Function reference
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CleanAmericanStates() - Clean states from the USA
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CleanCanadaStates() - Clean states from Canada
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CleanIndianStates() - Clean Indian States
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CleanSouthAfricanStates() - Clean states from South Africa
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CollapseLineageToVOCs() - Collpase pangolin lineage a list of VOCs
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CombineSequencedCases() - Create a combined dataframe of sequenced cases and confirmed cases
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CountsToPrevalence() - Convert monthwise counts to prevalence
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CovmullerTheme() - Set them
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FilterGISAIDIndia() - Filter GISAID India Metadata for India
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FixDate() - Fix date format
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FormatGISAIDMetadata() - Format metadata.tar.x file downloaded from GISAID with some missing columns
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GeocodeAddress() - Geocode a given address to get its latitude, longitude from Gooogle
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GetFiletype() - Determine filetype
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GetIndiaConfirmedCasesCumulative() - Get daily confirmed cases for India
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GetIndiaConfirmedCasesMonthlyLong() - Get India monthwose cases long
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GetIndiaConfirmedCasesWeeklyLong() - Get India weekwise cases long
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GetIndiaDailyCasesCumulative() - Get daily cases for India for a given status type
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GetIndiaDailyData() - Get daily statewise data for India
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GetIndiaDeceasedCasesCumulative() - Get daily deceased cases for India
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GetIndiaHospitalization() - Get hospitalization data for India
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GetIndianStates() - Get a list of Indian name states
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GetMonthYear() - Get MonthYear (zoo) from a dataframe string formatted data column
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GetVOCs() - Get variants of concern
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PlotSequencedPropHeatmap() - Plot heatmap of cases sequenced
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PlotTotalHeatmap() - Plot heatmap of total cases/sequences
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ReadAuspiceInstrument() - Read instrument metadata from GISAID batch downloads
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ReadAuspiceMetadata() - Read all metadata from GISAID batch downloads
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ReadGISAIDMetada() - Read metadata downloaded from GISAID
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SanitizeColumn() - Sanitize a vector to remove special characters and convert it to tile
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SummarizeVariantsDatewise() - Summarize the total number of variants per week
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SummarizeVariantsMonthwise() - Summarize the total number of variants per month
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SummarizeVariantsWeekwise() - Summarize the total number of variants per week
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TotalSequencesPerMonthCountrywise() - Get total sequenced samples per country
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TotalSequencesPerMonthStatewise() - Get total number of sequenced samples per month in a Country