Authors: Lianna Hovhannisyan, John Lee, Vadim Taskaev, Vanessa Yuen
The British Columbia Center for Disease Control (BCCDC) manages a range of provincial programs and clinics that contribute to public health and help control the spread of disease in BC. It administers and distributes the latest daily data on COVID-19 in British Columbia, which it provides in csv format along case-, lab- and regional-specific features as well as in comprehensive ArcGIS format via the COVID-19 webpage (under “Download the data”).
rbccovideeda leverages daily case-specific COVID-19 data, allowing users to conveniently download the latest case data, and - per specified date range interval - compute several key statistics, visualize time series progression along age-related and regional parameters, and generate exploratory data analysis in the form of histogram figures supporting on-demand analysis. COVID-19 case detail parameters extracted using this package:
You can install the development version of rbccovideda from GitHub with:
# install.packages("devtools")
devtools::install_github("UBC-MDS/rbccovideda")
get_data()
show_summary_stat()
plot_line_by_date()
plot_hist_by_cond()
Details documentation can be found on our Github page: https://ubc-mds.github.io/rbccovideda/
rbccovideda can be used to download and compute summary statistics, generate exploratory data analysis histogram plots, and plot time series chart data as follows:
## load library
library(rbccovideda)
library(dplyr, warn.conflicts = FALSE)
To download and save data from BCCDC, use get_data()
all_data <- get_data()
head(all_data)
#> # A tibble: 6 x 5
#> Reported_Date HA Sex Age_Group Classification_Reported
#> <date> <chr> <chr> <chr> <chr>
#> 1 2020-01-29 Out of Canada M 40-49 Lab-diagnosed
#> 2 2020-02-06 Vancouver Coastal F 50-59 Lab-diagnosed
#> 3 2020-02-10 Out of Canada F 20-29 Lab-diagnosed
#> 4 2020-02-10 Out of Canada M 30-39 Lab-diagnosed
#> 5 2020-02-18 Interior F 30-39 Lab-diagnosed
#> 6 2020-02-24 Fraser M 40-49 Lab-diagnosed
To generate summary statistics, call
show_summary_stat(startDate, endDate)
summary <- show_summary_stat("2022-01-01", "2022-01-31")
# to show the 15-columns tibble in a nice way
glimpse(summary)
#> Rows: 1
#> Columns: 15
#> $ total_cases_count <int> 327625
#> $ latest_date <date> 2022-02-01
#> $ latest_daily_cases_count <int> 1695
#> $ max_date <date> 2021-12-31
#> $ max_daily_cases_count <int> 4078
#> $ min_date <date> 2020-01-29
#> $ min_daily_cases_count <int> 1
#> $ max_age_group <chr> "20-29"
#> $ max_age_group_count <int> 67347
#> $ min_age_group <chr> "Unknown"
#> $ min_age_group_count <int> 90
#> $ max_region <chr> "Fraser"
#> $ max_region_count <int> 152269
#> $ min_region <chr> "Out of Canada"
#> $ min_region_count <int> 353
To plot a histogram by Age, use
plot_hist_by_cond("2021-01-01", "2021-12-31", "Age")
plot_hist_by_cond("2021-01-01", "2021-01-30", "Age")
To plot a time-series line chart, use
plot_line_by_date(startDate, endDate)
plot_line_by_date("2021-01-01", "2021-01-30")
Given the relatively adequate accessibility of latest aggregate COVID-19
data combined with its persistent impact on socio-economics since early
2020, there are some 40 related packages found in CRAN at time as of
January 2022. Examples of API wrapper packages that retrieve COVID-19
data include canadacovid
and
covidregionaldata,
while others provide functions to retrieve data, display summary
statistics and generate plots, such as
nCov2019 and
covid19.analytic. In
contrast to these existing packages, rbccovideda
provides a simple
user interface that focuses on the localized provincial context of
British Columbia, utilizing features specific to BCCDC’s data
administration conventions for generating a quick overview and on-demand
analysis of trends and statistics pertaining to age-related and regional
case characteristics.
Interested in contributing? Check out the contributing guidelines. Please note that this project is released with a Code of Conduct. By contributing to this project, you agree to abide by its terms.
Group 25 Contributors:
The rbccovideda
project was created by DSCI 524 (Collaborative
Software Development) Group 25 within the Master of Data Science program
at the University of British Columbia (2021-2022). It is licensed under
the terms of the MIT license.
R Packages, DSCI 524 Course Material (UBC MDS)
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