In appliedbinf/c19r-app: COVID-19 Event Risk Assessment Planning Tool

options(rmarkdown.html_vignette.check_title = FALSE)
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Setup

MySQL

The application is compatible with (most) databases with a {DBI} interface. It's been tested with MySQL and PostgreSQL. The production application uses a hosted instance of Aurora (MySQL) on AWS RDS. See below for the table schemaa. You may wish to use a connection manager, such as ProxySQL, to collate and proxy application instance connections to your Database server. The application has been tested with ProxySQL v2.3.2.

Creating MySQL database and tables

``{sql, eval=F} CREATE DATABASEc19r` /!40100 DEFAULT CHARACTER SET utf8 /;

-- c19r.risk_game_results definition

CREATE TABLE risk_game_results ( GEOID int(11) NOT NULL, data_ts varchar(100) NOT NULL, pred_20 int(11) NOT NULL, pred_50 int(11) NOT NULL, pred_100 int(11) NOT NULL, pred_1000 int(11) NOT NULL, g_20 int(11) NOT NULL, g_50 int(11) NOT NULL, g_100 int(11) NOT NULL, g_1000 int(11) NOT NULL, ip varchar(100) DEFAULT NULL, ts timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP, latitude float DEFAULT NULL, longitude float DEFAULT NULL, utm_source varchar(100) DEFAULT NULL, utm_medium varchar(100) DEFAULT NULL, utm_content varchar(100) DEFAULT NULL, utm_campaign varchar(100) DEFAULT NULL ) ENGINE=InnoDB DEFAULT CHARSET=utf8;

-- c19r.willingness definition

CREATE TABLE willingness ( source varchar(100) NOT NULL, ts timestamp NULL DEFAULT CURRENT_TIMESTAMP, asc_bias int(11) NOT NULL, event_size int(11) NOT NULL, answer varchar(40) NOT NULL, ip varchar(100) DEFAULT NULL, data_ts varchar(100) DEFAULT NULL, vacc_imm varchar(100) DEFAULT NULL, latitude float DEFAULT NULL, longitude float DEFAULT NULL, utm_source varchar(100) DEFAULT NULL, utm_medium varchar(100) DEFAULT NULL, utm_content varchar(100) DEFAULT NULL, utm_campaign varchar(100) DEFAULT NULL ) ENGINE=InnoDB DEFAULT CHARSET=utf8;

## Creating up to date data files

```{bash, eval=FALSE}
mkdir risk_data
docker pull appliedbioinformaticslab/c19r:latest
docker run -v $PWD/risk_data:/risk_data appliedbioinformaticslab/c19r R -e "c19rdata::create_c19r_data(output_prefix='/risk_data')"

If using an external directory for NYT case data

```{bash, eval=FALSE} base="/path/to/custom/dir" fname=$(date +%Y%m%d_%H%M%S) wget https://raw.githubusercontent.com/nytimes/covid-19-data/master/us-states.csv \ -O "${base}/states_current/${fname}.csv" \ -a "${base}/current.log";

# Deploying
```{base, eval=F}
docker run -d \
  -p 80:80 \
  -v $PWD/risk_data:/risk_data \
  -e C19R_RISK_DATA="/risk_data/usa_risk_counties.csv" 
  -e MYSQL_USERNAME="admin" \
  -e MYSQL_PASSWORD="password" \
  -e MYSQL_HOST="mysql.local" \
  appliedbioinformaticslab/c19r

appliedbinf/c19r-app documentation built on April 27, 2023, 11:54 p.m.