---
title: "Introduction"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Introduction}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r echo=FALSE, include=FALSE}
library(data.table)
library(magrittr)
```

# csfmt_rts_data_v2

`csfmt_rts_data_v2` (`vignette("csfmt_rts_data_v2", package = "cstidy")`) is the Core Surveillance data format for real-time surveillance of infectious diseases.

```{r}
d <- cstidy::generate_test_data()
cstidy::set_csfmt_rts_data_v2(d)

# Looking at the dataset
d[]
```

## Smart assignment

`csfmt_rts_data_v2` supports smart assignment for time and geography. When the **bold** variables below are set with `:=`, the associated variables are automatically derived.

**location_code**:

- granularity_geo
- country_iso3

**isoyear**:

- granularity_time
- isoweek
- isoyearweek
- season
- seasonweek
- calyear
- calmonth
- calyearmonth
- date

**isoyearweek**:

- granularity_time
- isoyear
- isoweek
- season
- seasonweek
- calyear
- calmonth
- calyearmonth
- date

**date**:

- granularity_time
- isoyear
- isoweek
- isoyearweek
- season
- seasonweek
- calyear
- calmonth
- calyearmonth

```{r}
d <- cstidy::generate_test_data()[1:5]
cstidy::set_csfmt_rts_data_v2(d)

# Looking at the dataset
d[]

# Smart assignment of time columns (note how granularity_time, isoyear, isoyearweek, date all change)
d[1,isoyearweek := "2021-01"]
d

# Smart assignment of time columns (note how granularity_time, isoyear, isoyearweek, date all change)
d[2,isoyear := 2019]
d

# Smart assignment of time columns (note how granularity_time, isoyear, isoyearweek, date all change)
d[4:5,date := as.Date("2020-01-01")]
d

# Smart assignment fails when multiple time columns are set
d[1,c("isoyear","isoyearweek") := .(2021,"2021-01")]
d

# Smart assignment of geo columns
d[1,c("location_code") := .("norge")]
d

# Collapsing down to different levels, and healing the dataset 
# (so that it can be worked on further with regards to real time surveillance)
d[, .(deaths_n = sum(deaths_n), location_code = "norge"), keyby=.(granularity_time)] %>%
  cstidy::set_csfmt_rts_data_v2(create_unified_columns = FALSE) %>%
  print()

# Collapsing to different levels, and removing the class csfmt_rts_data_v2 because
# it is going to be used in new output/analyses
d[, .(deaths_n = sum(deaths_n), location_code = "norge"), keyby=.(granularity_time)] %>%
  cstidy::remove_class_csfmt_rts_data() %>%
  print()
```

## Summary

`summary()` gives a concise overview of the data structure.

```{r}
cstidy::generate_test_data() %>%
  cstidy::set_csfmt_rts_data_v2() %>%
  summary()
```

## Identifying the data structure of one column

`cstidy::identify_data_structure()` inspects a single column and returns a plottable object.

```{r}
cstidy::generate_test_data() %>%
  cstidy::set_csfmt_rts_data_v2() %>%
  cstidy::identify_data_structure("deaths_n") %>%
  plot()
```