index.Rmd

---
title: "Steno Register-based Project: {{< var project.title >}}"
author:
  - name: Luke W. Johnston
    orcid: 0000-0003-4169-2616
    affiliations: 
        - name: Steno Diabetes Center Aarhus
        - name: Aarhus University
  - name: Omar Silverman
    affiliations: 
        - name: Steno Diabetes Center Aarhus
        - name: Aarhus University
  - name: Gunnar Toft
    affiliations: 
        - name: Steno Diabetes Center Aarhus
        - name: Aarhus University
---

The sidebar contains the applications sent to each of the different. If
you want to browse all the variables and registers we've requested, use
the table below.

## Searchable table

```{r setup}
#| message: false
#| warning: false
#| echo: false
#| column: page
#| tbl-cap: "Registers and variables requested from DST (as a searchable table)."
library(tidyverse)
library(here)
library(glue)
library(reactable)
source(here("R/functions.R"))
needed_registers <- here("data/needed-registers.csv") %>%
  read_csv(col_types = "lddccccc") %>%
  filter(!drop | is.na(drop))

dst_variables <- read_csv(here("data/dst-registers-with-variables-to-use.csv"))
dst_variables <- dst_variables %>%
  filter(
    register_id %in% unique(needed_registers$register_id)
  ) %>%
  mutate(across(ends_with("year"), str_extract, pattern = "^\\d{4}")) %>%
  mutate(
    start_year = case_when(
      is.na(variable_start_year) |
        variable_start_year == variable_end_year ~
        register_start_year,
      TRUE ~ variable_start_year
    ),
    year_range = glue::glue("{start_year} - {variable_end_year}")
  ) %>%
  mutate(across(ends_with("year"), as.numeric))

sds_variables <- read_csv(here("data/sds-registers-with-variables-to-use.csv"))
sds_variables <- sds_variables %>%
  mutate(periode = str_replace(periode, "\\s?-\\s?$", "-Latest")) %>%
  mutate(
    start_year = str_extract(periode, "^\\d{4}"),
    end_year = str_extract(periode, "-\\d{4}$")
  ) %>%
  mutate(across(ends_with("year"), as.numeric))

random_registers <- read_csv(here("data/random-undocumented.csv")) %>%
  mutate(
    start_year = if_else(is.na(start_year), "Earliest", as.character(start_year)),
    year_range = glue::glue("{start_year} - {end_year}")
  ) %>%
  mutate(across(ends_with("year"), as.numeric))

joined_registers <- list(
  dst_variables %>%
    select(
      "Register ID" = register_id,
      "Register" = register_name_dk,
      "Variable" = variable_name,
      "Start year" = variable_start_year,
      "End year" = variable_end_year,
      "Description" = description_english,
    ),
  sds_variables %>%
    select(
      "Register" = register_name,
      "Database Table" = table_name,
      "Variable" = variable_name,
      "Start year" = start_year,
      "End year" = end_year,
      "Description" = variable_description
    ),
  random_registers %>%
    select(
      "Register" = register_name,
      "Database Table" = register_table_name,
      "Variable" = variable_name,
      "Start year" = start_year,
      "End year" = end_year,
      "Description" = variable_description_dk
    )
) %>%
  reduce(bind_rows) 

joined_registers %>%
  as_reactable()
```

## Full variable list

```{r}
#| message: false
#| warning: false
#| echo: false
#| column: page
#| tbl-cap: "Registers and variables requested from DST (fully displayed list)."
options(knitr.kable.NA = "")
joined_registers %>% 
  knitr::kable()
```