diff --git a/R/utilities.R b/R/utilities.R index 93a596cf..361d1768 100644 --- a/R/utilities.R +++ b/R/utilities.R @@ -106,8 +106,8 @@ GetVOCs <- function() { beta = beta_voc, gamma = gamma_voc, delta = delta_voc, - omicron = omicron_voc, - B.1 = c("B.1") + omicron = omicron_voc + # B.1 = c("B.1") # lambda = lambda_voc, # mu = mu_voc, # epsilon = epsilon_voc, @@ -330,16 +330,23 @@ CollapseLineageToVOCs <- function(variant_df, vocs = GetVOCs(), custom_voc_mappi for (name in names(vocs)) { variant_df <- variant_df %>% mutate(lineage_collapsed = case_when( # pangolin_lineage %in% vocs[[!!name]] ~ str_to_title(!!name), - grepl(pattern = vocs[[!!name]], x = pangolin_lineage) ~ str_to_title(!!name), + grepl(pattern = paste(vocs[[!!name]], collapse = "|"), x = pangolin_lineage) ~ str_to_title(!!name), TRUE ~ lineage_collapsed )) } if (!is.null(custom_voc_mapping)) { for (name in names(custom_voc_mapping)) { - variant_df <- variant_df %>% mutate(lineage_collapsed = case_when( - grepl(pattern = !!name, x = pangolin_lineage) ~ custom_voc_mapping[[!!name]], - TRUE ~ lineage_collapsed - )) + if (grepl(pattern = "\\*", x = name)) { + variant_df <- variant_df %>% mutate(lineage_collapsed = case_when( + grepl(pattern = !!name, x = pangolin_lineage) ~ custom_voc_mapping[[!!name]], + TRUE ~ lineage_collapsed + )) + } else { + variant_df <- variant_df %>% mutate(lineage_collapsed = case_when( + pangolin_lineage %in% c(name) ~ custom_voc_mapping[[!!name]], + TRUE ~ lineage_collapsed + )) + } } } if (summarize) { diff --git a/docs/404.html b/docs/404.html index aca73001..9bd16e7b 100644 --- a/docs/404.html +++ b/docs/404.html @@ -30,7 +30,7 @@ covmuller - 0.1.2.0001 + 0.1.2.0003 + + + + + +
+ + + + +
+
+

Animation of projected weekly cases - Brazil

+ + + Source: vignettes/VariantAnimation-Brazil.Rmd +
VariantAnimation-Brazil.Rmd
+
+ + + +
suppressPackageStartupMessages({
+  library(covmuller)
+  library(COVID19)
+  library(tidyverse)
+})
+theme_set(CovmullerTheme())
+
+

Get variants data for Brazil

+
gisaid_metadata <- qs::qread("~/data/epicov/metadata_tsv_2024_01_11.qs")
+gisaid_brazil <- gisaid_metadata %>%
+  filter(Country == "Brazil") %>%
+  filter(Host == "Human")
+# format metadata
+gisaid_brazil <- FormatGISAIDMetadata(gisaid_brazil)
+gisaid_brazil <- gisaid_brazil %>%
+  arrange(State, MonthYearCollected) %>%
+  filter(pangolin_lineage != "Unknown")
+
+vocs <- GetVOCs()
+custom_voc_mapping <- list(
+  `JN.1` = "JN.1",
+  `JN.1.*` = "JN.1",
+  `HV.1` = "HV.1",
+  `HV.1.*` = "HV.1"
+)
+gisaid_brazil <- gisaid_brazil %>% filter(pangolin_lineage != "None")
+
+gisaid_brazil <- CollapseLineageToVOCs(
+  variant_df = gisaid_brazil,
+  vocs = vocs,
+  custom_voc_mapping = custom_voc_mapping,
+  summarize = FALSE
+)
+
+
+

