amadeus workflow

Mitchell Manware

2024-07-29

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.

Download

Download data for years 2021 and 2022 with download_data.

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.

list.files(paste0(dir, "/air.2m"))
[1] "air.2m.2021.nc" "air.2m.2022.nc"

Process

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

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.

temp_process
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

Calculate covariates

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

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.

temp_covar
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