Data update

saketkc · Jan 16, 2024 · 8cf33a1 · 8cf33a1
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diff --git a/docs/articles/Introduction_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/Introduction_files/figure-html/unnamed-chunk-4-1.png
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,4 +1,4 @@
-pandoc: 3.1.1
+pandoc: 3.1.11.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
@@ -9,10 +9,8 @@ articles:
   VariantAnimation-NYC: VariantAnimation-NYC.html
   VariantAnimation-NewYork: VariantAnimation-NewYork.html
   VariantAnimation-Singapore: VariantAnimation-Singapore.html
-  VariantAnimation-SouthAfrica: VariantAnimation-SouthAfrica.html
-  VariantAnimation-UK: VariantAnimation-UK.html
   VariantAnimation-USA: VariantAnimation-USA.html
-last_built: 2024-01-14T06:51Z
+last_built: 2024-01-16T04:47Z
 urls:
   reference: http://saket-choudhary.me/covmuller/reference
   article: http://saket-choudhary.me/covmuller/articles

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_11"
+current_date <- "2024_01_15"
 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_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.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_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_germany <- gisaid_metadata %>%
   filter(Country == "Germany") %>%
   filter(Host == "Human")

diff --git a/vignettes/VariantAnimation-India.Rmd b/vignettes/VariantAnimation-India.Rmd
@@ -29,7 +29,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.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_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.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_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.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_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_singapore <- gisaid_metadata %>%
   filter(Country == "Singapore") %>%
   filter(Host == "Human")

diff --git a/vignettes/VariantAnimation-USA.Rmd b/vignettes/VariantAnimation-USA.Rmd
@@ -32,7 +32,7 @@ theme_set(CovmullerTheme())
 # Get variants data for USA
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_usa <- gisaid_metadata %>%
   filter(Country == "USA") %>%
   filter(Host == "Human")

diff --git a/vignettes/_MultinomialModeling-Germany.Rmd b/vignettes/_MultinomialModeling-Germany.Rmd
@@ -15,7 +15,7 @@ theme_set(CovmullerTheme())
 ```
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_germany <- gisaid_metadata %>%
   filter(Country == "Germany") %>%
   filter(Host == "Human")

diff --git a/vignettes/_MultinomialModeling_Australia.Rmd b/vignettes/_MultinomialModeling_Australia.Rmd
@@ -15,7 +15,7 @@ theme_set(CovmullerTheme())
 ```
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_australia <- gisaid_metadata %>%
   filter(Country == "Australia") %>%
   filter(Host == "Human")

diff --git a/vignettes/_MultinomialModeling_Canada.Rmd b/vignettes/_MultinomialModeling_Canada.Rmd
@@ -15,7 +15,7 @@ theme_set(CovmullerTheme())
 ```
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_canada <- gisaid_metadata %>%
   filter(Country == "Canada") %>%
   filter(Host == "Human")

diff --git a/vignettes/_MultinomialModeling_India.Rmd b/vignettes/_MultinomialModeling_India.Rmd
@@ -15,7 +15,7 @@ theme_set(CovmullerTheme())
 ```
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 ```
 

diff --git a/vignettes/_MultinomialModeling_SouthAfrica.Rmd b/vignettes/_MultinomialModeling_SouthAfrica.Rmd
@@ -15,7 +15,7 @@ theme_set(CovmullerTheme())
 ```
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_southafrica <- gisaid_metadata %>%
   filter(Country == "South Africa") %>%
   filter(Host == "Human")

diff --git a/vignettes/_MultinomialModeling_UK.Rmd b/vignettes/_MultinomialModeling_UK.Rmd
@@ -15,7 +15,7 @@ theme_set(CovmullerTheme())
 ```
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_uk <- gisaid_metadata %>%
   filter(Country == "United Kingdom") %>%
   filter(Host == "Human")

diff --git a/vignettes/_SouthAfrica_contrast_India.Rmd b/vignettes/_SouthAfrica_contrast_India.Rmd
@@ -16,7 +16,7 @@ theme_set(CovmullerTheme())
 # Get data
 
 ```{r}
-current_date <- "2024_01_11"
+current_date <- "2024_01_15"
 fpath.tar <- paste0("~/data/epicov/metadata_tsv_", current_date, ".tar.xz")
 fpath.qs <- paste0("~/data/epicov/metadata_tsv_", current_date, ".qs")
 gisaid_metadata <- qs::qread(file = fpath.qs)

diff --git a/vignettes/_VariantAnimation-Bengaluru.Rmd b/vignettes/_VariantAnimation-Bengaluru.Rmd
@@ -19,7 +19,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

diff --git a/vignettes/_VariantAnimation-Chennai.Rmd b/vignettes/_VariantAnimation-Chennai.Rmd
@@ -19,7 +19,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

diff --git a/vignettes/_VariantAnimation-Delhi.Rmd b/vignettes/_VariantAnimation-Delhi.Rmd
@@ -19,7 +19,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

diff --git a/vignettes/_VariantAnimation-Gujarat.Rmd b/vignettes/_VariantAnimation-Gujarat.Rmd
@@ -20,7 +20,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

diff --git a/vignettes/_VariantAnimation-Hyderabad.Rmd b/vignettes/_VariantAnimation-Hyderabad.Rmd
@@ -19,7 +19,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

diff --git a/vignettes/_VariantAnimation-Jaipur.Rmd b/vignettes/_VariantAnimation-Jaipur.Rmd
@@ -19,7 +19,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

diff --git a/vignettes/_VariantAnimation-Kerala.Rmd b/vignettes/_VariantAnimation-Kerala.Rmd
@@ -20,7 +20,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

diff --git a/vignettes/_VariantAnimation-Maharashtra.Rmd b/vignettes/_VariantAnimation-Maharashtra.Rmd
@@ -20,7 +20,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

diff --git a/vignettes/_VariantAnimation-Mumbai.Rmd b/vignettes/_VariantAnimation-Mumbai.Rmd
@@ -20,7 +20,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

diff --git a/vignettes/_VariantAnimation-Pune.Rmd b/vignettes/_VariantAnimation-Pune.Rmd
@@ -19,7 +19,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

diff --git a/vignettes/_VariantAnimation-SouthAfrica.Rmd b/vignettes/_VariantAnimation-SouthAfrica.Rmd
@@ -32,7 +32,7 @@ theme_set(CovmullerTheme())
 # Get variants data for South Africa
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_South_Africa <- gisaid_metadata %>%
   filter(Country == "South Africa") %>%
   filter(Host == "Human")

diff --git a/vignettes/_VariantAnimation-Tamilnadu.Rmd b/vignettes/_VariantAnimation-Tamilnadu.Rmd
@@ -20,7 +20,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

diff --git a/vignettes/_VariantAnimation-Telangana.Rmd b/vignettes/_VariantAnimation-Telangana.Rmd
@@ -20,7 +20,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()

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_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_United_Kingdom <- gisaid_metadata %>%
   filter(Country == "United Kingdom") %>%
   filter(Host == "Human")

diff --git a/vignettes/_VarinatAnimation-Kolkata.Rmd b/vignettes/_VarinatAnimation-Kolkata.Rmd
@@ -19,7 +19,7 @@ theme_set(CovmullerTheme())
 # Get variants data for India
 
 ```{r, warning=FALSE, message=FALSE}
-gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_15.qs")
 gisaid_india <- FilterGISAIDIndia(gisaid_metadata_all = gisaid_metadata)
 
 vocs <- GetVOCs()