Initial commit

.Rprofile

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+source("renv/activate.R")

.gitignore

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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

analysis.R

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+library(tidyverse)
+library(janitor)
+
+# Get core data
+url <- "https://github.com/owid/covid-19-data/raw/master/public/data/owid-covid-data.csv"
+owid <- read_csv(url)
+
+# Get supplmental, auxilliary, hospitalisation data
+hosp_url <- "https://github.com/owid/covid-19-data/raw/master/public/data/hospitalizations/covid-hospitalizations.csv"
+hosp <- read_csv(hosp_url)
+hosp <-
+  hosp |>
+  pivot_wider(
+    id_cols = c("entity", "iso_code", "date"),
+    names_from = indicator,
+    values_from = value,
+    names_repair = \(x) make_clean_names(x) |> paste0("_aux")
+  ) |>
+  rename(
+    entity = entity_aux,
+    iso_code = iso_code_aux,
+    date = date_aux
+  )
+
+countries <- c("AUS", "NZL", "USA", "GBR", "CAN", "DEU", "FRA", "AUT", "BEL",
+  "SGP", "DNK", "ISR", "ITA", "JPN", "KOR", "NLD", "FIN", "NOR", "SWE", "ESP",
+  "CHE")
+start_date <- as.Date("2021-09-01")
+
+# Explore core OWID data
+
+owid |>
+  filter(
+    iso_code %in% countries,
+    date >= start_date
+  ) |>
+  select(
+    iso_code,
+    continent,
+    location,
+    new_cases_smoothed_per_million,
+    new_tests_smoothed_per_thousand,
+    people_fully_vaccinated_per_hundred,
+    hosp_patients_per_million,
+    weekly_hosp_admissions_per_million,
+    icu_patients_per_million,
+    weekly_icu_admissions_per_million,
+    new_deaths_smoothed_per_million,
+  ) |>
+  pivot_longer(
+    cols = !c("iso_code", "continent", "location"),
+  ) |>
+  group_by(iso_code, name) |>
+  summarise(n = n(), not_na = sum(!is.na(value))) |>
+  pivot_wider(
+    id_cols = name,
+    names_from = iso_code,
+    values_from = not_na
+  )
+
+# Explore aux hospitalisation data
+
+hosp |>
+  filter(
+    iso_code %in% countries,
+    date >= start_date
+  ) |>
+  pivot_longer(
+    cols = !c("entity", "iso_code", "date")
+  ) |>
+  group_by(iso_code, name) |>
+  summarise(n = n(), notna = sum(!is.na(value))) |>
+  pivot_wider(
+    id_cols = name,
+    names_from = iso_code,
+    values_from = notna
+  )
+
+# Join core with aux hospitalisatio data
+
+owid_aug <-
+  owid |>
+  left_join(hosp, by = c("iso_code", "location" = "entity", "date")) |>
+  filter(
+    iso_code %in% countries,
+    date >= start_date
+  )
+owid_aug |>
+  select(iso_code, date, contains("icu")) |>
+  filter(iso_code == "GBR")
+
+# Looks like the aux data is already in the core data set. Ignore this going
+# forward
+
+
+owid_long_tbl <-
+  owid |>
+  filter(
+    iso_code %in% countries,
+    date >= start_date
+  ) |>
+  select(
+    iso_code,
+    location,
+    date,
+    # "Tests conducted per new confirmed case of COVID-19, given as a rolling
+    #  7-day average (this is the inverse of positive_rate)"
+    new_tests_smoothed_per_thousand,
+    new_cases_smoothed_per_million,
+    tests_per_case,
+    hosp_patients_per_million, # stock, not flow.
+    icu_patients_per_million,  # stock, not flow.
+    new_deaths_smoothed_per_million
+  ) |>
+  pivot_longer(
+    cols = !c("iso_code", "location", "date"),
+    names_to = "indicator",
+    values_to = "value"
+  )
+
+ggplot(owid_long_tbl, aes(x = date, y = value, colour = iso_code)) +
+  geom_point(size = 0.5) +
+  facet_wrap(vars(indicator), scales = "free_y") +
+  theme_light()
+
+
+
+
+

covidanalysis.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes