From 4ec438ff4de54af5f2dae1f459fd3fcc6883e65f Mon Sep 17 00:00:00 2001 From: LucieContamin Date: Fri, 31 May 2024 14:20:14 -0400 Subject: [PATCH] update deadline information --- README.md | 5 +- hub-config/tasks.json | 2 +- model-output/README.md | 4 +- ...uet => 2024-06-18-team2-modelb.gz.parquet} | Bin ...uet => 2024-06-18-team5-modele.gz.parquet} | Bin rounds/round1_phase1.md | 52 +++++++++++------- 6 files changed, 38 insertions(+), 25 deletions(-) rename model-output/team2-modelb/{2024-05-15-team2-modelb.gz.parquet => 2024-06-18-team2-modelb.gz.parquet} (100%) rename model-output/team5-modele/{2024-05-15-team5-modele.gz.parquet => 2024-06-18-team5-modele.gz.parquet} (100%) diff --git a/README.md b/README.md index 55a3d97..5c9dcd8 100644 --- a/README.md +++ b/README.md @@ -237,7 +237,7 @@ documentation associated with the In this round, the required target for trajectories will be **weekly incident infections, cases, and deaths in California and North Carolina for a set of specified racial/ethnic groups.** Trajectories will need to be paired across -racial/ethnic groups ann horizaom (i.e., for a given model, location, scenario +racial/ethnic groups and horizon (i.e., for a given model, location, scenario and horizon, all race/ethnicity data for simulation 1 corresponds to the sum of race/ethnicity-specific estimates for simulation 1). @@ -290,7 +290,8 @@ The folder contains multiple sub-folders: - Start date for scenarios: Sunday November 15, 2020 (first date of simulated transmission/outcomes) - Simulation end date: April 3, 2021 (20-week horizon) -- **Phase 1 projections due: Mid-May 2024 (soft deadline)** +- Mid-May 2024 (soft deadline) +- **Phase 1 projections due: 2024-06-18** ##### Submission requirements diff --git a/hub-config/tasks.json b/hub-config/tasks.json index cafeda5..ffc78c8 100644 --- a/hub-config/tasks.json +++ b/hub-config/tasks.json @@ -2,7 +2,7 @@ "schema_version": "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/tasks-schema.json", "rounds": [ { - "round_id": "2024-05-15", + "round_id": "2024-06-18", "round_id_from_variable": false, "model_tasks": [ { diff --git a/model-output/README.md b/model-output/README.md index c2fe7bf..f8774a9 100644 --- a/model-output/README.md +++ b/model-output/README.md @@ -93,8 +93,8 @@ arrow::read_parquet(filename) ``` For the disparities round, the date YYYY-MM-DD should correspond to the -**due date**, for example: "`2024-05-15`" from -"Phase 1 projections due: mid-May" as noted in the scenario +**due date**, for example: "`2024-06-18`" from +"Phase 1 projections due: 2024-06-18" as noted in the scenario description on the main [README, Submission Information](https://github.com/midas-network/rsv-scenario-modeling-hub)). diff --git a/model-output/team2-modelb/2024-05-15-team2-modelb.gz.parquet b/model-output/team2-modelb/2024-06-18-team2-modelb.gz.parquet similarity index 100% rename from model-output/team2-modelb/2024-05-15-team2-modelb.gz.parquet rename to model-output/team2-modelb/2024-06-18-team2-modelb.gz.parquet diff --git a/model-output/team5-modele/2024-05-15-team5-modele.gz.parquet b/model-output/team5-modele/2024-06-18-team5-modele.gz.parquet similarity index 100% rename from model-output/team5-modele/2024-05-15-team5-modele.gz.parquet rename to model-output/team5-modele/2024-06-18-team5-modele.gz.parquet diff --git a/rounds/round1_phase1.md b/rounds/round1_phase1.md index 50d7902..46445bc 100644 --- a/rounds/round1_phase1.md +++ b/rounds/round1_phase1.md @@ -19,10 +19,10 @@ consultation with academic modeling teams and government agencies (e.g., CDC). ### Disparities Round Phase 1: Can we accurately predict COVID-19 death disparities by race/ethnicity? In Phase 1, teams will calibrate to case and death data by race/ethnicity from -5/1/2020 – 11/14/2020 and project forward 11/15/2020 – 4/3/2021 in a single +5/1/2020 – 11/14/2020 and project forward to 11/15/2020 – 4/3/2021 in a single Scenario A. Teams are required to incorporate health inequities that contribute to differential transmission risk and severity by race/ethnicity, where -severity is defined at the probability of death given infection. Teams will be +severity is defined as the probability of death given infection. Teams will be evaluated on their ability to model race/ethnicity-specific death time series throughout the projection period in Phase 1. We will assume that we have prescribed the perfect scenario conditions; thus full information about new @@ -163,23 +163,24 @@ documentation associated with the In this round, the required target for trajectories will be **weekly incident infections, cases, and deaths in California and North Carolina for a set of specified racial/ethnic groups.