Update VOCs

saketkc · Jan 13, 2024 · ecddcd5 · ecddcd5
1 parent e39bf9b
commit ecddcd5
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diff --git a/vignettes/VariantAnimation-NewYork.Rmd b/vignettes/VariantAnimation-NewYork.Rmd
@@ -39,34 +39,12 @@ gisaid_NY <- gisaid_usa %>% filter(State == "New York")
 
 vocs <- GetVOCs()
 custom_voc_mapping <- list(
-  `XBB` = "XBB",
-  `XBB.1.5` = "XBB",
-  `XBB.1` = "XBB",
-  `XBB.1.*` = "XBB",
-  `XBB.*` = "XBB",
-  `XBB.*.*` = "XBB",
-  `XBB.*.*.*` = "XBB",
-  `BQ.1` = "BQ.1",
-  `BQ.1.*` = "BQ.1",
-  `EG.5` = "EG.5",
-  `EG.5.1` = "EG.5",
-  `EG.5.1.1` = "EG.5",
-  `EG.5.*` = "EG.5",
-  `EG.5.1` = "EG.5",
-  # `EG.6.*` = "EG.6",
-  # `EG.6.1` = "EG.6",
-  `FL.1.*` = "FL.1",
-  `FU.1` = "FU.1",
-  `FU.1.*` = "FU.1",
-  `GJ.1.2` = "GJ.1",
-  `GJ.1.*` = "GJ.1",
   `JN.1` = "JN.1",
   `JN.1.*` = "JN.1",
   `HV.1` = "HV.1",
   `HV.1.*` = "HV.1"
 )
 gisaid_NY <- gisaid_NY %>% filter(pangolin_lineage != "None")
-
 gisaid_NY <- CollapseLineageToVOCs(
   variant_df = gisaid_NY,
   vocs = vocs,

diff --git a/vignettes/VariantAnimation-Singapore.Rmd b/vignettes/VariantAnimation-Singapore.Rmd
@@ -40,30 +40,7 @@ gisaid_singapore <- gisaid_singapore %>%
   filter(State != "Unknown")
 
 vocs <- GetVOCs()
-omicron <- vocs[["omicron"]]
-vocs[["omicron"]] <- NULL
 custom_voc_mapping <- list(
-  `XBB` = "XBB",
-  `XBB.1.5` = "XBB",
-  `XBB.1` = "XBB",
-  `XBB.1.*` = "XBB",
-  `XBB.*` = "XBB",
-  `XBB.*.*` = "XBB",
-  `XBB.*.*.*` = "XBB",
-  `BQ.1` = "BQ.1",
-  `BQ.1.*` = "BQ.1",
-  `EG.5` = "EG.5",
-  `EG.5.1` = "EG.5",
-  `EG.5.1.1` = "EG.5",
-  `EG.5.*` = "EG.5",
-  `EG.5.1` = "EG.5",
-  # `EG.6.*` = "EG.6",
-  # `EG.6.1` = "EG.6",
-  `FL.1.*` = "FL.1",
-  `FU.1` = "FU.1",
-  `FU.1.*` = "FU.1",
-  `GJ.1.2` = "GJ.1",
-  `GJ.1.*` = "GJ.1",
   `JN.1` = "JN.1",
   `JN.1.*` = "JN.1",
   `HV.1` = "HV.1",

diff --git a/vignettes/VariantAnimation-SouthAfrica.Rmd b/vignettes/VariantAnimation-SouthAfrica.Rmd
@@ -41,30 +41,7 @@ gisaid_sa <- gisaid_sa %>%
   filter(State != "Unknown")
 
 vocs <- GetVOCs()
-omicron <- vocs[["omicron"]]
-vocs[["omicron"]] <- NULL
 custom_voc_mapping <- list(
-  `XBB` = "XBB",
-  `XBB.1.5` = "XBB",
-  `XBB.1` = "XBB",
-  `XBB.1.*` = "XBB",
-  `XBB.*` = "XBB",
-  `XBB.*.*` = "XBB",
-  `XBB.*.*.*` = "XBB",
-  `BQ.1` = "BQ.1",
-  `BQ.1.*` = "BQ.1",
-  `EG.5` = "EG.5",
-  `EG.5.1` = "EG.5",
-  `EG.5.1.1` = "EG.5",
-  `EG.5.*` = "EG.5",
-  `EG.5.1` = "EG.5",
-  # `EG.6.*` = "EG.6",
-  # `EG.6.1` = "EG.6",
-  `FL.1.*` = "FL.1",
-  `FU.1` = "FU.1",
-  `FU.1.*` = "FU.1",
-  `GJ.1.2` = "GJ.1",
-  `GJ.1.*` = "GJ.1",
   `JN.1` = "JN.1",
   `JN.1.*` = "JN.1",
   `HV.1` = "HV.1",