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Rate multipliers and IgG count #260

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merged 77 commits into from
Feb 26, 2024
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9cb728a
Added RateMultiplier class in the utility package
mghosh00 Feb 2, 2024
6fbf65e
Update test_rate_multiplier.py
mghosh00 Feb 2, 2024
cda5193
Changed documentation
mghosh00 Feb 2, 2024
f78ca43
create_waning_transition_matrix
abbie-evans Feb 3, 2024
5d00840
Made changes to host_progression_sweep.py with waning rate multipliers
mghosh00 Feb 4, 2024
cd63bbe
Flake8
abbie-evans Feb 4, 2024
b0da924
Functional tests for waning immunity
abbie-evans Feb 7, 2024
8336314
Passing functional tests
mghosh00 Feb 7, 2024
9d85810
Flake8
abbie-evans Feb 7, 2024
d974a15
Updated entry
abbie-evans Feb 7, 2024
015bb53
Updated igg_foi_multiplier.py
mghosh00 Feb 13, 2024
1cefd2f
Merge remote-tracking branch 'origin/waning-immunity' into waning-imm…
mghosh00 Feb 13, 2024
3389303
Susceptibility of person with waning immunity change
abbie-evans Feb 13, 2024
504af4c
Update person_susc
abbie-evans Feb 13, 2024
479b960
Update default param values
abbie-evans Feb 13, 2024
5520c5e
Added validation graph for igg levels
tomcodewizard Feb 14, 2024
1f2e80b
Added graph png
tomcodewizard Feb 14, 2024
954b2b6
Added reference image
tomcodewizard Feb 14, 2024
261c89e
flake8
tomcodewizard Feb 14, 2024
da633e4
Update person_susc
abbie-evans Feb 14, 2024
3d5c5cd
Update README.md
abbie-evans Feb 14, 2024
909d960
Updated .json with antibody params
abbie-evans Feb 14, 2024
b586162
Created test_igg_foi_multiplier.py
mghosh00 Feb 14, 2024
913482a
Merge remote-tracking branch 'origin/waning-immunity' into waning-imm…
mghosh00 Feb 14, 2024
724a2b5
update labels
tomcodewizard Feb 14, 2024
3a55950
Ensure infection start time is not None
abbie-evans Feb 14, 2024
fa9b93d
Update to include waning multipliers
abbie-evans Feb 14, 2024
3f064d3
Removed unnecessary checks
mghosh00 Feb 14, 2024
4924fd0
Merge remote-tracking branch 'origin/waning-immunity' into waning-imm…
mghosh00 Feb 14, 2024
d373969
Added new test to test_host_progression_sweep.py
mghosh00 Feb 14, 2024
456a58a
Flake8 fixes
mghosh00 Feb 14, 2024
3dfa998
Flake8 and typing fixes
mghosh00 Feb 14, 2024
500e14d
Merge branch 'main' into waning-immunity
mghosh00 Feb 14, 2024
46c41bb
Merge branch 'main' into waning-immunity
abbie-evans Feb 14, 2024
2381fad
flake8
tomcodewizard Feb 14, 2024
2252eaa
Merge branch 'waning-immunity' of github.com:SABS-R3-Epidemiology/epi…
tomcodewizard Feb 14, 2024
88aa797
Delete python_examples/gibraltar_example/simulation_outputs/demograph…
mghosh00 Feb 14, 2024
b83c8ec
Delete python_examples/gibraltar_example/simulation_outputs/gibraltar…
mghosh00 Feb 14, 2024
baa5921
Delete python_examples/gibraltar_example/simulation_outputs/inf_statu…
mghosh00 Feb 14, 2024
80a33af
Delete python_examples/gibraltar_example/simulation_outputs/inf_statu…
mghosh00 Feb 14, 2024
59a2f0d
Delete python_examples/gibraltar_example/simulation_outputs/infectiou…
mghosh00 Feb 14, 2024
ba21c02
Delete python_examples/gibraltar_example/simulation_outputs/output_gi…
mghosh00 Feb 14, 2024
c8cb0ac
Update antibody_igG_test_graph.py
tomcodewizard Feb 14, 2024
5ee5a3b
Update README.rst
abbie-evans Feb 14, 2024
a262856
Gibraltar simulation outputs
abbie-evans Feb 14, 2024
cfa5bb1
Update README.md
abbie-evans Feb 14, 2024
a922515
Update class docstring
abbie-evans Feb 21, 2024
af8163d
Merge branch 'waning-immunity' of github.com:SABS-R3-Epidemiology/epi…
abbie-evans Feb 21, 2024
824f5d3
test_waning_status_count update
abbie-evans Feb 21, 2024
4e30e25
Added num_times_infected to person.py
mghosh00 Feb 21, 2024
9ee6db3
Merge remote-tracking branch 'origin/waning-immunity' into waning-imm…
mghosh00 Feb 21, 2024
1faa3f9
Modified Luxembourg example to incorporate waning immunity
tomcodewizard Feb 21, 2024
606f7b3
Merge branch 'waning-immunity' of github.com:SABS-R3-Epidemiology/epi…
tomcodewizard Feb 21, 2024
3f8251d
Reverting to without waning immunity
abbie-evans Feb 21, 2024
19b980e
Update README.md
abbie-evans Feb 21, 2024
6ced00b
flake8
tomcodewizard Feb 21, 2024
312999f
Merge branch 'waning-immunity' of github.com:SABS-R3-Epidemiology/epi…
tomcodewizard Feb 21, 2024
d8006cc
Update rate_multiplier.py
abbie-evans Feb 21, 2024
358a4ab
save images for differening seeds
tomcodewizard Feb 21, 2024
3ef61bc
flake8
tomcodewizard Feb 21, 2024
41e9e6f
Changed foi to include IgG counts. Also ensured that infection_start_…
mghosh00 Feb 21, 2024
7cb7367
Merge remote-tracking branch 'origin/waning-immunity' into waning-imm…
mghosh00 Feb 21, 2024
195865f
Flake8
mghosh00 Feb 21, 2024
5e1ae2b
added diagram image
tomcodewizard Feb 21, 2024
7fe54d4
Waning transition matrix only generated when waning immunity active
abbie-evans Feb 21, 2024
dbc8660
Update pyEpiabm/pyEpiabm/sweep/transition_matrices.py
mghosh00 Feb 21, 2024
c16b9b8
Changed error messages and changed arguments of update_next_infection…
mghosh00 Feb 21, 2024
8b4e8d5
Merge remote-tracking branch 'origin/waning-immunity' into waning-imm…
mghosh00 Feb 21, 2024
dc4d71b
Fixed compression error
abbie-evans Feb 25, 2024
a019f49
test_waning_status_count susceptible
abbie-evans Feb 26, 2024
3ad7b44
Added link to docstring
abbie-evans Feb 26, 2024
3790ac0
Flake8
abbie-evans Feb 26, 2024
7b4a8f4
Changed IgGFOIMultiplier to AntibodyMultiplier
mghosh00 Feb 26, 2024
68fb20a
Merge remote-tracking branch 'origin/waning-immunity' into waning-imm…
mghosh00 Feb 26, 2024
46af5e5
Removed commented code
mghosh00 Feb 26, 2024
195e835
Comment fix
mghosh00 Feb 26, 2024
19e0732
Parameter name change
abbie-evans Feb 26, 2024
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Removed unnecessary checks
mghosh00 committed Feb 14, 2024
commit 3f064d36bd79c6f467579d5c8a7a4ace1f9a48b8
Original file line number Diff line number Diff line change
@@ -58,17 +58,6 @@ def test__calculate_igg_titre(self):
titre = self.multiplier._calculate_igg_titre(time_since_max, age_group)
self.assertAlmostEqual(3.312, titre, places=3)

