update Readme + target-data

README.md

@@ -1 +1,61 @@
-# covid19-smh-research
+# COVID-19 Scenario Modeling Hub - Research
+
+
+This repository follows the guidelines and standards outlined by the hubverse, 
+which provides a set of data formats and open source tools for modeling hubs.
+
+The Consortium of Infectious Disease Modeling Hubs. The hubverse: open tools for 
+collaborative modeling. GitHub release v2.0.0, 14 Jul 2023. URL: https://github.com/Infectious-Disease-Modeling-Hubs
+
+## How to participate    
+
+The Scenario Modeling Hub is open to any team willing to provide projections
+at the right temporal and spatial scales, with minimal gatekeeping. We only 
+require that participating teams share point estimates and uncertainty bounds, 
+along with a short model description and answers to a list of key questions 
+about design. A major output of the projection hub is ensemble estimates of 
+epidemic outcomes (e.g., infection, hospitalizations, and deaths), for different
+time points, intervention scenarios, and US jurisdictions.
+
+Those interested to participate, please read the README file and email us at 
+[email protected] 
+
+
+## Target Data
+
+The repository contains a [target-data](./target-data/) folder relevant to the modeling efforts.
+It contains COVID-19 case and death time series by race/ethnicity. 
+
+For more information, please consult the associated [README file](./target-data/README.md)
+
+## Data license and reuse
+
+All source code that is specific to the overall project is available under an 
+open-source [MIT license](https://opensource.org/licenses/MIT). We note that 
+this license does NOT cover model code from the various teams, model scenario 
+data (available under specified licenses as described above) and auxiliary data.
+
+## Computational power
+
+Those teams interested in accessing additional computational power should 
+contact Katriona Shea at [email protected]. Additional resources might be available 
+from the ]MIDAS Coordination Center](https://midasnetwork.us/) - please 
+contact [email protected] for information.
+
+## The RSV Scenario Modeling Hub Coordination Team    
+
+ - Shaun Truelove, Johns Hopkins University
+ - Cécile Viboud, NIH Fogarty
+ - Justin Lessler, University of North Carolina
+ - Sara Loo, Johns Hopkins University
+ - Lucie Contamin, University of Pittsburgh
+ - Emily Howerton, Penn State University
+ - Claire Smith, Johns Hopkins University
+ - Harry Hochheiser, University of Pittsburgh
+ - Katriona Shea, Penn State University
+ - Michael Runge, USGS
+ - Erica Carcelen, John Hopkins University
+ - Sung-mok Jung, University of North Carolina
+ - Jessi Espino, University of Pittsburgh
+ - John Levander, University of Pittsburgh
+ - Katie Yan, Penn State University

target-data/README.md

@@ -0,0 +1,50 @@
+# Target Data
+
+This folder is used to store target data (also called "ground truth" or 
+"truth data") relevant to the modeling efforts.
+
+It contains the calibration data for phase 1 and 2 of the COVID-19
+Scenario Modeling Hub (SMH) Disparities Round. 
+
+For any questions or issues, please contact [email protected]. 
+
+### Demographic data
+
+Data is reported for incident cases and deaths. 
+
+Race/ethnicity grouping in North Carolina 
+includes `"black"`, `"white"`,  `"asian"`, and `"other"`. 
+Here `"other"`  represents the sum of other and Hispanic/Latino. 
+
+Race/ethnicity 
+grouping in California includes `"latino"`, `"black"`, `"white"`, 
+`"asian"`, and `"other"`. All non-Latino groups are non-Hispanic and 
+`"latino"` represents both Latino and Hispanic. 
+
+[`target_data_phase1.csv`](./target_data_phase1.csv): Calibration 
+data to be used for Phase 1. 
+This file contains incident cases and deaths for California and 
+North Carolina as reported to respective public health departments 
+up until 11/14/2020. 
+
+[target_data_phase2.csv](./target_data_phase2.csv): Calibration data 
+to be used for Phase 2. 
+This file contains incident cases and deaths for California and 
+North Carolina as reported to respective public health departments 
+up until 4/3/2021.
+
+Case demographic data is sourced from the 
+[COVID-19 Race-Ethnicity Timeseries](https://data.chhs.ca.gov/dataset/covid-19-equity-metrics/resource/ef29f30e-320c-46cf-86cd-37a36663616d) from 
+California Department of Public Health and 
+[NC COVID-19 Dashboard Data](https://covid19.ncdhhs.gov/dashboard/data-behind-dashboards)
+from the North Carolina Department of Public Health. 
+Death demographic data is sourced from 
+[The National Center for Health Statistics](https://wonder.cdc.gov/mcd-icd10-provisional.html) 
+
+### Overall population data
+
+[cases_overall_jhu.csv](./cases_overall_jhu.csv): Overall cases reported 
+to Johns Hopkins Center for Systems Science and Engineering (JHU-CSSE) 
+in California and North Carolina. This gives full cases reported, whereas 
+the public health department case data has some missingness by 
+race/ethnicity.

