nert

The goal of {nert} is to provide access to Australian TERN (Terrestrial Ecosystem Research Network) data in your R session.

Installation

You can install the development version of {nert} from GitHub with:

o <- options() # store original options

options(pkg.build_vignettes = TRUE)

if (!require("pak")) {
  install.packages("pak")
}

pak::pak("AAGI-AUS/nert")
options(o) # reset options

Example: reading a COG as a spatial object

This is a basic example which shows you how you can fetch one day’s data from the SMIPS data (currently the only supported data set in TERN) and visualise it:

library(nert)
r <- read_smips(day = "2024-01-01")
#> Warning in check_tzones(e1, e2): 'tzone' attributes are inconsistent

# `autoplot` is re-exported from {tidyterra}
autoplot(r)
#> <SpatRaster> resampled to 501270 cells.

Extract Values Given Lat/Lon Values

Extract Soil Moisture for Corrigin and Merriden, WA and Tamworth, NSW given latitude and longitude values for each.

library(terra)
#> terra 1.8.42
df <- structure(
  list(
    location = c("Corrigin", "Merredin", "Tamworth"),
    x = c(117.87, 118.28, 150.84),
    y = c(-32.33, -31.48, -31.07)
  ),
  row.names = c(NA, -3L),
  class = "data.frame"
)

cog_df <- extract(x = r, y = df[, c("x", "y")], xy = TRUE)

cog_df <- cbind(df$location, cog_df)
names(cog_df) <- c("location", "ID", "smips_totalbucket_mm_20240101", "x", "y")
cog_df
#>   location ID smips_totalbucket_mm_20240101        x         y
#> 1 Corrigin  1                    0.06715473 117.8688 -32.33328
#> 2 Merredin  2                    0.22716530 118.2787 -31.48353
#> 3 Tamworth  3                   93.44989014 150.8408 -31.07365

Development

Dev Container

Set up the container.

devcontainer up --workspace-folder .

Run tests and check stuff.

devcontainer exec --workspace-folder . R -e "devtools::check()"

Render this file.

devcontainer exec --workspace-folder . R -e "devtools::build_readme()"

Citing {nert}

To cite nert:

citation("nert")
#> Warning in citation("nert"): could not determine year for 'nert' from package
#> DESCRIPTION file
#> To cite package 'nert' in publications use:
#> 
#>   Sparks A, Pipattungsakul W, Edson R, Rogers S, Moldovan M (2025).
#>   _nert: An API Client for TERN Data_. R package version 0.0.1,
#>   https://github.com/AAGI-AUS/nert, <https://aagi-aus.github.io/nert/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {nert: An API Client for TERN Data},
#>     author = {Adam H. Sparks and Wasin Pipattungsakul and Russell Edson and Sam Rogers and Max Moldovan},
#>     year = {2025},
#>     note = {R package version 0.0.1, https://github.com/AAGI-AUS/nert},
#>     url = {https://aagi-aus.github.io/nert/},
#>   }