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 index 6fe20f27..fda5b081 100644 Binary files a/docs/articles/Introduction_files/figure-html/unnamed-chunk-4-1.png and b/docs/articles/Introduction_files/figure-html/unnamed-chunk-4-1.png differ diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 2c6fa4d1..4e975636 100644 --- 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 index d509ba53..5e5ad94f 100644 --- 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 index 5adc9e2f..8364f7b4 100644 --- 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 index aec0fc82..a2dedcb7 100644 --- 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 index e2b4979a..577b19b0 100644 --- 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 index 5470ab55..2e64e1fe 100644 --- 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 index 8308dceb..35a728c2 100644 --- 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 index ea9c16ff..126be6d1 100644 --- 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 index bb944a89..2ed741dc 100644 --- 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 index 12227cc4..48d125a7 100644 --- 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 index c52fcb8c..5a126d0d 100644 --- 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 index 87307b67..0861add1 100644 --- 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 index 90b97c8f..7bfc8c96 100644 --- 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 index d8e1b530..4a2c2cb9 100644 --- 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 index 0adc1329..b5da7f35 100644 --- 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 index ddd507be..e7a4b792 100644 --- 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 index 40e25060..76af1173 100644 --- 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 index 7e214b1d..993ee2d3 100644 --- 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 index c0d4b6af..5f038241 100644 --- 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 index 443af046..de504123 100644 --- 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 index 7af3ed3c..1e482706 100644 --- 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 index c796a628..314f2cdb 100644 --- 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 index c4081adf..8457e34c 100644 --- 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 index 955e8bf9..9b50d4b6 100644 --- 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 index a7cc777d..a746997e 100644 --- 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 index a5a453b3..9f6bef7d 100644 --- 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 index 0c9fe0f3..2f50a4d2 100644 --- 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 index b6255320..fb48c93b 100644 --- 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 index 4604b88c..7f6eebc2 100644 --- 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 index 19007fee..a3945a60 100644 --- 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 index 52b4f862..360fe14a 100644 --- 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()