Get weekly cases for Brazil

+
GetCases <- function() {
+  data <- read.csv("https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/cases_deaths/new_cases.csv")
+  confirmed <- data %>% select(date, Brazil)
+  colnames(confirmed)[2] <- c("cases")
+  confirmed$MonthYear <- GetMonthYear(confirmed$date)
+  confirmed$WeekYear <- tsibble::yearweek(confirmed$date)
+  return(confirmed)
+}
+
+
+GetCasesLong <- function() {
+  data <- read.csv("https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/cases_deaths/new_cases.csv")
+  confirmed <- data %>% select(date, Brazil)
+  colnames(confirmed)[2] <- c("cases")
+  confirmed$MonthYear <- GetMonthYear(confirmed$date)
+  confirmed$WeekYear <- tsibble::yearweek(confirmed$date)
+  confirmed_subset_weekwise <- confirmed %>%
+    group_by(WeekYear) %>%
+    summarise(cases = mean(cases, na.rm = T)) %>%
+    arrange(WeekYear)
+  confirmed_subset_weekwise$cases <- ceiling(confirmed_subset_weekwise$cases)
+  confirmed_subset_dateweekwise_long_india <- confirmed_subset_weekwise %>%
+    rename(n = cases) %>%
+    rename(WeekYearCollected = WeekYear)
+}
+
+
+confirmed <- GetCases()
+confirmed_subset_dateweekwise_long <- GetCasesLong()
+gisaid_brazil_weekwise <- SummarizeVariantsWeekwise(gisaid_brazil)
+
+
+

Distribution of variants

+
state_month_counts <- SummarizeVariantsMonthwise(gisaid_brazil)
+state_month_counts$State <- "Brazil"
+state_month_prevalence <- CountsToPrevalence(state_month_counts)
+vocs <- GetVOCs()
+
+state_month_prevalence <- CollapseLineageToVOCs(
+  variant_df = state_month_prevalence,
+  vocs = vocs,
+  custom_voc_mapping = custom_voc_mapping, summarize = FALSE
+)
+
+p5 <- StackedBarPlotPrevalence(state_month_prevalence)
+p5
+

+
+
+

Project weekly cases to variant prevalence data from GISAID

+
voc_to_keep <- gisaid_brazil_weekwise %>%
+  group_by(lineage_collapsed) %>%
+  summarise(n_sum = sum(n)) %>%
+  filter(n_sum > 50) %>%
+  pull(lineage_collapsed) %>%
+  unique()
+gisaid_brazil_weekwise <- gisaid_brazil_weekwise %>% filter(lineage_collapsed %in% voc_to_keep)
+
+brazil_cases_pred_prob_sel_long <- FitMultinomWeekly(gisaid_brazil_weekwise, confirmed_subset_dateweekwise_long)
+#> # weights:  24 (15 variable)
+#> initial  value 439814.238114 
+#> iter  10 value 256033.720738
+#> iter  20 value 142234.034232
+#> iter  30 value 120096.926154
+#> iter  40 value 115996.408661
+#> iter  50 value 101694.726489
+#> iter  60 value 101679.150425
+#> iter  60 value 101679.150298
+#> iter  60 value 101679.150294
+#> final  value 101679.150294 
+#> converged
+the_anim <- PlotVariantPrevalenceAnimated(brazil_cases_pred_prob_sel_long, title = "Estimated cases (weekly average) in Brazil by variant", caption = "**Source: gisaid.org and ourworldindata.org/coronavirus**<br>", date_breaks = "100 days")
+gganimate::anim_save(filename = here::here("docs/articles/Brazil_animated.gif"), animation = the_anim)
+

+

Look at cases from 2022,

+
confirmed_subset_dateweekwise_long <- GetCasesLong() %>%
+  filter(WeekYearCollected >= tsibble::yearweek("2021 W35"))
+
+gisaid_brazil_subset <- gisaid_brazil %>% filter(MonthYearCollected > "Oct 2021")
+gisaid_brazil_weekwise <- SummarizeVariantsWeekwise(gisaid_brazil_subset)
+
+voc_to_keep <- gisaid_brazil_weekwise %>%
+  group_by(lineage_collapsed) %>%
+  summarise(n_sum = sum(n)) %>%
+  filter(n_sum > 50) %>%
+  pull(lineage_collapsed) %>%
+  unique()
+gisaid_brazil_weekwise <- gisaid_brazil_weekwise %>% filter(lineage_collapsed %in% voc_to_keep)
+
+brazil_cases_pred_prob_sel_long <- FitMultinomWeekly(gisaid_brazil_weekwise, confirmed_subset_dateweekwise_long)
+#> # weights:  24 (15 variable)
+#> initial  value 242593.481577 
+#> iter  10 value 67367.516549
+#> iter  20 value 50299.321008
+#> iter  30 value 48568.582744
+#> iter  40 value 48399.528910
+#> iter  50 value 48216.001702
+#> final  value 48215.991366 
+#> converged
+the_anim <- PlotVariantPrevalenceAnimated(brazil_cases_pred_prob_sel_long, title = "Estimated cases (weekly average) in Brazil by variant", caption = "**Source: gisaid.org and ourworldindata.org/coronavirus**<br>", date_breaks = "100 days")
+gganimate::anim_save(filename = here::here("docs/articles/Brazil_animated_2021.gif"), animation = the_anim)
+

