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| /doc/ | ||
| /Meta/ | ||
| inst/doc | ||
| inst/extdata/air.2m | ||
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| --- | ||
| 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) | ||
| ``` | ||
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| 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} | ||
|
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| ## Download | ||
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| Download data for years 2021 and 2022 with `download_data`. | ||
|
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| ```{r, eval = FALSE} | ||
| download_data( | ||
| dataset_name = "narr", | ||
| variable = "air.2m", | ||
| year = c(2021, 2022), | ||
| directory_to_save = "./inst/extdata", | ||
| acknowledgement = TRUE, | ||
| download = TRUE, | ||
| remove_command = TRUE | ||
| ) | ||
| ``` | ||
|
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| Check for the downloaded files. | ||
|
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| ```{r, eval = FALSE} | ||
| list.files("./inst/extdata/air.2m") | ||
| ``` | ||
| ```{r, echo = FALSE} | ||
| cat('[1] "air.2m.2021.nc" "air.2m.2022.nc"\n') | ||
| ``` | ||
|
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| ## Process | ||
|
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| Process data for all dates from December 28, 2021 to January 3, 2022 with `process_covariates`. | ||
|
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| ```{r, eval = FALSE} | ||
| temp_process <- process_covariates( | ||
| covariate = "narr", | ||
| variable = "air.2m", | ||
| date = c("2021-12-28", "2022-01-03"), | ||
| path = "./inst/extdata/air.2m" | ||
| ) | ||
| ``` | ||
|
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| Check the processed `SpatRaster` object. | ||
|
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| ```{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" | ||
| ) | ||
| ``` | ||
|
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| ## Calculate covariates | ||
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| Calculate covariates for North Carolina county boundaries with `calc_covariates`. | ||
| County boundaries are accessed with the `tigris::counties` function.\insertRef{package_tigris} | ||
| `geom = TRUE` will return the covariates as a `SpatVector` object. | ||
|
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| ```{r, eval = FALSE} | ||
| library(tigris) | ||
| temp_covar <- calc_covariates( | ||
| covariate = "narr", | ||
| from = temp_process, | ||
| locs = tigris::counties("NC", year = 2021), | ||
| locs_id = "NAME", | ||
| radius = 0, | ||
| geom = TRUE | ||
| ) | ||
| ``` | ||
|
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| Check the calculated covariates `SpatVector` object. | ||
|
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| ```{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") | ||
| ``` |