Load and Analyze Live Data from the COVID-19 Pandemic

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Documentation for package ‘covid19.analytics’ version 2.1.3.3

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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