diff --git a/hub-config/tasks.json b/hub-config/tasks.json index 7f84bf78..054a7d72 100644 --- a/hub-config/tasks.json +++ b/hub-config/tasks.json @@ -25,7 +25,7 @@ }, "horizon": { "required": [1, 2, 3, 4], - "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, @@ -142,7 +142,7 @@ } ] }, - { + { "task_ids": { "origin_date": { "required": null, @@ -162,7 +162,7 @@ }, "horizon": { "required": [1, 2, 3, 4], - "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, @@ -264,231 +264,9 @@ "time_unit": "week" } ] - }, - { - "task_ids": { - "origin_date": { - "required": null, - "optional": [ - "2023-11-12", "2023-11-19", "2023-11-26", "2023-12-03", - "2023-12-10", "2023-12-17", "2023-12-24", "2023-12-31", - "2024-01-07", "2024-01-14", "2024-01-21", "2024-01-28", - "2024-02-05", "2024-02-11", "2024-02-18", "2024-02-25", - "2024-03-03", "2024-03-10", "2024-03-17", "2024-03-24", - "2024-03-31", "2024-04-07", "2024-04-14", "2024-04-21", - "2024-04-28", "2024-05-05", "2024-05-12" - ] - }, - "target": { - "required": null, - "optional": ["peak size hosp"] - }, - "horizon": { - "required": null, - "optional": null - }, - "location": { - "required": null, - "optional": [ - "US", - "01", - "02", - "04", - "05", - "06", - "08", - "09", - "10", - "11", - "12", - "13", - "15", - "16", - "17", - "18", - "19", - "20", - "21", - "22", - "23", - "24", - "25", - "26", - "27", - "28", - "29", - "30", - "31", - "32", - "33", - "34", - "35", - "36", - "37", - "38", - "39", - "40", - "41", - "42", - "44", - "45", - "46", - "47", - "48", - "49", - "50", - "51", - "53", - "54", - "55", - "56", - "72", - "78" - ] - }, - "age_group":{ - "required":["0-130"], - "optional":["0-0.99","1-4","5-17","5-64","18-49","50-64","65-130"] - } - }, - "output_type": { - "quantile":{ - "output_type_id":{ - "required":[0.01,0.025,0.05,0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5,0.55,0.6,0.65,0.7,0.75,0.8,0.85,0.9,0.95,0.975,0.99], - "optional":[0,1] - }, - "value":{ - "type":"double", - "minimum":0 - } - } - }, - "target_metadata": [ - { - "target_id": "peak size hosp", - "target_name": "Peak size of hospitalization", - "target_units": "count", - "target_keys": { - "target": ["peak size hosp"] - }, - "target_type": "discrete", - "is_step_ahead": false - } - ] - }, - { - "task_ids": { - "origin_date": { - "required": null, - "optional": [ - "2023-11-12", "2023-11-19", "2023-11-26", "2023-12-03", - "2023-12-10", "2023-12-17", "2023-12-24", "2023-12-31", - "2024-01-07", "2024-01-14", "2024-01-21", "2024-01-28", - "2024-02-05", "2024-02-11", "2024-02-18", "2024-02-25", - "2024-03-03", "2024-03-10", "2024-03-17", "2024-03-24", - "2024-03-31", "2024-04-07", "2024-04-14", "2024-04-21", - "2024-04-28", "2024-05-05", "2024-05-12" - ] - }, - "target": { - "required": null, - "optional": ["peak time hosp"] - }, - "horizon": { - "required": null, - "optional": null - }, - "location": { - "required": null, - "optional": [ - "US", - "01", - "02", - "04", - "05", - "06", - "08", - "09", - "10", - "11", - "12", - "13", - "15", - "16", - "17", - "18", - "19", - "20", - "21", - "22", - "23", - "24", - "25", - "26", - "27", - "28", - "29", - "30", - "31", - "32", - "33", - "34", - "35", - "36", - "37", - "38", - "39", - "40", - "41", - "42", - "44", - "45", - "46", - "47", - "48", - "49", - "50", - "51", - "53", - "54", - "55", - "56", - "72", - "78" - ] - }, - "age_group":{ - "required":["0-130"], - "optional":["0-0.99","1-4","5-17","5-64","18-49","50-64","65-130"] - } - }, - "output_type": { - "cdf":{ - "output_type_id":{ - "required":null, - "optional":null - }, - "value":{ - "type":"double", - "minimum":0, - "maximum":1 - } - } - }, - "target_metadata": [ - { - "target_id": "peak time hosp", - "target_name": "Peak timing of hospitalization", - "target_units": "population", - "target_keys": { - "target": ["peak time hosp"] - }, - "target_type": "discrete", - "is_step_ahead": false, - "time_unit": "week" - } - ] } + + ], "submissions_due": { "relative_to": "origin_date", diff --git a/model-metadata/CEPH-Rtrend_rsv.yaml b/model-metadata/CEPH-Rtrend_rsv.yaml new file mode 100644 index 00000000..447996d1 --- /dev/null +++ b/model-metadata/CEPH-Rtrend_rsv.yaml @@ -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": "majelli@iu.edu", + }, + { + "name": "Paulo C. Ventura", + "affiliation": "Indiana University Bloomington", + "email": "pventura@iu.edu", + }, + { + "name": "Maria Litvinova", + "affiliation": "Indiana University Bloomington", + "email": "malitv@iu.edu", + }, + { + "name": "Allisandra G. Kummer", + "affiliation": "Indiana University Bloomington", + "email": "alkummer@iu.edu", + }, + { + "name": "Shreeya Mhade", + "affiliation": "Indiana University Bloomington", + "email": "smhade@iu.edu", + }, +] +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 diff --git a/model-output/CEPH-Rtrend_rsv/2024-02-25-CEPH-Rtrend_rsv.parquet b/model-output/CEPH-Rtrend_rsv/2024-02-25-CEPH-Rtrend_rsv.parquet new file mode 100644 index 00000000..e0e5b955 Binary files /dev/null and b/model-output/CEPH-Rtrend_rsv/2024-02-25-CEPH-Rtrend_rsv.parquet differ