oxcovid19.R
In oxcovid19: An R API to the Oxford COVID-19 Database

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----workflow, echo = FALSE, eval = FALSE, fig.width = 8, fig.height = 10, fig.pos = "center"----
#  DiagrammeR::grViz("
#    digraph oxcovid19 {
#  
#      # a 'graph' statement
#      graph [overlap = false, fontsize = 12, fontname = Helvetica]
#  
#      # Terminal nodes
#      node [shape = oval, width = 1.5, penwidth = 2, fontsize = 14]
#  
#      a [label = '@@1'; color = darkgreen; fontcolor = darkgreen];
#      h [label = '@@8'; color = crimson; fontcolor = crimson];
#  
#      # Input/output nodes
#      node [shape = parallelogram, fixedsize = true, height = 1, width = 1.5, penwidth = 2, color = royalblue1, fontcolor = royalblue1]
#  
#      b [label = '@@2'];
#  
#      # Process nodes
#      node [shape = rect]
#  
#      d [label = '@@4'];
#      f [label = '@@6'];
#  
#      # Package nodes
#      node [shape = oval, fixedsize = TRUE, width = 2, penwidth = 2, fontsize = 10, fontname = Courier, color = darkviolet, fontcolor = darkviolet]
#  
#      c [label = '@@3';];
#      e [label = '@@5'];
#      g [label = '@@7'];
#  
#      edge [minlen = 2, arrowsize = 0.75, penwidth = 2, color = dimgray]
#  
#      a -> b
#      b -> d
#      d -> f
#      f -> h
#  
#      edge [minlen = 3]
#  
#      b -> c
#      c -> b
#      d -> e
#      e -> d
#      f -> g
#      g -> f
#  
#      subgraph {
#        rank = same; b; c;
#      }
#  
#      subgraph {
#        rank = same; d; e;
#      }
#  
#      subgraph {
#        rank = same; f; g;
#      }
#  
#    }
#  
#      [1]: 'START'
#      [2]: 'Step 1:\\nConnect\\nto server'
#      [3]: 'oxcovid19\\nconnect_oxcovid19()'
#      [4]: 'Step 2:\\nRetrieve\\ntable'
#      [5]: 'oxcovid19\\nget_table; get_layer'
#      [6]: 'Step 3:\\nQuery\\ntable'
#      [7]: 'dplyr - filter; select\\nsf - st_read'
#      [8]: 'END'
#  ")

## ----workflowB, echo = FALSE, eval = TRUE, out.width = "80%", fig.align = "center"----
knitr::include_graphics("../man/figures/oxcovid19workflow.png")

## ----workflow1, echo = TRUE, eval = TRUE--------------------------------------
library(oxcovid19)

## Step 1: Create a connection to OxCOVID19 PostgreSQL server
con <- connect_oxcovid19()

## Step 2: Access epidemiology table from OxCOVID19 PostgreSQL server
epi_tab <- get_table(con = con, tbl_name = "epidemiology")

## Step 3: Query the epidemiology table to show data for Great Britain
gbr_epi_tab <- dplyr::filter(.data = epi_tab, countrycode == "GBR")

## ----workflow2, echo = FALSE, eval = TRUE-------------------------------------
gbr_epi_tab

## ----workflow3, echo = TRUE, eval = TRUE--------------------------------------
## Load magrittr to use pipe operator %>%
library(magrittr)

connect_oxcovid19() %>%
  get_table(tbl_name = "epidemiology") %>%
  dplyr::filter(countrycode == "GBR")