---
title: "amadeus workflow"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{amadeus workflow}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
date: "2024-07-29"
author: "Mitchell Manware"
---

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

The following vignette will demonstrate how to download, process, and calculate covariates using `amadeus` functions.
The examples will utilize air temperature at 2m height ("air.2m") data from the NOAA North American Regional Reanalysis (NARR) dataset.\insertRef{web_NARRabout}

## Download

Download data for years 2021 and 2022 with `download_data`.

```{r, eval = FALSE}
dir <- tempdir()
download_data(
  dataset_name = "narr",
  variable = "air.2m",
  year = c(2021, 2022),
  directory_to_save = dir,
  acknowledgement = TRUE,
  download = TRUE,
  remove_command = TRUE
)
```

Check for the downloaded files.

```{r, eval = FALSE}
list.files(paste0(dir, "/air.2m"))
```
```{r, echo = FALSE}
cat('[1] "air.2m.2021.nc" "air.2m.2022.nc"\n')
```

## Process

Process data for all dates from December 28, 2021 to January 3, 2022 with `process_covariates`.

```{r, eval = FALSE}
temp_process <- process_covariates(
  covariate = "narr",
  variable = "air.2m",
  date = c("2021-12-28", "2022-01-03"),
  path = paste0(dir, "/air.2m")
)
```

Check the processed `SpatRaster` object.

```{r, eval = FALSE}
temp_process
```
```{r, echo = FALSE}
cat(
"class       : SpatRaster 
dimensions  : 277, 349, 7  (nrow, ncol, nlyr)
resolution  : 32462.99, 32463  (x, y)
extent      : -16231.49, 11313351, -16231.5, 8976020  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=lcc +lat_0=50 +lon_0=-107 +lat_1=50 +lat_2=50 +x_0=5632642.22547 +y_0=4612545.65137 +datum=WGS84 +units=m +no_defs 
sources     : air.2m.2021.nc:air  (4 layers) 
              air.2m.2022.nc:air  (3 layers) 
varnames    : air (Daily Air Temperature at 2 m) 
              air (Daily Air Temperature at 2 m) 
names       : air.2~11228, air.2~11229, air.2~11230, air.2~11231, air.2~20101, air.2~20102, ... 
unit        :           K,           K,           K,           K,           K,           K, ... 
time        : 2021-12-28 to 2022-01-03 UTC\n"
)
```

## Calculate covariates

Calculate covariates for North Carolina county boundaries with `calculate_covariates`.
County boundaries are accessed with the `tigris::counties` function.\insertRef{package_tigris}
`geom = TRUE` will return the covariates as a `SpatVector` object.

```{r, eval = FALSE}
library(tigris)
temp_covar <- calculate_covariates(
  covariate = "narr",
  from = temp_process,
  locs = tigris::counties("NC", year = 2021),
  locs_id = "NAME",
  radius = 0,
  geom = TRUE
)
```

Check the calculated covariates `SpatVector` object.

```{r, eval = FALSE}
temp_covar
```
```{r, echo = FALSE}
cat(
"class       : SpatVector 
geometry    : polygons 
dimensions  : 700, 3  (geometries, attributes)
extent      : 7731783, 8506154, 3248490, 3694532  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=lcc +lat_0=50 +lon_0=-107 +lat_1=50 +lat_2=50 +x_0=5632642.22547 +y_0=4612545.65137 +datum=WGS84 +units=m +no_defs 
names       :     NAME       time air.2m_0
type        :    <chr>   <POSIXt>    <num>
values      :   Chatham 2021-12-28    289.3
               Alamance 2021-12-28    288.8
               Davidson 2021-12-28    289.1\n")
```