matched_groups.Rmd

---
title: "Matched groups"
author: "Jan Savinc"
date: "15/07/2020"
output: html_document
editor_options: 
  chunk_output_type: console
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

# Libraries

```{r}
library(tidyverse)
library(readxl)
library(lubridate)
library(knitr)
```

# Load data

Note: these are the eDRIS-provided provisional matches, not the final matches used in the analysis!

```{r}
group2 <- read_excel(path = "../group2_controls.xlsx", trim_ws = TRUE) %>% mutate(group = "pre-ICJ, Glasgow")
group3 <- read_excel(path = "../group3_controls.xlsx", trim_ws = TRUE) %>% mutate(group = "same period, RoS")
```

# Overlap of individuals between groups

```{r}
table_individuals_counts <-
  tribble(
    ~group, ~N,
    "ICJ individuals, total", n_distinct(c(group2$id,group3$id)),
    "ICJ individuals with 2 controls", n_distinct(intersect(group2$id,group3$id)),
    "ICJ individuals with only pre-ICJ Glasgow controls", n_distinct(base::setdiff(group2$id, group3$id)),
    "ICJ individuals with only RoS controls", n_distinct(base::setdiff(group3$id, group2$id)),
    "Pre-ICJ Glasgow controls", n_distinct(group2$id_c),
    "RoS controls", n_distinct(group3$id_c)
  ) %>% mutate(
    Percent = if_else(condition = str_starts(group,"ICJ"), true = scales::percent(N/n_distinct(c(group2$id,group3$id))), false = "")
  )

table_individuals_counts %>% kable(caption = "Number of individuals in cases & controls")
```

# Time period

```{r}
table_time_periods <- 
  bind_rows(
    bind_rows(group2,group3) %>% select(id, AssessmentStartDate, INCIDENCE_DATE) %>% mutate(group = "ICJ") %>% distinct,
    group2 %>% select(INCIDENCE_DATE=INCIDENCE_DATE_c, group),
    group3 %>% select(INCIDENCE_DATE=INCIDENCE_DATE_c, group)
  ) %>%
    group_by(group) %>%
    summarise(
      "ICJ use" = paste0(year(min(AssessmentStartDate)),"-",year(max(AssessmentStartDate))),
      "Cancer incidence" = paste0(year(min(INCIDENCE_DATE)),"-",year(max(INCIDENCE_DATE)))
    )

table_time_periods %>% kable(caption = "Time periods of data for cases & controls")
```