target-data/cases_overall_jhu.csv

@@ -0,0 +1,127 @@
+"location","date","value","race_ethnicity","target"
+"06","2020-01-25",0,"overall","inc case"
+"06","2020-02-01",3,"overall","inc case"
+"06","2020-02-08",3,"overall","inc case"
+"06","2020-02-15",2,"overall","inc case"
+"06","2020-02-22",0,"overall","inc case"
+"06","2020-02-29",3,"overall","inc case"
+"06","2020-03-07",81,"overall","inc case"
+"06","2020-03-14",241,"overall","inc case"
+"06","2020-03-21",1061,"overall","inc case"
+"06","2020-03-28",6118,"overall","inc case"
+"06","2020-04-04",5320,"overall","inc case"
+"06","2020-04-11",8627,"overall","inc case"
+"06","2020-04-18",9181,"overall","inc case"
+"06","2020-04-25",11790,"overall","inc case"
+"06","2020-05-02",11451,"overall","inc case"
+"06","2020-05-09",13378,"overall","inc case"
+"06","2020-05-16",12208,"overall","inc case"
+"06","2020-05-23",14077,"overall","inc case"
+"06","2020-05-30",17986,"overall","inc case"
+"06","2020-06-06",18378,"overall","inc case"
+"06","2020-06-13",20765,"overall","inc case"
+"06","2020-06-20",26769,"overall","inc case"
+"06","2020-06-27",39932,"overall","inc case"
+"06","2020-07-04",49494,"overall","inc case"
+"06","2020-07-11",61250,"overall","inc case"
+"06","2020-07-18",62557,"overall","inc case"
+"06","2020-07-25",66880,"overall","inc case"
+"06","2020-08-01",57986,"overall","inc case"
+"06","2020-08-08",46413,"overall","inc case"
+"06","2020-08-15",65502,"overall","inc case"
+"06","2020-08-22",41872,"overall","inc case"
+"06","2020-08-29",36280,"overall","inc case"
+"06","2020-09-05",32449,"overall","inc case"
+"06","2020-09-12",23025,"overall","inc case"
+"06","2020-09-19",24011,"overall","inc case"
+"06","2020-09-26",24654,"overall","inc case"
+"06","2020-10-03",23631,"overall","inc case"
+"06","2020-10-10",23439,"overall","inc case"
+"06","2020-10-17",21876,"overall","inc case"
+"06","2020-10-24",31733,"overall","inc case"
+"06","2020-10-31",29834,"overall","inc case"
+"06","2020-11-07",41873,"overall","inc case"
+"06","2020-11-14",57118,"overall","inc case"
+"06","2020-11-21",89098,"overall","inc case"
+"06","2020-11-28",101640,"overall","inc case"
+"06","2020-12-05",155691,"overall","inc case"
+"06","2020-12-12",225121,"overall","inc case"
+"06","2020-12-19",310548,"overall","inc case"
+"06","2020-12-26",277574,"overall","inc case"
+"06","2021-01-02",282372,"overall","inc case"
+"06","2021-01-09",295678,"overall","inc case"
+"06","2021-01-16",278911,"overall","inc case"
+"06","2021-01-23",172340,"overall","inc case"
+"06","2021-01-30",139182,"overall","inc case"
+"06","2021-02-06",98940,"overall","inc case"
+"06","2021-02-13",70839,"overall","inc case"
+"06","2021-02-20",46798,"overall","inc case"
+"06","2021-02-27",38740,"overall","inc case"
+"06","2021-03-06",31349,"overall","inc case"
+"06","2021-03-13",24392,"overall","inc case"
+"06","2021-03-20",20587,"overall","inc case"
+"06","2021-03-27",18753,"overall","inc case"
