In saketkc/covmuller: A tool to model COVID19 variant prevalence using data from GISAID

suppressPackageStartupMessages({
  library(covmuller)
  library(tidyverse)
})
theme_set(CovmullerTheme())

gisaid_metadata <- qs::qread(file = "~/data/epicov/metadata_tsv_2024_04_11.qs")
gisaid_australia <- gisaid_metadata %>%
  filter(Country == "Australia") %>%
  filter(Host == "Human")
gisaid_australia <- FormatGISAIDMetadata(gisaid_australia)
gisaid_australia$State <- gsub(pattern = "?", replacement = "", x = gisaid_australia$State)

gisaid_australia <- gisaid_australia %>%
  filter(State != "") %>%
  arrange(State, MonthYearCollected)
gisaid_australia <- gisaid_australia %>% filter(State != "Unknown")

Plot total sequenced cases

country_seq_stats <- TotalSequencesPerMonthCountrywise(gisaid_australia, rename_country_as_state = TRUE)
p0 <- BarPlot(country_seq_stats, ylabel = "Sequenced per month", color = "slateblue1", label_si = TRUE, xangle = 90, title = "Australia")
p0

Get VOCs

vocs <- GetVOCs()
omicron <- vocs[["omicron"]]
vocs[["omicron"]] <- NULL
custom_voc_mapping <- list(
  `BA.1.1` = "BA.1",
  `BA.1` = "BA.1",
  `BA.2` = "BA.2",
  `BA.2.10` = "BA.2.X",
  `BA.2.10.1` = "BA.2.X",
  `BA.2.12` = "BA.2.X",
  `BA.2.12.1` = "BA.2.X",
  `BA.3` = "BA.3",
  `BA.4` = "BA.4",
  `BA.5` = "BA.5",
  `BA.2.74` = "BA.2.X",
  `BA.2.75` = "BA.2.75",
  `BA.2.76` = "BA.2.X",
  `XBB.*` = "XBB",
  `BQ.1` = "BQ.1+",
  `BQ.1.*` = "BQ.1+"
)

gisaid_australia_collapsed <- CollapseLineageToVOCs(
  variant_df = gisaid_australia,
  vocs = vocs,
  custom_voc_mapping = custom_voc_mapping,
  summarize = FALSE
)

gisaid_australia_collapsed_sel <- gisaid_australia_collapsed %>%
  filter(MonthYearCollected >= "Oct 2022") %>%
  filter(lineage_collapsed != "Unassigned")

vocs_to_keep <- table(gisaid_australia_collapsed_sel$lineage_collapsed)
vocs_to_keep <- vocs_to_keep[vocs_to_keep > 100]

gisaid_australia_collapsed_sel <- gisaid_australia_collapsed_sel %>% filter(lineage_collapsed %in% names(vocs_to_keep))
gisaid_australia_shared_dateweek <- SummarizeVariantsDatewise(gisaid_australia_collapsed_sel, by_state = TRUE)
head(gisaid_australia_shared_dateweek)

fit_australia_multi_predsbystate <- FitMultinomStatewiseDaily(gisaid_australia_shared_dateweek)
head(fit_australia_multi_predsbystate)

Plot Smooth Muller Plots

muller_australiabystate_mfit <- PlotMullerDailyPrevalence(fit_australia_multi_predsbystate, ncol = 3)
muller_australiabystate_mfit

saketkc/covmuller documentation built on April 19, 2024, 10:14 a.m.