Summary.Rmd

---
title: "Weekly Testing Dataset Summary"
author: "Cam Appel"
date: "03/04/2021"
output: md_document
---
# Weekly Testing Dataset Summary `r Sys.Date()`
```{r, echo=FALSE, warning=FALSE,message=FALSE}
library(readr)
library(lubridate)
library(dplyr)

# inactive countries
data <- read_csv(url("https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/testing/covid-testing-all-observations.csv")) %>%
  select(1, 3, 4) %>%
  group_by(Entity) %>%
  summarise(max(Date), `Source URL` = first(`Source URL`), Counts=n())
data['active'] <- NA
for (i in 1:nrow(data)) {
  if(data[[i,2]] > Sys.Date()-21) {
    data$active[[i]] = "active"
  } else {
    data$active[[i]] = "inactive"
  } 
}

inactive <- filter(data, active == "inactive")


names(inactive)[2] <- 'Last updated'
inactive <- inactive[, c(1,2,3,4)]
inactive <- inactive[order(inactive$`Last updated`),]

# missing countries
# df_loc <- data
# df_loc$Entity <- gsub("[^ ][^-]*$","",data$Entity) %>%
#   trimws()
# df_pop <- read_csv("https://raw.githubusercontent.com/owid/covid-19-data/master/scripts/input/un/population_2020.csv")
# 
# miss <- list()
# 
# for (i in df_pop$entity) {
#   match <- i %in% df_loc$Entity
#   if(!match) {
#     miss[[length(miss)+1]] <- i
#   }
# }
```
## Out of date countries:
```{r echo=FALSE}
knitr::kable(inactive)
```
## Missing countries:
```{r echo=FALSE}
# cat(paste('-',miss),sep='\n')
```

<iframe src="https://ourworldindata.org/grapher/countries-included-in-the-covid-19-testing-dataset" loading="lazy" style="width: 100%; height: 600px; border: 0px none;"></iframe>