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saketkc · Jan 19, 2024 · 92163f5 · 92163f5
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diff --git a/docs/articles/Brazil_animated.gif b/docs/articles/Brazil_animated.gif
diff --git a/docs/articles/Brazil_animated_2021.gif b/docs/articles/Brazil_animated_2021.gif
diff --git a/docs/articles/Brazil_animated_2023.gif b/docs/articles/Brazil_animated_2023.gif
diff --git a/docs/articles/Brazil_animated_2024.gif b/docs/articles/Brazil_animated_2024.gif
diff --git a/docs/articles/Germany_animated.gif b/docs/articles/Germany_animated.gif
diff --git a/docs/articles/Germany_animated_2021.gif b/docs/articles/Germany_animated_2021.gif
diff --git a/docs/articles/Germany_animated_2023.gif b/docs/articles/Germany_animated_2023.gif
diff --git a/docs/articles/Germany_animated_2024.gif b/docs/articles/Germany_animated_2024.gif
diff --git a/docs/articles/IN_animated.gif b/docs/articles/IN_animated.gif
diff --git a/docs/articles/IN_animated_2021.gif b/docs/articles/IN_animated_2021.gif
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diff --git a/docs/articles/IN_animated_latest.gif b/docs/articles/IN_animated_latest.gif
diff --git a/docs/articles/Introduction.html b/docs/articles/Introduction.html
diff --git a/docs/articles/Introduction_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/Introduction_files/figure-html/unnamed-chunk-10-1.png
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diff --git a/docs/articles/NYC_animated.gif b/docs/articles/NYC_animated.gif
diff --git a/docs/articles/NYC_animated_2023.gif b/docs/articles/NYC_animated_2023.gif
diff --git a/docs/articles/NY_animated.gif b/docs/articles/NY_animated.gif
diff --git a/docs/articles/NY_animated_2023.gif b/docs/articles/NY_animated_2023.gif
diff --git a/docs/articles/Singapore_animated.gif b/docs/articles/Singapore_animated.gif
diff --git a/docs/articles/Singapore_animated_2021.gif b/docs/articles/Singapore_animated_2021.gif
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diff --git a/docs/articles/Singapore_animated_2024.gif b/docs/articles/Singapore_animated_2024.gif
diff --git a/docs/articles/USA_animated.gif b/docs/articles/USA_animated.gif
diff --git a/docs/articles/USA_animated_2021.gif b/docs/articles/USA_animated_2021.gif
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diff --git a/docs/articles/United_Kingdom_animated.gif b/docs/articles/United_Kingdom_animated.gif
diff --git a/docs/articles/United_Kingdom_animated_2021.gif b/docs/articles/United_Kingdom_animated_2021.gif
diff --git a/docs/articles/United_Kingdom_animated_2023.gif b/docs/articles/United_Kingdom_animated_2023.gif
diff --git a/docs/articles/United_Kingdom_animated_2024.gif b/docs/articles/United_Kingdom_animated_2024.gif
diff --git a/docs/articles/VariantAnimation-Brazil.html b/docs/articles/VariantAnimation-Brazil.html
diff --git a/docs/articles/VariantAnimation-Brazil_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/VariantAnimation-Brazil_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/VariantAnimation-Germany.html b/docs/articles/VariantAnimation-Germany.html
diff --git a/docs/articles/VariantAnimation-Germany_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/VariantAnimation-Germany_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/VariantAnimation-India.html b/docs/articles/VariantAnimation-India.html
diff --git a/docs/articles/VariantAnimation-India_files/figure-html/unnamed-chunk-11-1.png b/docs/articles/VariantAnimation-India_files/figure-html/unnamed-chunk-11-1.png
diff --git a/docs/articles/VariantAnimation-India_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/VariantAnimation-India_files/figure-html/unnamed-chunk-4-1.png
diff --git a/docs/articles/VariantAnimation-NYC.html b/docs/articles/VariantAnimation-NYC.html
diff --git a/docs/articles/VariantAnimation-NYC_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/VariantAnimation-NYC_files/figure-html/unnamed-chunk-4-1.png
diff --git a/docs/articles/VariantAnimation-NewYork.html b/docs/articles/VariantAnimation-NewYork.html
diff --git a/docs/articles/VariantAnimation-NewYork_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/VariantAnimation-NewYork_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/VariantAnimation-Singapore.html b/docs/articles/VariantAnimation-Singapore.html
diff --git a/docs/articles/VariantAnimation-Singapore_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/VariantAnimation-Singapore_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/VariantAnimation-UK.html b/docs/articles/VariantAnimation-UK.html
diff --git a/docs/articles/VariantAnimation-UK_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/VariantAnimation-UK_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/VariantAnimation-USA.html b/docs/articles/VariantAnimation-USA.html
diff --git a/docs/articles/VariantAnimation-USA_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/VariantAnimation-USA_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
   VariantAnimation-Singapore: VariantAnimation-Singapore.html
   VariantAnimation-UK: VariantAnimation-UK.html
   VariantAnimation-USA: VariantAnimation-USA.html
-last_built: 2024-01-16T23:41Z
+last_built: 2024-01-18T18:31Z
 urls:
   reference: http://saket-choudhary.me/covmuller/reference
   article: http://saket-choudhary.me/covmuller/articles

