SoPhy {SoPhy} | R Documentation

## Soil physics tools

### Description

This package provides a collection of tools that might be useful in soil physics. It is a first version of work in progress.

### Details

Currently, the following functionalities are provided:

- Physical modelling
  - `swms2d` : R interface to SWMS_2d, an algorithm by Simunek et. al based on finite elements to simulate water flux and solute transport in soil
  - `xswms2d` : interactive plot to define soil structure and to simulate water flux and solute transport
  - various functions for the modified simulation of the water flux or the solute transport in a profile; see `calculate.horizons` for an example
- Stochastic modelling
  - `flowpattern` stochastic simulation of dye tracer profiles
- Estimation of the risk index
  - `analyse.profile` : analysis of Brilliant Blue tracer experiments w.r.t. the contamination risk index
  - `BrilliantBlue` : examples of profile pictures
  - `Pareto` : the Pareto distribution
  - `risk.index` : esimation of the risk index
- Estimation of the variability of the tortuosity
  - `tortuosity` : estimation of tortuosity from Brilliant Blue tracer experiments
- Graphics
  - `my.legend` : legend giving a colour spectrum
  - `quader` : tools for 3d perspective plot
  - `read.picture`, `plotRGB` : Conversion of tiff pictures to RGBA array and plotting RGB figures
- Code used in publications by Schlather and Huwe
  - `sh.jh` : Schlather, M. and Huwe, B. (2005a)
  - `sh.jch` : Schlather, M. and Huwe, B. (2005b)

### Acknowledgement

The author thanks Rien van Genuchten, Carl A. Mendoza, Rene Therrien, and Edward Sudicky for kindly changing the former copyright to the GNU copyleft licence, hence making their code directly available for this package.

The work has been financially supported by the German Federal Ministry of Research and Technology (BMFT) grant PT BEO 51-0339476C during 2000-03.

### Installation

LINUX: The tiff-library is avalailable from http://www.remotesensing.org/libtiff. SuSe-users install libtiff and libtiff-devel.

WINDOWS: The binaries are available from gnuwin32.sourceforge.net/packages/tiff.htm. Before starting the R session, add in the system variable $PATH the path to the libtiff3.dll file; the standard path to be added is C:\Programme\GnuWin32\bin. Further, make sure that zlib1.dll and jpeg62.dll are present.

### Author(s)

Martin Schlather, schlath@hsu-hh.de http://www.unibw-hamburg.de/WWEB/math/schlath/schlather.html

The Fortran code has been published as ‘swms_2d’ by Jirka Simunek, T. Vogel and Martinus Th. van Genuchten, http://www.ussl.ars.usda.gov/MODELS/MODELS.HTM; the file ORTHOFEM.f was written by Edward A. Sudicky and Carl A. Mendoza, based on code by Frank W. Letniowshi and contributions by Rene Therrien, and modified by Jirka Simunek.

### References

Schlather, M. (2006) SOPHY - a package for the simulation and the analysis of water flux in soil In preparation

Schlather, M. and Huwe, B. (2005a) A stochastic model for 3-dimensional flow patterns in dye tracer experiments. J. Hydrol. 310, 17-27.

Schlather, M. and Huwe, B. (2005b) A risk index for characterising flow pattern in soils using dye tracer distributions J. Contam. Hydrol. 79, to appear.

Schlather, M. and Huwe, B. (2006) Modelling inhomogeneous soils: Part I, Theory In preparation

Schlather, M. and Huwe, B. (2006) SOPHY - an interactive programme for water flow modelling In preparation

Schlather, M., Zeilinger, J. and Huwe, B. (2006) Modelling inhomogeneous soils: Part II, Applications In preparation

Simunek., J., Vogel, T., and van Genuchten, M.Th. (1994) The SWMS_2D code for simulating water flow and solute transport in two-dimensional variably saturated media, Version 1.21. Research Report No. 132, 197 p., U.S. Salinity Laboratory, USDA, ARS, Riverside, California.

[Package SoPhy version 1.0.28 Index]