R: Load and Analyze Live Data from the COVID-19 Pandemic

# Load and Analyze Live Data from the COVID-19 Pandemic

## Documentation for package ‘covid19.analytics’ version 2.1.3.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

c19.fasta.data | function to obtain FASTA sequence of the SARS-CoV-2 virus
c19.genomic.data | function to obtain genomic data from SARS-CoV-2019
c19.NPs.data | function to obtain data for nucleotides or proteins from SARS-CoV-2
c19.NP_fasta.data | function to obtain FASTA seqs for nucleotides or proteins from SARS-CoV-2
c19.OWID.data | function to read data from OWID repos
c19.ptree.data | function to obtain "Tree of complete SARS-CoV-2 Sequences as obtained from NCBI"
c19.refGenome.data | function to obtain sequencing data grom NCBI Reference: https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2
consistency.check | function that determines whether there are consistency issues within the data, such as, anomalies in the cumulative quantities of the data as reported by JHU/CCSEGIS
covid19.Canada.data | function to import data for Canada as reported by Health Canada https://health-infobase.canada.ca/src/data/covidLive/covid19.csv
covid19.data | function to read "live" data from reported covid19 cases
covid19.genomic.data | main master (wrapper) function to obtain different types of genomic data for the SARS-CoV-2 virus
covid19.JHU.data | function to read "live" data as reported by JHU's CCSE repository
covid19.testing.data | function to read data related to covid19 Testing from OWID repo
covid19.Toronto.data | function to import data from the city of Toronto, ON - Canada as reported by the City of Toronto OR Open Data Toronto
covid19.Toronto_city.data | function to import data from the city of Toronto, ON - Canada as reported by the City of Toronto https://www.toronto.ca/home/covid-19/covid-19-pandemic-data/
covid19.Toronto_OD.data | function to import data from the city of Toronto, ON - Canada as reported by Open Data Toronto https://open.toronto.ca/dataset/covid-19-cases-in-toronto/ This dataset is updated WEEKLY.
covid19.URL_csv.data | function to read CSV from URLs or local replicas
covid19.US.data | function to read the TimeSeries US detailed data
covid19.vaccination | function to read data related to covid19 vaccinations
covid19dashboard | covid19.analytics explorer dashboard
covid19Explorer | covid19.analytics explorer dashboard
data.checks | function to check for data integrity and data consistency
estimateRRs | estimate rolling rates for a given geographical location for an specific TS data
generate.SIR.model | function to generate a simple SIR (Susceptible-Infected-Recovered) model based on the actual data of the coivd19 cases
geographicalRegions | function to define continents and its constituent countries
getFile | auxiliary function to download files in a protected fashion, i.e. against errors in the downloading procedure
growth.rate | function to compute daily changes and "Growth Rates" per location; "Growth Rates" defined as the ratio between changes in consecutive days
integrity.check | function that determines whether there are integrity issues within the datasets or changes to the structure of the data as reported by JHU/CCSEGIS
itrends | function to visualize trends in daily changes in time series data interactively
live.map | function to map cases in an interactive map
movingFn | generic fn that computes the "fn" on a moving window
mrollingRates | function to compute a rolling fn (rate) of multiple quantities from TS data, eg. fatality and recovery rate
mtrends | function to visualize different indicators for trends in daily changes of cases reported as time series data, for mutliple (or single) locations
nullify.data | remove inconsistencies from data by removing 'suspicious' entries
OWID.repos | function to define the OWID repos URLs
pandemics.data | function to retrieve historical pandemics data
pandemics.loaddata | internal function to retrieve historical data on pandemics
plt.SIR.model | function to plot the results from the SIR model fn
preProcessingData | auxiliary function to pre-process data per geographical location
red.devel.ver | function to redirect users to install devel version from github
report.summary | function to summarize the current situation, will download the latest data and summarize the top provinces/cities per case
report.Tor | function to obtain main indicators from Toronto data
rollingRate | function to compute a rolling fn of a TS data
single.trend | function to visualize different indicators for trends in daily changes of cases reported as time series data
sweep.SIR.models | function to perform a sweep of models and generate values of R0
totals.plt | function to plot total number of cases per day for different groups
tots.per.location | function to compute totals per location
X.covid19.genomic.data | function to obtain sequencing data grom NCBI Reference: https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2