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Peter Jentsch
CovidAlertABM
Commits
133000c9
Commit
133000c9
authored
May 27, 2021
by
Peter Jentsch
Browse files
fixed silly distribution adjust bug
parent
0bfd9b1d
Changes
5
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5 changed files
with
23 additions
and
18 deletions
+23
-18
CovidAlertVaccinationModel/Manifest.toml
CovidAlertVaccinationModel/Manifest.toml
+4
-4
CovidAlertVaccinationModel/abm_fit_parameters.jl
CovidAlertVaccinationModel/abm_fit_parameters.jl
+1
-3
CovidAlertVaccinationModel/prem_mixing_approx.jl
CovidAlertVaccinationModel/prem_mixing_approx.jl
+6
-5
CovidAlertVaccinationModel/src/ABM/mixing_distributions.jl
CovidAlertVaccinationModel/src/ABM/mixing_distributions.jl
+2
-0
CovidAlertVaccinationModel/src/ABM/model_setup.jl
CovidAlertVaccinationModel/src/ABM/model_setup.jl
+10
-6
No files found.
CovidAlertVaccinationModel/Manifest.toml
View file @
133000c9
...
...
@@ -8,9 +8,9 @@ version = "1.0.1"
[[AbstractMCMC]]
deps
=
[
"BangBang"
,
"ConsoleProgressMonitor"
,
"Distributed"
,
"Logging"
,
"LoggingExtras"
,
"ProgressLogging"
,
"Random"
,
"StatsBase"
,
"TerminalLoggers"
,
"Transducers"
]
git-tree-sha1
=
"
21279159f6be4b2fd00e1a4a1f736893100408fc
"
git-tree-sha1
=
"
06e46b94299b6d0d9fb4f7833c7b1df3df6f9678
"
uuid
=
"80f14c24-f653-4e6a-9b94-39d6b0f70001"
version
=
"3.
2
.0"
version
=
"3.
0
.0"
[[AbstractTrees]]
git-tree-sha1
=
"03e0550477d86222521d254b741d470ba17ea0b5"
...
...
@@ -520,8 +520,8 @@ uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
version
=
"0.6.3"
[[KissABC]]
deps
=
[
"AbstractMCMC"
,
"Distributed"
,
"Distributions"
,
"MonteCarloMeasurements"
,
"Random"
]
path
=
"/home/peterj/Projects/PRs/KissABC.jl/
"
deps
=
[
"AbstractMCMC"
,
"Distributions"
,
"MonteCarloMeasurements"
,
"Random"
]
git-tree-sha1
=
"693d4bd4cbb9ad6515414e0935bbd646b15fc16a
"
uuid
=
"9c9dad79-530a-4643-a18b-2704674d4108"
version
=
"3.0.1"
...
...
CovidAlertVaccinationModel/abm_fit_parameters.jl
View file @
133000c9
using
Distributed
addprocs
(
15
)
@everywhere
using
CovidAlertVaccinationModel
using
CovidAlertVaccinationModel
CovidAlertVaccinationModel
.
fit_parameters
(
CovidAlertVaccinationModel
.
get_parameters
())
\ No newline at end of file
CovidAlertVaccinationModel/prem_mixing_approx.jl
View file @
133000c9
using
CovidAlertVaccinationModel
:
ModelSolution
,
get_parameters
,
neighbors
,
GraphEdge
,
get_weight
using
CovidAlertVaccinationModel
:
abm
,
ModelSolution
,
get_parameters
,
neighbors
,
GraphEdge
,
get_weight
function
approximate_mixing_matricies
()
sol
=
abm
(
get_parameters
(),
nothing
)
p
=
get_parameters
()
sol
=
abm
(
p
,
nothing
)
mean_mixing
=
zeros
(
3
,
3
)
display
(
mean_mixing
)
display
(
sol
.
inf_network
)
display
(
p
.
O_distribution_shift
)
for
(
node_i
,
demo_i
)
in
enumerate
(
sol
.
demographics
)
for
g_list
in
sol
.
inf_network
.
graph_list
for
g
in
g_list
...
...
@@ -19,6 +19,7 @@ function approximate_mixing_matricies()
display
(
mean_mixing
)
return
sol
end
approximate_mixing_matricies
()
approximate_mixing_matricies
();
println
(
"dasdlkjasdas"
)
#rerun with weights
#
\ No newline at end of file
CovidAlertVaccinationModel/src/ABM/mixing_distributions.jl
View file @
133000c9
...
...
@@ -8,7 +8,9 @@ function adjust_distributions_mean!(distribution_matrix,mean_shift_percentage)
for
i
in
eachindex
(
distribution_matrix
)
dist
=
distribution_matrix
[
i
]
new_mean
=
mean
(
dist
)
+
mean_shift_percentage
distribution_matrix
[
i
]
=
from_mean
(
typeof
(
dist
),
new_mean
)
end
end
...
...
CovidAlertVaccinationModel/src/ABM/model_setup.jl
View file @
133000c9
...
...
@@ -83,19 +83,23 @@ mutable struct ModelSolution{T,InfNet,SocNet,WSMixingDist,RestMixingDist}
demographics
,
base_network
,
index_vectors
=
generate_population
(
num_households
)
nodes
=
length
(
demographics
)
pop_sizes
=
length
.
(
index_vectors
)
ws_mixing_tuple_preshift
=
deepcopy
(
workschool_mixing
)
rest_mixing_tuple_preshift
=
deepcopy
(
rest_mixing
)
map
(
workschool_mixing
)
do
md
for
md
in
ws_mixing_tuple_preshift
adjust_distributions_mean!
(
md
[
1
:
3
,
3
],
params
.
O_distribution_shift
)
adjust_distributions_mean!
(
md
[
3
,
1
:
3
],
params
.
O_distribution_shift
)
adjust_distributions_mean!
(
md
[
3
,
1
:
2
],
params
.
O_distribution_shift
)
#dont shift OO twice
end
map
(
rest_mixing
)
do
md
for
md
in
rest_mixing
_tuple_preshift
adjust_distributions_mean!
(
md
[
1
:
3
,
3
],
params
.
O_distribution_shift
)
adjust_distributions_mean!
(
md
[
3
,
1
:
3
],
params
.
O_distribution_shift
)
adjust_distributions_mean!
(
md
[
3
,
1
:
2
],
params
.
O_distribution_shift
)
#dont shift OO twice
end
map_symmetrize
(
m_tuple
)
=
map
(
md
->
symmetrize_means
(
pop_sizes
,
md
),
m_tuple
)
ws_matrix_tuple
=
map_symmetrize
(
workschool_mixing
)
rest_matrix_tuple
=
map_symmetrize
(
rest_mixing
)
ws_matrix_tuple
=
map_symmetrize
(
ws_mixing_tuple_preshift
)
rest_matrix_tuple
=
map_symmetrize
(
rest_mixing_tuple_preshift
)
is_app_user
=
app_users
(
demographics
,
params
.
app_user_fraction
)
app_user_list
=
zeros
(
nodes
)
app_user_index
=
findall
(
==
(
true
),
is_app_user
)
...
...
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