example_report.Rmd

---
title: "ISARIC-4C data example report"
date: "`r Sys.time()`"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(tidyverse)
library(lubridate)
library(finalfit)
library(kableExtra)

# Save image to spare the API:
# source("00_source_all.R")
# save.image(file = "00_source_all.RData")
load("00_source_all.RData")
```


## Admissions plot


```{r admissions_plot, message=FALSE, warning=FALSE}
topline %>%
  filter(sex != "Not specified") %>% 
  filter(hostdat < Sys.Date()) %>% 
  arrange(hostdat) %>% 
  group_by(sex) %>% 
  mutate(
    cum = seq_along(hostdat)
  ) %>%  
  drop_na(sex) %>% 
  ggplot_lancet(aes(x = hostdat, y = cum, colour = sex)) +
  geom_line() +
  scale_colour_brewer(palette = "Set1") +
  labs(x = "Admission date", y = "Number of patients") +
  theme(legend.position = c(0.05, 1),
        legend.justification = c(0, 1)) +
  # facet_wrap(.~sex) +
  coord_cartesian(xlim = c(ymd(20200201,NA))) +
  ggtitle("Hospital admission with COVID-19 by sex",
          "Figure 1A")
```

## Demographics table

```{r dem_table, warning=FALSE}
topline %>% 
  mutate_if(is.factor, fct_explicit_na) %>% 
  summary_factorlist(
    explanatory = c(
      "age", "sex",
      "healthwork_erterm", "labwork_erterm",  
      "onset2admission",
      "hooccur", 
      "travel_erterm"), 
    na_include = TRUE, 
    add_col_totals = TRUE
  ) %>% 
  mytable(longtable = FALSE)
```