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Author SHA1 Message Date
Nicolas Mounet
c2f2ca1bf6 Merge branch 'feature/BLO_data' into 'feature/scientific_model_update' 
BLO particle concentration emission value update

See merge request cara/cara!253
 2021-09-22 09:06:50 +02:00
Nicolas Mounet
cbb17e4950 Updating test_expiration_aerosols 2021-09-22 08:55:39 +02:00
Luis Aleixo
66ebf8a2bb Correct Cn values for B and L factors 2021-09-21 17:16:01 +02:00
Nicolas Mounet
c5a849f653 Merge branch 'feature/probability_infection' into 'feature/scientific_model_update' 
Changed probability of infection formula

See merge request cara/cara!262
 2021-09-21 12:05:02 +02:00
Luis Aleixo
364f20930e Changed P(I) formula and added host immunity for exposed Population 
Fixed values for viable_to_RNA_ratio and transmissibility_factor of each Virus variant

Updated probability of infection formula
 2021-09-21 11:49:22 +02:00
Luis Aleixo
e00d7982a8 Added a uniform distribution for the infectious dose 2021-09-21 11:46:04 +02:00
Andre Henriques
414b133856 Merge branch 'feature/infectious_dose_dist' into 'feature/scientific_model_update' 
Infectious dose with uniform distribution

See merge request cara/cara!261
 2021-09-20 16:23:12 +02:00
Luis Aleixo
35ea838933 Added a uniform distribution for the infectious dose 2021-09-20 16:15:46 +02:00
Nicolas Mounet
38a8870535 Merge branch 'feature/infectious_virus_fraction' into 'feature/scientific_model_update' 
Updated inhaled dose with Infectious virus fraction

See merge request cara/cara!260
 2021-09-20 14:26:03 +02:00
Luis Aleixo
e2327ee82d Deactivate pipeline 2021-09-20 14:20:51 +02:00
Luis Aleixo
0929bfc0b0 Changed the f_inf calculation to the InfectedPopulation class 2021-09-20 12:12:31 +02:00
Luis Aleixo
153896ec7e Updated host immunity declaration to model generator 2021-09-20 12:12:31 +02:00
Luis Aleixo
61be4a57f5 Updated infected probability with f_inf that considers the host immunity and the viable-to-RNA distribution 2021-09-17 14:46:45 +02:00
Andre Henriques
86ab306dd9 Merge branch 'feature/diameter_dependence' into 'feature/scientific_model_update' 
Monte-Carlo sampling of the aerosol diameters with BLO model

See merge request cara/cara!259
 2021-09-17 12:11:18 +02:00
Nicolas Mounet
396339f7bb Modifying condition to trigger the averaging of the exposure in cara/models.py 2021-09-17 09:34:00 +02:00
Nicolas Mounet
84fcddcd86 Preventing MultipleExpiration to be used with distributions 2021-09-17 09:34:00 +02:00
Nicolas Mounet
efe35da414 Taking the mean of the exposure only when diameter is an array (represents a distribution) 2021-09-16 18:15:25 +02:00
Nicolas Mounet
30eb90099b Introducing cn as parameter for the Expiration, and proper normalization of the exposure 2021-09-16 18:15:25 +02:00
Nicolas Mounet
acdd22cb07 Bugs fixed in monte_carlo/data.py; updating ExposureModel for diameter dependent exposure 2021-09-16 18:15:25 +02:00
Nicolas Mounet
28a9e5d5b3 Adding expiration diameter distributions from the BLO model 2021-09-16 18:15:25 +02:00
Nicolas Mounet
7d3a83c629 Removing completely the previous BLO implementation for Expiration; tests updated accordingly 2021-09-16 18:09:35 +02:00
Nicolas Mounet
ab90b04349 Introducing diameter as a vectorised parameter of Expiration. Providing equivalent diameters for each expiration type (gives the same emission rate as before) 2021-09-16 17:48:49 +02:00
Nicolas Mounet
936c72f76c Adding optional total concentration parameter in Expiration 2021-09-16 17:22:32 +02:00
Nicolas Mounet
ca6e70f2f9 Removing completely the previous BLO implementation for Expiration; tests updated accordingly 2021-09-16 16:33:31 +02:00
Nicolas Mounet
85f0f1708e Removing infectious dose in emission rate when using known_individual_emission_rate 2021-09-16 16:33:31 +02:00
Nicolas Mounet
d1ec990255 Remove suprespreading event from the expiration types; replace by an optional parameter to fix directly the emission rate; updates the corresponding tests 2021-09-16 16:33:31 +02:00
Nicolas Mounet
46465c499d Vectorising the Mask exhale_efficiency method 2021-09-16 16:33:30 +02:00
Nicolas Mounet
83e2185763 Introducing diameter as a vectorised parameter of Expiration. Providing equivalent diameters for each expiration type (gives the same emission rate as before) 2021-09-16 14:41:06 +02:00
Andre Henriques
686c709cc9 Merge branch 'feature/remove_superspreading' into 'master' 
Remove suprespreading event from the expiration types