diff --git a/docs/search.json b/docs/search.json
diff --git a/vignettes/Introduction.Rmd b/vignettes/Introduction.Rmd
@@ -56,7 +56,7 @@ p1
 We utilize [GISAID](https://www.gisaid.org/) data to look at prevalence of variants. To access this data, GISAID requires registration.
 
 ```{r}
-current_date <- "2024_01_15"
+current_date <- "2024_01_18"
 fpath.tar <- paste0("~/data/epicov/metadata_tsv_", current_date, ".tar.xz")
 fpath.qs <- paste0("~/data/epicov/metadata_tsv_", current_date, ".qs")
 

diff --git a/vignettes/VariantAnimation-Brazil.Rmd b/vignettes/VariantAnimation-Brazil.Rmd
@@ -32,7 +32,7 @@ theme_set(CovmullerTheme())
 # Get variants data for Brazil
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_18.qs")
 gisaid_brazil <- gisaid_metadata %>%
   filter(Country == "Brazil") %>%
   filter(Host == "Human")

diff --git a/vignettes/VariantAnimation-Germany.Rmd b/vignettes/VariantAnimation-Germany.Rmd
@@ -32,7 +32,7 @@ theme_set(CovmullerTheme())
 # Get variants data for Germany
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_18.qs")
 gisaid_germany <- gisaid_metadata %>%
   filter(Country == "Germany") %>%
   filter(Host == "Human")

diff --git a/vignettes/VariantAnimation-India.Rmd b/vignettes/VariantAnimation-India.Rmd
@@ -30,7 +30,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_18.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

diff --git a/vignettes/VariantAnimation-NYC.Rmd b/vignettes/VariantAnimation-NYC.Rmd
@@ -20,7 +20,7 @@ theme_set(CovmullerTheme())
 ```{r, warning=FALSE, message=FALSE}
 counties <- c("New York", "New York City", "New York County", "Queens County", "Bronx County", "Bronx", "Brooklyn", "Manhattan", "Queens", "Richmond County")
 
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_18.qs")
 gisaid_usa <- gisaid_metadata %>%
   filter(Country == "USA") %>%
   filter(Host == "Human")

diff --git a/vignettes/VariantAnimation-NewYork.Rmd b/vignettes/VariantAnimation-NewYork.Rmd
@@ -26,7 +26,7 @@ theme_set(CovmullerTheme())
 # Get variants data for NY state
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_18.qs")
 gisaid_usa <- gisaid_metadata %>%
   filter(Country == "USA") %>%
   filter(Host == "Human")

diff --git a/vignettes/VariantAnimation-Singapore.Rmd b/vignettes/VariantAnimation-Singapore.Rmd
@@ -32,7 +32,7 @@ theme_set(CovmullerTheme())
 # Get variants data for Singapore
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_18.qs")
 gisaid_singapore <- gisaid_metadata %>%
   filter(Country == "Singapore") %>%
   filter(Host == "Human")

diff --git a/vignettes/VariantAnimation-UK.Rmd b/vignettes/VariantAnimation-UK.Rmd
@@ -32,7 +32,7 @@ theme_set(CovmullerTheme())
 # Get variants data for United Kingdom
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_18.qs")
 gisaid_United_Kingdom <- gisaid_metadata %>%
   filter(Country == "United Kingdom") %>%
   filter(Host == "Human")