In tjtnew/reportfactory: Lightweight Infrastructure for Handling Multiple Rmarkdown Documents

knitr::opts_chunk$set(echo = TRUE, collapse = TRUE, fig.width = 8, fig.height = 6, dpi = 150)

This is an example report to illustrate how reportfactory can be used. It uses a cutdown snapshot of NHS pathways data that is available in the outbreaks package. These data include all reports classified as ‘potential COVID-19 cases’ notified via calls to 111, 999, and 111-online systems. These data are not confirmed cases, and are subject to unknown reporting biases.

library(here)
library(incidence2)
dat <- read.csv(here("data", "raw", "example_data.csv"))
inci <- incidence(dat, date, groups = nhs_region, count = count)
if (params$grouped_plot) {
  plot(inci, angle = 45, ylab = "", title = "Reports by date", centre_ticks = TRUE)
} else {
  facet_plot(inci, angle = 45, ylab = "", title = "Reports by day", centre_ticks = TRUE)
}

tjtnew/reportfactory documentation built on Dec. 31, 2020, 8:40 a.m.