Look at cases from 2023

+
confirmed_subset_dateweekwise_long <- GetCasesLong() %>%
+  filter(WeekYearCollected >= tsibble::yearweek("2022 W35"))
+
+gisaid_brazil_subset <- gisaid_brazil %>% filter(MonthYearCollected > "October 2022")
+gisaid_brazil_weekwise <- SummarizeVariantsWeekwise(gisaid_brazil_subset)
+
+voc_to_keep <- gisaid_brazil_weekwise %>%
+  group_by(lineage_collapsed) %>%
+  summarise(n_sum = sum(n)) %>%
+  filter(n_sum > 50) %>%
+  pull(lineage_collapsed) %>%
+  unique()
+gisaid_brazil_weekwise <- gisaid_brazil_weekwise %>% filter(lineage_collapsed %in% voc_to_keep)
+
+brazil_cases_pred_prob_sel_long <- FitMultinomWeekly(gisaid_brazil_weekwise, confirmed_subset_dateweekwise_long)
+#> # weights:  16 (9 variable)
+#> initial  value 42782.430279 
+#> iter  10 value 25591.413964
+#> iter  20 value 24307.240935
+#> iter  20 value 24307.240870
+#> final  value 24307.240870 
+#> converged
+the_anim <- PlotVariantPrevalenceAnimated(brazil_cases_pred_prob_sel_long, title = "Estimated cases (weekly average) in Brazil by variant", caption = "**Source: gisaid.org and ourworldindata.org/coronavirus**<br>")
+gganimate::anim_save(filename = here::here("docs/articles/Brazil_animated_2023.gif"), animation = the_anim)
+

+

Look at cases in the past few weeks

+
confirmed_subset_dateweekwise_long <- GetCasesLong() %>%
+  filter(WeekYearCollected >= tsibble::yearweek("2023 W23"))
+
+gisaid_brazil_subset <- gisaid_brazil %>% filter(MonthYearCollected > "June 2023")
+gisaid_brazil_weekwise <- SummarizeVariantsWeekwise(gisaid_brazil_subset)
+
+voc_to_keep <- gisaid_brazil_weekwise %>%
+  group_by(lineage_collapsed) %>%
+  summarise(n_sum = sum(n)) %>%
+  filter(n_sum > 50) %>%
+  pull(lineage_collapsed) %>%
+  unique()
+gisaid_brazil_weekwise <- gisaid_brazil_weekwise %>% filter(lineage_collapsed %in% voc_to_keep)
+
+brazil_cases_pred_prob_sel_long <- FitMultinomWeekly(gisaid_brazil_weekwise, confirmed_subset_dateweekwise_long)
+#> # weights:  16 (9 variable)
+#> initial  value 7589.961627 
+#> iter  10 value 3097.145675
+#> iter  20 value 2913.994381
+#> iter  30 value 2912.954507
+#> final  value 2905.363627 
+#> converged
+the_anim <- PlotVariantPrevalenceAnimated(brazil_cases_pred_prob_sel_long, title = "Estimated cases (weekly average) in Brazil by variant", caption = "**Source: gisaid.org and ourworldindata.org/coronavirus**<br>")
+gganimate::anim_save(filename = here::here("docs/articles/Brazil_animated_2024.gif"), animation = the_anim)
+

+
+
+ + + +
+

Developed by Saket Choudhary.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + 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 new file mode 100644 index 00000000..01bbcc52 Binary files /dev/null and b/docs/articles/VariantAnimation-Brazil_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/docs/articles/VariantAnimation-Germany.html b/docs/articles/VariantAnimation-Germany.html index 049be50a..9a5ff9e7 100644 --- a/docs/articles/VariantAnimation-Germany.html +++ b/docs/articles/VariantAnimation-Germany.html @@ -32,7 +32,7 @@ covmuller - 0.1.2.0001 + 0.1.2.0003 + + + + + +
+
+
+

Fix date format

+ Source: R/utilities.R +
FixDate.Rd
+
+ +
+

Fix date format

+
+ +
+

Usage

+ 
FixDate(datecol, datefmt = "%Y-%m-%d")
+
+ + +
+ + +
+

Developed by Saket Choudhary.

+
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + diff --git a/docs/reference/FormatGISAIDMetadata.html b/docs/reference/FormatGISAIDMetadata.html index 64b7e852..668bc41d 100644 --- a/docs/reference/FormatGISAIDMetadata.html +++ b/docs/reference/FormatGISAIDMetadata.html @@ -16,7 +16,7 @@ covmuller - 0.1.2.0001 + 0.1.2.0003