v4.1.5 Fix phantom incorporation effect and add NEWS.md

See release title above.

Full Changelog: v4.1.3...v4.1.5
Or: ed5e90b...f1fb70f

v4.1.3 Documentation update and other small improvements

Corrections to documentation in alfam2.Rd, where the description of the parameter sets had been outdated in v4.0.
Some other improvements as well.
See NEWS.md for details.
This version is on CRAN.

v4.0 First CRAN version

This is the first version on CRAN.

More minor improvements

Minor improvements related to unusual uses of the alfam2 function, including use of flatout option with incorporation, extreme parameter values, and preparation for parameter set 3.

Bug fix

There was a bug in the add.incorp.rows option related to the row order. Interval emission and flux for any added row (but not cumulative emission) could have been wrong, maybe usually obviously wrong. This new version should no longer have this problem.

Avoiding errors in incorporation inputs

Version 3.5 accepts NAs in both incorporation time and incorporation method columns with mixed scenarios (with and without incorporation).

Faster evaluation with C++/Rcpp, more checks, r5 par

Version 3.2 of the ALFAM2 package has the core calculations in C++ code, giving a major improvement in speed. This version also includes several more checks of input data with more helpful warning or error messages than the defaults. A new r5 parameter has been added, requiring changes in core equations for the size of pools and emission over time. But it is not yet present in the included parameter sets, so has no effect for most users.

Simpler function name alfam2() and small improvements

The model function can be called with alfam2() instead of the original ALFAM2mod() now (although the original name is still an alias, and so still works as before). This version also includes some new checks to input arguments and associated warning messages, that should make use easier.

You can install this release directly within R with

devtools::install_github('sashahafner/ALFAM2@v2.0')

To update (if you already have ALFAM2 installed), remove the older version first with this

remove.packages('ALFAM2')

Fix parallel processing bug

This release addresses a bug present in v1.5.0 and earlier versions related to the use of the parallel argument.

You can install this release directly within R with

devtools::install_github('sashahafner/ALFAM2@v1.5.1')

Automatic dummy variable prep and bug fix

Version 1.5.0 introduces a prep argument for automatic processing of dummy variables. By default it is FALSE, so the addition is backwards-compatible. When prep = TRUE ALFAM2mod() will create dummy variables for application method, incorporation, and manure source, significantly simplifying external data prep. See the updated vignette for more details.

A bug related to incorporation is also fixed in this release. It would have caused problems only when incorporation variables were FALSE or 0 but incorporation time was still specified as a numeric value.

You can install this release directly within R with

devtools::install_github('sashahafner/ALFAM2@v1.5.0')