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README-africa.Rmd
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README-africa.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
dpi=200,
comment = "#>",
fig.path = "man/figures/README-africa-",
out.width = "100%"
)
```
# COVID19analytics
<!-- . -->
This package curate (downloads, clean, consolidate, smooth) [data from Johns Hokpins](https://github.com/CSSEGISandData/COVID-19/) for analysing international outbreak of COVID-19.
It includes several visualizations of the COVID-19 international outbreak.
Yanchang Zhao, COVID-19 Data Analysis with Tidyverse and Ggplot2 - China. RDataMining.com, 2020.
URL: http://www.rdatamining.com/docs/Coronavirus-data-analysis-china.pdf.
* COVID19DataProcessor generates curated series
* [visualizations](https://www.r-bloggers.com/coronavirus-data-analysis-with-r-tidyverse-and-ggplot2/) by [Yanchang Zhao](https://www.r-bloggers.com/author/yanchang-zhao/) are included in ReportGenerator R6 object
* More visualizations included int ReportGeneratorEnhanced R6 object
* Visualizations ReportGeneratorDataComparison compares all countries counting epidemy day 0 when confirmed cases > n (i.e. n = 100).
# Consideration
Data is still noisy because there are missing data from some regions in some days. We are working on in it.
# Package
<!-- badges: start -->
| Release | Usage | Development |
|:--------|:------|:------------|
| | [](https://cran.r-project.org/) | [](https://travis-ci.org/rOpenStats/COVID19analytics) |
| [](https://cran.r-project.org/package=COVID19analytics) | | [](https://codecov.io/gh/rOpenStats/COVID19analytics) |
|||[](https://www.repostatus.org/#active)|
<!-- badges: end -->
# How to get started (Development version)
Install the R package using the following commands on the R console:
```R
# install.packages("devtools")
devtools::install_github("rOpenStats/COVID19analytics", build_opts = NULL)
```
# How to use it
```{r load}
library(COVID19analytics)
library(dplyr)
```
```{r}
data.processor <- COVID19DataProcessor$new(provider = "JohnsHopkingsUniversity", missing.values = "imputation")
#dummy <- data.processor$preprocess() is setupData + transform is the preprocess made by data provider
dummy <- data.processor$setupData()
dummy <- data.processor$transform()
# Curate is the process made by missing values method
dummy <- data.processor$curate()
current.date <- max(data.processor$getData()$date)
rg <- ReportGeneratorEnhanced$new(data.processor)
rc <- ReportGeneratorDataComparison$new(data.processor = data.processor)
top.countries <- data.processor$top.countries
international.countries <- unique(c(data.processor$top.countries,
"China", "Japan", "Singapore", "Korea, South"))
africa.countries <- sort(data.processor$countries$getCountries(division = "continent", name = "Africa"))
```
```{r}
# Top 10 daily cases confirmed increment
(data.processor$getData() %>%
filter(date == current.date) %>%
select(country, date, rate.inc.daily, confirmed.inc, confirmed, deaths, deaths.inc) %>%
arrange(desc(confirmed.inc)) %>%
filter(confirmed >=10))[1:10,]
```
```{r}
# Top 10 daily deaths increment
(data.processor$getData() %>%
filter(date == current.date) %>%
select(country, date, rate.inc.daily, confirmed.inc, confirmed, deaths, deaths.inc) %>%
arrange(desc(deaths.inc)))[1:10,]
```
```{r, dataviz-4-africa-countries}
rg$ggplotTopCountriesStackedBarDailyInc(included.countries = africa.countries,
countries.text = "Africa")
rc$ggplotComparisonExponentialGrowth(included.countries = africa.countries, min.cases = 20)
rg$ggplotCountriesLines(included.countries = africa.countries, countries.text = "Africa countries",
field = "confirmed.inc", log.scale = TRUE)
rc$ggplotComparisonExponentialGrowth(included.countries = africa.countries,
field = "deaths", y.label = "deaths", min.cases = 1)
```
```{r, dataviz-5-top-countries}
rg$ggplotTopCountriesStackedBarDailyInc(top.countries)
rc$ggplotComparisonExponentialGrowth(included.countries = international.countries,
min.cases = 100)
```
```{r, dataviz-6-top-countries-inc-daily}
rg$ggplotCountriesLines(field = "confirmed.inc", log.scale = TRUE)
rg$ggplotCountriesLines(field = "rate.inc.daily", log.scale = TRUE)
```
```{r, dataviz-7-top-countries-inc-legacy}
rg$ggplotTopCountriesPie()
rg$ggplotTopCountriesBarPlots()
rg$ggplotCountriesBarGraphs(selected.country = "Ethiopia")
```