def test___call___erroneous(self):
multiplier = IgGFOIMultiplier(1.0, 2.0, 0.1, 0.2, 3)
with self.assertRaises(ValueError) as ve_1:
multiplier(-1.0, 5)
self.assertEqual("time_since_infection must be non-negative",
str(ve_1.exception))
with self.assertRaises(ValueError) as ve_2:
multiplier(1.0, 17)
self.assertEqual("age_group must be between 0 and 16",
str(ve_2.exception))

def test___call___before_max_igg(self):
p = self.multiplier(20.0, 6)
self.assertEqual(0, p)
6 changes: 0 additions & 6 deletions pyEpiabm/pyEpiabm/utility/igg_foi_multiplier.py
Original file line number Diff line number Diff line change
@@ -85,12 +85,6 @@ def __call__(self, time_since_infection: float, age_group: int) -> float:
float
An IgG multiplier for the force of infection
"""
# Parameter checks
if time_since_infection < 0:
raise ValueError("time_since_infection must be non-negative")
if not 0 <= age_group <= 16:
raise ValueError("age_group must be between 0 and 16")

# If time_since_infection < days_positive_pcr_to_max_igg, then the
# person cannot be reinfected yet, so set their multiplier to 0.
if time_since_infection < self.days_positive_pcr_to_max_igg: