covid19.genomic.data

main master (wrapper) function to obtain different types of genomic data for the SARS-CoV-2 virus

Load and analyze updated time series worldwide data of reported cases for the Novel Coronavirus Disease (COVID-19) from different sources, including the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE) data repository <https://github.com/CSSEGISandData/COVID-19>, "Our World in Data" <https://github.com/owid/> among several others. The datasets reporting the COVID-19 cases are available in two main modalities, as a time series sequences and aggregated data for the last day with greater spatial resolution. Several analysis, visualization and modelling functions are available in the package that will allow the user to compute and visualize total number of cases, total number of changes and growth rate globally or for an specific geographical location, while at the same time generating models using these trends; generate interactive visualizations and generate Susceptible-Infected-Recovered (SIR) model for the disease spread.

Marcelo Ponce

covid19.analytics

Load and Analyze Live Data from the COVID-19 Pandemic

covid19.genomic.data function

<dl><dt>type</dt>
<dd>type of data to retrieve, options are: 'genome', 'genomic', 'fasta', 'nucleotide', 'protein', 'ptree'</dd>
<dt>src</dt>
<dd>source of the data: "livedata", "repo" or "local"</dd>
<dt>graphics.ON</dt>
<dd>boolean option for display associated graphics</dd>
<dt>accOnly</dt>
<dd>boolean indicator for getting only accession codes or whole records</dd></dl>

Arguments

main master (wrapper) function to obtain different types of genomic data for the SARS-CoV-2 virus — covid19.genomic.data

<dl>

<dt>type</dt>
<dd>type of data to retrieve, options are: 'genome', 'genomic', 'fasta', 'nucleotide', 'protein', 'ptree'</dd>


<dt>src</dt>
<dd>source of the data: "livedata", "repo" or "local"</dd>


<dt>graphics.ON</dt>
<dd>boolean option for display associated graphics</dd>


<dt>accOnly</dt>
<dd>boolean indicator for getting only accession codes or whole records</dd>

</dl>

covid19.genomic.data: main master (wrapper) function to obtain different types of genomic data for the SARS-CoV-2 virus

Description

Usage

Arguments