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AU-BCE-EE / ALFAM2

Model and data on ammonia volatilization (loss) from field-applied manure
GNU General Public License v3.0
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ALFAM2

Model for ammonia volatilization (loss) from field-applied manure.

Maintainer

Sasha D. Hafner. Contact information here: https://www.au.dk/vis/person/sasha.hafner@bce.au.dk.

Installation

The ALFAM2 package is now on CRAN, so it can be installed in the normal way:

install.packages("ALFAM2")

This will install the latest version available on CRAN.

Earlier versions can still be found here on the ALFAM2 GitHub repository. And as package development continues, there will be times when the CRAN version is not the latest one. Installation of packages from GitHub requires a package called devtools. You can run the code below to install devtools and ALFAM2.

If you don't already have it, first install devtools from CRAN.

install.packages("devtools")

Then install the latest ALFAM2 release from this ALFAM2 repository with the following command.

devtools::install_github("AU-BCE-EE/ALFAM2@*release", build_vignettes = TRUE)

The build_vignettes argument is needed in order to get the vignette.

You can just pull from the master branch (AU-BCE-EE/ALFAM2), but you may get some new changes not yet included in a release. And you can get any specific release (e.g., to check out a specific version used in a particular paper) with the following syntax.

devtools::install_github("AU-BCE-EE/ALFAM2@v3.2", build_vignettes = TRUE)

See the Releases page for all available releases. The @v3.2 bit in the command above is from the release tag.

For other branches using the ref argument, but based on how the branches are used, this doesn't typically make sense for regular users.

Package use

Once the package is installed, load it.

library(ALFAM2)

And see a vignette to get started.

vignette("ALFAM2-start")

Or download the CRAN version here.

Citations

When referring to the ALFAM2 model predictions in publications, be sure to include

  1. the version of the software used (e.g., "R package version 4.1.8") and
  2. the parameter set used (e.g., "parameter set 3").

You can get citations to the R package and relevant publications with citation('ALFAM2') in R.

Model description

The following paper describes the model in some detail:

Hafner, S.D., Pacholski, A., Bittman, S., Carozzi, M., Chantigny, M., Génermont, S., Häni, C., Hansen, M.N., Huijsmans, J., Kupper, T., Misselbrook, T., Neftel, A., Nyord, T., Sommer, S.G., 2019. A flexible semi-empirical model for estimating ammonia volatilization from field-applied slurry. Atmospheric Environment 199: 474-484. https://doi.org/10.1016/j.atmosenv.2018.11.034

Download a copy here.

As shown in the figure below, the ALFAM2 model tracks applied ammonia (as "total ammoniacal nitrogen", TAN) after field application. The numerical value of the "primary" parameters shown below (r and f terms) determine the rate and trajectory of emission. The value of these parameters are determined by the value of predictor variables and the "secondary" parameter set.

schematic

Bugs and requests

Please use the Issues page.

Project information

See www.alfam.dk for more information and resources.