This repo serves as documentation of code used by the routine reporting team to generate IM slide 1 during the COVID-19 response for the Case Surveillance Section. Intially, this slide (IM slide 1) was generated in excel but was transitioned to R during July 2020. Within this repo, each of these files discussed below is also included as example input and output.
Once all packages are installed, one can just 'source' the entire script to generate 3 different outputs after adjusting the date for the file names of the 3 outputs (L164, L294, and L381). Those outputs include:
- 2 png images
- 1 excel file with updated information generated in R
The png images are epi-curves; one with correction to exclude high number of probable deaths reported during June (slide2). The input to generate these files is a csv file consisting of 5 columns - submission date, total cases, new cases, new deaths, and total deaths. This file was generated daily from DCIPHER and made available to those on the routine reporting team.
This code was developed while on COVID19 response by
As of this writing and because we are no longer on the response changes may have been made to generate these images, but hope that this repo could be helpful for others. We encourage others that are on response and participating in making these figures to provide addtional updates as they see fit.
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