+"06","2021-04-03",18793,"overall","inc case"
+"37","2020-01-25",0,"overall","inc case"
+"37","2020-02-01",0,"overall","inc case"
+"37","2020-02-08",0,"overall","inc case"
+"37","2020-02-15",0,"overall","inc case"
+"37","2020-02-22",0,"overall","inc case"
+"37","2020-02-29",0,"overall","inc case"
+"37","2020-03-07",2,"overall","inc case"
+"37","2020-03-14",30,"overall","inc case"
+"37","2020-03-21",255,"overall","inc case"
+"37","2020-03-28",818,"overall","inc case"
+"37","2020-04-04",1530,"overall","inc case"
+"37","2020-04-11",1900,"overall","inc case"
+"37","2020-04-18",1989,"overall","inc case"
+"37","2020-04-25",2405,"overall","inc case"
+"37","2020-05-02",3000,"overall","inc case"
+"37","2020-05-09",3073,"overall","inc case"
+"37","2020-05-16",3752,"overall","inc case"
+"37","2020-05-23",4569,"overall","inc case"
+"37","2020-05-30",5413,"overall","inc case"
+"37","2020-06-06",6985,"overall","inc case"
+"37","2020-06-13",8574,"overall","inc case"
+"37","2020-06-20",8714,"overall","inc case"
+"37","2020-06-27",9727,"overall","inc case"
+"37","2020-07-04",11043,"overall","inc case"
+"37","2020-07-11",12713,"overall","inc case"
+"37","2020-07-18",14002,"overall","inc case"
+"37","2020-07-25",13633,"overall","inc case"
+"37","2020-08-01",12953,"overall","inc case"
+"37","2020-08-08",11147,"overall","inc case"
+"37","2020-08-15",9793,"overall","inc case"
+"37","2020-08-22",10869,"overall","inc case"
+"37","2020-08-29",11488,"overall","inc case"
+"37","2020-09-05",10318,"overall","inc case"
+"37","2020-09-12",8250,"overall","inc case"
+"37","2020-09-19",9321,"overall","inc case"
+"37","2020-09-26",9508,"overall","inc case"
+"37","2020-10-03",9112,"overall","inc case"
+"37","2020-10-10",12866,"overall","inc case"
+"37","2020-10-17",13973,"overall","inc case"
+"37","2020-10-24",14567,"overall","inc case"
+"37","2020-10-31",16343,"overall","inc case"
+"37","2020-11-07",16610,"overall","inc case"
+"37","2020-11-14",17873,"overall","inc case"
+"37","2020-11-21",23143,"overall","inc case"
+"37","2020-11-28",25697,"overall","inc case"
+"37","2020-12-05",30594,"overall","inc case"
+"37","2020-12-12",41224,"overall","inc case"
+"37","2020-12-19",42492,"overall","inc case"
+"37","2020-12-26",41662,"overall","inc case"
+"37","2021-01-02",44507,"overall","inc case"
+"37","2021-01-09",55918,"overall","inc case"
+"37","2021-01-16",53471,"overall","inc case"
+"37","2021-01-23",44890,"overall","inc case"
+"37","2021-01-30",39911,"overall","inc case"
+"37","2021-02-06",38894,"overall","inc case"
+"37","2021-02-13",27203,"overall","inc case"
+"37","2021-02-20",21372,"overall","inc case"
+"37","2021-02-27",18452,"overall","inc case"
+"37","2021-03-06",13628,"overall","inc case"
+"37","2021-03-13",10539,"overall","inc case"
+"37","2021-03-20",12548,"overall","inc case"
+"37","2021-03-27",10265,"overall","inc case"
+"37","2021-04-03",10631,"overall","inc case"