Man pages for saketkc/covmuller
A tool to model COVID19 variant prevalence using data from GISAID
| CleanAmericanStates | Clean states from the USA |
| CleanCanadaStates | Clean states from Canada |
| CleanIndianStates | Clean Indian States |
| CleanSouthAfricanStates | Clean states from South Africa |
| CollapseLineageToVOCs | Collpase pangolin lineage a list of VOCs |
| CombineSequencedCases | Create a combined dataframe of sequenced cases and confirmed... |
| CountsToPrevalence | Convert monthwise counts to prevalence |
| CovmullerTheme | Set them |
| FilterGISAIDIndia | Filter GISAID India Metadata for India |
| FixDate | Fix date format |
| FormatGISAIDMetadata | Format metadata.tar.x file downloaded from GISAID with some... |
| GeocodeAddress | Geocode a given address to get its latitude, longitude from... |
| GetFiletype | Determine filetype |
| GetIndiaConfirmedCasesCumulative | Get daily confirmed cases for India |
| GetIndiaConfirmedCasesMonthlyLong | Get India monthwose cases long |
| GetIndiaConfirmedCasesWeeklyLong | Get India weekwise cases long |
| GetIndiaDailyCasesCumulative | Get daily cases for India for a given status type |
| GetIndiaDailyData | Get daily statewise data for India |
| GetIndiaDeceasedCasesCumulative | Get daily deceased cases for India |
| GetIndiaHospitalization | Get hospitalization data for India |
| GetIndianStates | Get a list of Indian name states |
| GetMonthYear | Get MonthYear (zoo) from a dataframe string formatted data... |
| GetVOCs | Get variants of concern |
| PlotSequencedPropHeatmap | Plot heatmap of cases sequenced |
| PlotTotalHeatmap | Plot heatmap of total cases/sequences |
| ReadAuspiceInstrument | Read instrument metadata from GISAID batch downloads |
| ReadAuspiceMetadata | Read all metadata from GISAID batch downloads |
| ReadGISAIDMetada | Read metadata downloaded from GISAID |
| SanitizeColumn | Sanitize a vector to remove special characters and convert it... |
| SummarizeVariantsDatewise | Summarize the total number of variants per week |
| SummarizeVariantsMonthwise | Summarize the total number of variants per month |
| SummarizeVariantsWeekwise | Summarize the total number of variants per week |
| TotalSequencesPerMonthCountrywise | Get total sequenced samples per country |
| TotalSequencesPerMonthStatewise | Get total number of sequenced samples per month in a Country |
