liuyanguu/coverage_plot

Make descriptive plots for COVerAGE-DB: COVID-19 cases, deaths, and tests by age and sex

COVerAge_Plot : Age Pyramid for the COVerAGE-DB Dataset

COVerAGE-DB dataset project page

Plots using the harmonized dataset (Output_5.zip)

The Github page (updated in February 2022) shows the aggregated plots for global cases and deaths based on the 5-year age interval harmonized datasets from COVerAGE-DB The pages are rendered from the .Rmd files.

Age distribution of global COVID-19 cases and deaths

Age distribution of global COVID-19 cases and deaths by sex

Plots using the raw input dataset (inputDB.zip)

Notice that it's harder to work on the input database directly now since it is quite large (~1.5GB). The cleaning step might take an hour.

The script plot_raw_dataset.R walks through the process

Download raw data from OSF: https://osf.io/mpwjq/

source("plotting_funcs.R") # all the plotting functions
source("00_Functions_convert_to_count.R") # borrow to distribute total if Metric is "Fraction"
inputDB <- refresh_data() # re-download and calculate fraction into numbers 

This cleaning step might take an hour:

dt1 <- clean_inputDB(inputDB = inputDB)

Country-specific plot

• Age pyramid for each country showing Cases, Deaths, and CFR (Death/Case), whichever is available
• Showing sex-specific if available
• Showing in title the latest date used as it is different for each country

all_countries <- get_cnames(dt1)
cname0 <- all_countries[1]
p1 <- make_country_plot(cname0)

Aggregated plots for all countries

• Only choose those with both case and death data with matching age intervals, thus can calculate CFR
• By assigning a common age interval, only those countries whose age interval are adaptable are used (i.e. through combining intervals into a wider one, 0-5 & 5-10 -> 0-10)
• Fewer countries will be included if set a stricter/narrower interval, or set get_f_m = TRUE to ask for sex-specific data

# this example shows the countries available with 0 to 80 by 10 years age intervals
data_total1 <- rbindlist(lapply(all_countries, get_dt_for_total, 
                                data = dt1,
                                target_interval = seq(0, 80, by = 10),
                                get_f_m = TRUE))
# a three-panel plot (Case, Death, CFR) for a specific given interval
g1 <- plot_aggregated_total(data_total1)

coverage_plot's Issues

Save pictures for readme

Example of country age-pyramid

Example of aggregated age-pyramid

All in one