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outbreak-info
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R-outbreak-info
R package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info.
https://outbreak-info.github.io/R-outbreak-info/
MIT License
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Clean up outputs from cumulative getPrevalence calls
#59
flaneuse
opened
2 years ago
0
Allow worldwide data in getPrevalenceByLocation
#58
flaneuse
closed
2 years ago
0
enable getPrevalenceByLocation to take an array of lineages as inputs
#57
flaneuse
closed
2 years ago
0
lineages are case sensitive in `other_exclude`
#56
flaneuse
opened
2 years ago
1
Add Genomics Location Lookup function
#55
flaneuse
closed
2 years ago
1
Bad error for "location not found"
#54
flaneuse
closed
2 years ago
1
Improve @return statements in all documentation
#53
flaneuse
closed
2 years ago
1
Fix collection/submission date responses
#52
flaneuse
closed
2 years ago
1
After refactoring of epi pipeline, remove sunsetted variables
#51
flaneuse
closed
2 years ago
0
Allow prevalence of a mutation
#50
flaneuse
closed
2 years ago
0
Add authentication to all examples in documentation
#49
flaneuse
closed
2 years ago
0
Fix / suppress the `muffleWarning` output when user isn't authenticated
#48
flaneuse
closed
2 years ago
1
README
#47
sabahzero
closed
2 years ago
4
Update 'master' branch name to 'main'
#46
sabahzero
closed
2 years ago
3
Full testing of R client with authentication
#45
flaneuse
closed
2 years ago
0
Investigate rpy2 package error
#44
flaneuse
closed
2 years ago
1
Add other vignette links to README
#43
flaneuse
closed
2 years ago
0
In last table, use more meaningful variable name(s)
#42
flaneuse
closed
3 years ago
0
Mods to characteristic mutations heatmap
#41
flaneuse
closed
3 years ago
0
Change the color scheme on the lineage prevalence plots
#40
flaneuse
closed
3 years ago
0
Add percent complete feedback for API calls that require lots of time
#39
flaneuse
closed
3 years ago
0
Lineage Report vignette mapping
#38
flaneuse
closed
2 years ago
0
Simplify ggplot code in Lineage Report Rmd
#37
flaneuse
closed
3 years ago
0
Add ggtitle to plotPrevalenceByLocation
#36
flaneuse
closed
3 years ago
3
Add a nicer error message for slow internet connections
#35
flaneuse
closed
3 years ago
3
getMutationDetails - would be nice to return total number of observations
#34
flaneuse
opened
3 years ago
0
getLag should return dates, not strings
#33
flaneuse
closed
3 years ago
0
Add ggtitle to plotPrevalenceByLocation
#32
flaneuse
closed
3 years ago
0
getSeqCounts broken (?)
#31
flaneuse
closed
3 years ago
5
Merge genomics branch into main branch
#30
flaneuse
closed
2 years ago
0
Add intro to Location Report vignette
#29
flaneuse
closed
2 years ago
0
Add intro to Lineage Report vignette
#28
flaneuse
closed
2 years ago
0
Add intro to Genomic data vignette
#27
flaneuse
closed
2 years ago
0
Create a homepage
#26
flaneuse
closed
2 years ago
1
Improve function call perf and/or offer users more options to limit their results
#25
flaneuse
opened
3 years ago
0
Add check if date is a string in getEpiData()
#24
gkarthik
closed
3 years ago
0
searchLocations needs a better example
#23
flaneuse
opened
3 years ago
1
getCountryByRegion is broken
#22
flaneuse
closed
3 years ago
0
`getByAdmnLevel(-1)` is broken
#21
flaneuse
closed
3 years ago
0
Improve helper text displayed to user
#20
flaneuse
closed
3 years ago
1
`plotCovid` is broken
#19
flaneuse
closed
3 years ago
0
getEpiData function is broken
#18
flaneuse
closed
3 years ago
1
R manual only lists one help page and no vignettes
#17
flaneuse
closed
2 years ago
0
Vignette `getAdmn2ByState` function is broken
#16
flaneuse
closed
3 years ago
1
Vignette `getLocationData` function is broken
#15
flaneuse
closed
3 years ago
2
Add introduction to README and vignette.
#14
gkarthik
closed
2 years ago
0
Allow user to use browseVignettes(package = "outbreakinfo")
#13
gkarthik
opened
4 years ago
0
Document use of list of locations names in vignette
#12
gkarthik
opened
4 years ago
0
Geographic synonym lookup in searchLocations()
#11
gkarthik
opened
4 years ago
0
Set date as a date type, not a string.
#10
gkarthik
closed
3 years ago
0
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