** Trajectories will need to be paired across -racial/ethnic groups (i.e., for a given model, location, scenario and horizon, -all race/ethnicity data for simulation 1 corresponds to the sum of +racial/ethnic groups and horizon (i.e., for a given model, location, scenario +and horizon, all race/ethnicity data for simulation 1 corresponds to the sum of race/ethnicity-specific estimates for simulation 1). In California, required racial/ethnic groups are `"latino"`, `"black"`, -`"white"`, `"asian"`, and `"other"`, where `"other"` represents American Indian -Alaska Native and Native Hawaiian and Pacific Islander. +`"white"`, `"asian"`, `"other"`, and `"overall"`. In North Carolina, required racial/ethnic groups are `"white"`, `"black"`, `"asian"`, -and `"other"`, where `"other"` represents non-White Hispanic and American Indian -Alaska Native. +`"other"`, and `"overall"`. -Given the missingness in demographic disease data and limited data available on -case reporting rates by race/ethnicity, infections and cases will not be evaluated. +The definitions of race/ethnicity can differ across various datasets. + +Given the missingness in demographic disease data and limited data available on case +reporting rates by race/ethnicity, it will be optional for teams to submit cases. +Infections and deaths will be required and only weekly death targets will be evaluated. + +For more information please consult the [target data README](./target-data/README.md). -Teams will be submitting cases and infections for the purpose of model comparison and -weekly death targets will be evaluated. ### Additional Information @@ -198,7 +199,7 @@ The folder contains multiple sub-folders: - Population Data: state-level population structure data by age and race/ethnicity - Hospitalization: hospitalization time series by race/ethnicity, in a rate per 100,000 people for California and number of hospitalizations for North Carolina -- Contact Matrix: synthetic daily contact matrices by race/ethnicity in the household, +- Contacts: synthetic daily contact matrices by race/ethnicity in the household, school, community, workplace setting in the pre-pandemic and pandemic period ### Submission Information @@ -211,7 +212,8 @@ The folder contains multiple sub-folders: - Start date for scenarios: Sunday November 15, 2020 (first date of simulated transmission/outcomes) - Simulation end date: April 3, 2021 (20-week horizon) -- **Phase 1 projections due: March 26, 2024** +- Mid-May 2024 (soft deadline) +- **Phase 1 projections due: 2024-06-18** ##### Submission requirements @@ -219,14 +221,24 @@ The folder contains multiple sub-folders: Saturday, April 3, 2021 (20 week projection period). Weeks follow epi-weeks (Sun-Sat) dated by the last day of the week. -- Weekly targets: Weekly incident infections, cases, and deaths by location +- Weekly targets: Weekly incident infections, deaths by location and major racial/ethnic group. We require the following racial/ethnic groups by state: - - California: `"latino"`, `"black"`, `"white"`, `"asian"`, and `"other"`. - - North Carolina: `"black"`, `"white"`, `"asian"`, and `"other"`. + - California: `"latino"`, `"black"`, `"white"`, `"asian"`, `"other"`, and `"overall"`. + - North Carolina: `"black"`, `"white"`, `"asian"`, `"other"`, and `"overall"`. -- 100-300 individual trajectories for each target. Trajectories should be sampled - in such a way that they will be most likely to produce the uncertainty of the - simulated process. +- Optional target: weekly incident cases by location and major + racial/ethnic group (as previously stated) + +- We required 100-300 individual trajectories for each target. Trajectories + should be sampled in such a way that they will be most likely to produce + the uncertainty of the simulated process. Projection quantiles are optional. + - For teams who wish to submit quantiles, the format is in accordance with + prior SMh rounds. We ask for the following quantiles: + 0.01, 0.025, 0.05, every 5% to 0.95, 0.975, and 0.99 - Metadata: We will require a brief meta-data from all teams. + +- Filename: the date YYYY-MM-DD should correspond to the **due date**. + For phase 1: the date will be "2024-05-15". For more information, + please consult the [model-output/README](./model-output/README.md) \ No newline at end of file