README.md

In julienmoeys/rmacrolite: R interface for the pesticide fate models MACRO In FOCUS and MACRO

R interface for MACRO, a model of water flow and solute transport in macroporous soil, or its regulatory variant MACRO In FOCUS. The package provides functions to read, write and modify the model parameter files (.par-files). Parameter modifications are done either with low-level generic functions, or with high-level functions designed for specific parameters or groups of parameters. High-level functions are currently limited to modifications of the substance properties.

rmacrolite was written as an infrastructure for the R packages macroutils2 and macrounchained

rmacrolite is derived from the R package rmacro, written by the author while at the Center for Chemical Pesticides (CKB), Swedish University of Agricultural Sciences (SLU), during the R&D project PERFORM (2013-2016; Funding: "Pour et Sur le Plan Ecophyto" (PSPE)). Compared to rmacro, the package has been significantly refactored, and there is no backward compatibility. Compared to rmacro, rmacrolite does not contain any MACRO-executable, and it uses an existing installation of MACRO or MACRO In FOCUS.

• Development status: pre-release. Do not use for production purpose, as the interface may still evolve if needed.

• General information: See DESCRIPTION (including author(s), package-version, minimum R version required, ...).

• Change log: See NEWS.

• Operating system: rmacrolite will only work on Windows, because MACRO is a Windows-only program.

• License: MIT License. See LICENSE.

Either MACRO or MACRO In FOCUS or both need to be installed for using rmacrolite (see below).

Installation

End-users should manually install the package from Windows binary package (a .zip-archive). The binary package provided on the website indicated below are presumably stable versions of the package, for release or pre-release (see status above).

Experienced users and developers may prefer to install the development version of the package, from GitHub. The later should not be seen as a stable version and may not work at all.

Before you install the package, check in the DESCRIPTION file what is the minimum version of R needed to run this package (field "Depends", see "R (>= ...)"). As I don't have time to test the package on multiple R major versions, the package will generally require the latest major-release at the time of testing the latest (pre-)release of the package. If needed, the code can be loaded as an R-script instead of installed as a package (see below), and used on any R-version presumably compatible with the code.

Installing the package from Windows binaries

Windows binary-installer (a .zip file) and source tar of the package (a .tar.gz file) can be downloaded from the following address: https://rpackages.julienmoeys.info/macrounchained/.

Choose both the binary-installer for rmacrolite and macroutils2.

Save the files to a local folder on your computer.

As I cannot guarantee the integrity of the website above, it is recommended to scan the file(s) with an antivirus, not least if you work in a corporation or a public institution.

Do not unpack the .zip archive (nor the .tar.gz archive) before installing the package.

See also: https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Windows-packages

Method 1 (R graphical user interface for Windows):

Open R graphical user interface for Windows. Click on the 'Packages'-menu and select 'Install package(s) from local zip file...'. Select the package .zip binary package that you just downloaded, so that it is installed. When done, type library("macroutils2") and then library("rmacrolite") to check if the installation was successful.

Method 2 (install the zip binary package using the command line):

Open R command line prompt or R graphical user interface for Windows and type:

install.packages( 
    pkgs = "C:/path/to/binary/file/macroutils2_x.y.z.zip", 
    repos = NULL ) 
install.packages( 
    pkgs = "C:/path/to/binary/file/rmacrolite_x.y.z.zip", 
    repos = NULL ) 

where C:/path/to/binary/file/ should be replaced by the actual path to the folder where the binary package was downloaded and macroutils2_x.y.z.zip and rmacrolite_x.y.z.zip by the actual file-names (x.y.z being the version number, different for different packages). It is important to use a slash (/) as path separator, or alternatively a double backslash (\\), instead of a single backslash (\; Windows standard), as the later is a reserved character in R.

Method 3 (install the source package using the command line:

Open R command line prompt or R graphical user interface for Windows and type:

install.packages( 
    pkgs = "C:/path/to/source/file/macroutils2_x.y.z.tar.gz", 
    repos = NULL, type = "source" ) 
install.packages( 
    pkgs = "C:/path/to/source/file/rmacrolite_x.y.z.tar.gz", 
    repos = NULL, type = "source" ) 

where C:/path/to/source/file/ should be replaced by the actual path to the folder where the source package was downloaded and macroutils2_x.y.z.tar.gz and rmacrolite_x.y.z.tar.gz by the actual file-name (x.y.z being the version number). See above the remark on the path separator.

Installing the package from GitHub

This method is reserved for experienced R users and developers. If you don't know what you are doing, choose one of the installation method above.

The development version of macroutils2 is publicly available on GitHub (here), as well as the development version of rmacrolite (here)

to install the development version of the packages, you will need to install the package devtools first. It is available on CRAN and can be easily installed. Simply type install.packages("devtools") in R command prompt. See also the package README page.

You can then install the development version of macroutils2 and rmacrolite by typing in R command prompt:

devtools::install_github("julienmoeys/macroutils2")
devtools::install_github("julienmoeys/rmacrolite")

Source the package as an R script instead of installing the package

It is also possible to source the package as an R-script instead of installing the package. This method has some drawbacks (help pages not available; R workspace polluted with many objects otherwise invisible to end-users; sourced-code may be accidentally modified by the user; lack of traceability), but may be useful to some users, for example with restricted possibilities to install new R packages, as a bootstrap.

First, open the following .r-file https://raw.githubusercontent.com/julienmoeys/rmacrolite/master/R/rmacrolite.r and save it on your computer. This file contains the full R source code of the package.

Open R command line prompt or R graphical user interface for Windows and type:

library("macroutils2") 
source( "C:/path/to/file/rmacrolite.r" ) 

where C:/path/to/file/ should be replaced by the actual path to the folder where the file was downloaded. See above the remark on the path separator.

About

This package is a personal project of the author. It is not funded or supported by any corporation or public body.

Report issues

Your are very welcome to report any (suspected) error or issue on this page: https://github.com/julienmoeys/rmacrolite/issues

Before reporting on this page, try to reproduce the issue on a generic example that you can provide together with your issue.

User Support

Currently, I cannot provide user-support for this tool. In my experience, many questions are general R questions rather than questions specific to my R packages, so it may help to get support from an experienced R programmer.

Credits

The original version of this tool (rmacro`) was funded by the R&D project PERFORM (2013-2016; Funding: "Pour et Sur le Plan Ecophyto" (PSPE)), in a collaboration between INRA Versailles-Grignon (Sabine Karen Lammoglia and Laure Mamy) and SLU Uppsala (Julien Moeys, with a significant contribution from Mats Larsbo concerning the core MACRO model).

Disclaimer

This tool is not an official regulatory tool.

It is not endorsed by FOCUS DG SANTE, SLU/CKB or the author's employer.

It does not engage these institutions nor reflects any official position on regulatory exposure assessment.

Indeed, the website of FOCUS DG SANTE "is the one and only definitive source of the currently approved version of the FOCUS scenarios and associated models and input files.". Thus, please refer to FOCUS DG SANTE or to the competent authorities in each EU regulatory zone for guidance on officially accepted tools and methods.

As stated in the LICENSE, the package is provided without any warranty.

julienmoeys/rmacrolite documentation built on May 22, 2019, 6:31 p.m.