See merge request cara/cara!256
 2021-09-16 13:55:05 +02:00
Nicolas Mounet
af3ded7935 Remove suprespreading event from the expiration types 2021-09-16 13:55:04 +02:00
Andre Henriques
092d566dbe Merge branch 'feature/delta_default' into 'master' 
Changes default strain in calculator to Delta.

See merge request cara/cara!257
 2021-09-14 23:51:49 +02:00
jdevine
5d4dc4b91d reverted model_generator default virus type 2021-09-14 16:22:49 +02:00
Andre Henriques
705485b1d5 Merge branch 'feature/concentration_normalization' into 'master' 
Normalization of the computation of the concentration

See merge request cara/cara!255
 2021-09-14 16:11:45 +02:00
Nicolas Mounet
92f9bce7e5 Normalization of the computation of the concentration 2021-09-14 16:11:44 +02:00
jdevine
8fbe7856b9 Addressed comments from Andre. 2021-09-14 14:57:48 +02:00
jdevine
fdca7da53a Changed default strain in calculator to Delta. 
Also applies retroactively to QR codes missing delta.
The rational for the retrospective change is that old simulations (wild type)
re-run need to be re-run with the current dominant strain.
 2021-09-13 13:50:12 +02:00
Philip Elson
743d4ab706 Merge branch 'feature/no_computing_before_first_time' into 'master' 
Model optimisation: avoid computing before first presence time

See merge request cara/cara!254
 2021-09-13 12:00:07 +02:00
Nicolas Mounet
9ed65a2b04 Model optimisation: avoid computing before first presence time 2021-09-13 12:00:06 +02:00
Philip Elson
97ac2ab743 Merge branch 'feature/alternative_scenario_d3' into 'master' 
Alternative scenarios plot with D3

See merge request cara/cara!246
 2021-09-07 06:43:23 +02:00
Luis Aleixo
250b7c0582 Plot alternative scenarios in report using D3.js, speeding up the response time and improving user interactivity 2021-09-07 06:43:22 +02:00
Philip Elson
0414e15e4b Merge branch 'feature/masks_efficiency' into 'master' 
Inward efficiency of masks

See merge request cara/cara!250
 2021-09-02 17:15:06 +02:00
Luis Aleixo
ab153ca781 added inward mask efficiency references 2021-09-02 15:23:49 +02:00
Luis Aleixo
bdc51d81b8 Changed relevant references for mask distributions 2021-09-02 12:11:22 +02:00
Andre Henriques
72681b9895 Merge branch 'feature/climate_function' into 'master' 
Allow location selection as part of the calculator, with temp profile from local weather station

See merge request cara/cara!211
 2021-09-02 11:58:33 +02:00
James Devine
db02132853 Allow location selection as part of the calculator, with temp profile from local weather station 2021-09-02 11:58:32 +02:00
Luis Aleixo
cbb3846eb7 Added uniform distribution for masks 2021-09-01 14:59:13 +02:00
Andre Henriques
3f38897099 Merge branch 'feature/update-nginx' into 'master' 
Update the nginx version to 1.18

See merge request cara/cara!248
 2021-08-31 09:19:58 +02:00
Andre Henriques
fcdab9506c Merge branch 'feature/report_reformulation' into 'master' 
Feature/report reformulation

See merge request cara/cara!234
 2021-08-30 18:48:58 +02:00
gaazzopa
cfb43aa259 Update calculator minor version 2021-08-30 17:52:23 +02:00
Luis Aleixo
e556f4d4bd revert d3 resizable plot changes 2021-08-27 17:29:49 +02:00