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First submission #9

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merged 9 commits into from
Feb 29, 2024
Merged

First submission #9

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86cb401
Add CEPH metadata file
paulocv Feb 26, 2024
f8507a9
CEPH_2024-02-25
paulocv Feb 26, 2024
2062089
Move and rename forecast file
paulocv Feb 26, 2024
76ec30a
Fix typo on metadata
paulocv Feb 26, 2024
9fb0abe
Update metadata for missing fields
paulocv Feb 27, 2024
279ce87
Add horizon = 4
paulocv Feb 27, 2024
2ab8420
Remove file with wrong name
paulocv Feb 27, 2024
215f04f
Add horizon = 4 (fix filename)
paulocv Feb 27, 2024
7e34d11
Fix validation
kjsato Feb 29, 2024
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232 changes: 5 additions & 227 deletions hub-config/tasks.json
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@
},
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},
"location": {
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Expand Down Expand Up @@ -142,7 +142,7 @@
}
]
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{
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Expand All @@ -162,7 +162,7 @@
},
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"optional": [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]
"optional": [0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]
},
"location": {
"required": null,
Expand Down Expand Up @@ -264,231 +264,9 @@
"time_unit": "week"
}
]
},
{
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],
"submissions_due": {
"relative_to": "origin_date",
Expand Down
40 changes: 40 additions & 0 deletions model-metadata/CEPH-Rtrend_rsv.yaml
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@@ -0,0 +1,40 @@
schema_version: "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/admin-schema.json"
team_name: "CEPH Lab at Indiana University"
team_abbr: "CEPH"
model_name: "Rtrend RSV"
model_abbr: "Rtrend_rsv"
model_version: 2024-01-08
model_contributors: [
{
"name": "Marco Ajelli",
"affiliation": "Indiana University Bloomington",
"email": "[email protected]",
},
{
"name": "Paulo C. Ventura",
"affiliation": "Indiana University Bloomington",
"email": "[email protected]",
},
{
"name": "Maria Litvinova",
"affiliation": "Indiana University Bloomington",
"email": "[email protected]",
},
{
"name": "Allisandra G. Kummer",
"affiliation": "Indiana University Bloomington",
"email": "[email protected]",
},
{
"name": "Shreeya Mhade",
"affiliation": "Indiana University Bloomington",
"email": "[email protected]",
},
]
license: "CC-BY-4.0"
data_inputs: "Weekly incident RSV hospitalizations from RSV-NET"
methods: "A renewal equation method based on Bayesian estimation of Rt from past hospitalization data."
methods_long: "Model forecasts are obtained by using a renewal equation based on the estimated net reproduction number Rt. We use a spline interpolation to obtain daily data from weekly incidence, then apply a lowpass filter to extract the main trend. We then use MCMC Metropolis-Hastings sampling to estimate the posterior distribution of Rt based on the filtered data, considering an informed prior on Rt based on RSV literature. The estimated Rt in the last weeks of available data is used to forecast Rt in the upcoming weeks, with a drift term proportional to the current incidence. Finally, we use the renewal equation with the posterior distribution and trend of the estimated Rt to forecast RSV hospitalization trajectories."
ensemble_of_models: false
ensemble_of_hub_models: false
website_url: https://publichealth.indiana.edu/research/faculty-directory/profile.html?user=majelli
Binary file added model-output/CEPH-Rtrend_rsv/2024-02-25-CEPH-Rtrend_rsv.parquet
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