assignment action (Alex Coleman) #146
• [ceacb64]: cache workplaces #142 (Nick Malleson) #145
• [c41f8a2]: added issue-branch.yml file in .github (Alex Coleman) #146
• [5c876d3]: turned off danger reduction at work now that we don't have big virtual workplaces (Nick Malleson)
• [884ffce]: bump version number (Alex Coleman) #151

v0.3.0

Commits

• [1620c6e]: added tagged-release github action for automated release creation (Alex Coleman) #137