Original papers
soilphysics: An R package for calculating soil water availability to plants by different soil physical indices

https://doi.org/10.1016/j.compag.2015.11.003Get rights and content

Highlights

  • We presented an R package called soilphysics.

  • Water availability to plants can be calculated.

  • LLWR and IWC indices can be determine through a few easy-to-use functions.

  • The salinity effect on soil available water was also employed for IWC index.

  • High-quality graphics are created for both indices.

Abstract

Soil available water is an important factor for plant growth. It has been estimated by different soil physical indices, such as the least limiting water range (LLWR), integral water capacity (IWC) and integral energy (EI). Moreover, salinity is an important limitation for soil water availability to plants. Despite the advances in the quantification of LLWR, IWC and EI, a comprehensive description of the computational methods, including data management, curve fitting procedures and graphing techniques, is still lacking. The salinity effect on these quantities has still not been implemented in a computer package. In this paper, we present an R package soilphysics and its implementations to determine LLWR, IWC and EI. We described the theory behind each implementation, illustrated the functionalities and validated the outcomes of soilphysics with other software packages for LLWR, IWC and EI calculations (an Excel® algorithm and SAWCal). The salinity effect on soil available water was also employed in the package. The outcomes are basically the same as other software available, with small differences (<4%). The package soilphysics takes advantage of all the power of R for dealing with extensive algorithms and for building high-quality graphics. It is currently available from the CRAN website (http://cran.r-project.org/web/packages/soilphysics/index.html).

Introduction

The concept of soil available water (SAW) for plants was stated by Veihmeyer and Hendrickson, 1927, Veihmeyer and Hendrickson, 1931 in its simplest form as the water content available between field capacity (FC) and wilting point (WP). The concept aims to estimate, by a soil physical index, the water available for plant growth.

Letey (1985) elaborated the concept of SAW by considering some soil physical factors that could restrict plants growth in addition to SAW, such as aeration and penetration resistance. He suggested the term non-limiting water range (NLWR) for which the limiting effects of aeration, penetration resistance and matric head are non-limiting. Then, Silva et al. (1994) quantitatively developed the concept introduced by Letey (1985), and renamed it the least limiting water range (LLWR).

The LLWR is an important index for the evaluation of soil physical quality and soil available water, as it allows the integration of three main plant growth-limiting factors (i.e. penetration resistance, aeration and soil water potential) into a single parameter (Silva et al., 1994, Leão et al., 2005, Leão and da Silva, 2004, Guedes Filho et al., 2013), which is related to the bulk density variation.

Groenevelt et al. (2001) introduced the integral water capacity (IWC) to determine the SAW. In order to calculate SAW by the IWC approach, continuous weighting functions accounting for various soil physical restrictions are multiplied by the differential water capacity (C(h)) and the effective values of C(h) are integrated over the full matric head (h) range (Asgarzadeh et al., 2014). Groenevelt et al. (2001) presented the IWC theory and considered four limiting factors at wet and dry ranges. At the wet range, they considered rapid drainage by gravity and lack of sufficient aeration. At the dry range, the low hydraulic conductivity and root penetrability were considered. The weighting functions were constructed as functions of the matric head so that they ranged between zero and unity at appropriate limits (Asgarzadeh et al., 2014).

In addition to limiting factors used by Groenevelt et al. (2001) and Asgarzadeh et al. (2014) for calculating the IWC, Groenevelt et al. (2004) proposed a weighting function to account for the effect of salinity on the water available for plants. Salinity can significantly decrease the SAW through the osmotic effect.

The energy required for plants to remove a defined amount of water from the soil is also considered as an index of soil water availability. Minasny and McBratney (2003) introduced the integral energy (EI) concept to quantify the energy required of a plant to take up an unit amount of water from the soil at a given water content or matric head range (Asgarzadeh et al., 2014). This concept was extended for the LLWR and IWC (Asgarzadeh et al., 2011, Asgarzadeh et al., 2014) to quantify the energy required to extract water in the LLWR and IWC ranges.

Many researchers have used the LLWR and IWC approaches to evaluate soil physical quality (e.g. Asgarzadeh et al., 2010, Asgarzadeh et al., 2014, Guedes Filho et al., 2013). These researchers considered the LLWR and IWC as important indicators of SAW for plant growth.

According to Leão et al. (2005) and Asgarzadeh et al. (2014), despite advances in the quantification of the LLWR, IWC and EI, a detailed description of the computational methodology for calculating these indexes from soil properties data, including data management, curve fitting procedures, and graphing techniques, is still lacking. In addition, salinity effect on these quantities has not been included in a user-friendly computer package so far. Leão and da Silva (2004) and Leão et al. (2005) proposed a simplified algorithm for calculation of the LLWR using the spreadsheet software Microsoft Excel® and Statistical Analysis System (SAS), respectively. Asgarzadeh et al. (2014) proposed a software called SAWCal (Soil Available Water Calculator) to calculate LLWR, IWC, and EI. These algorithms and softwares are important tools for determination and popularization of soil physical indices.

The software R (R Core Team, 2015) is a distribution-free computing environment that receives contributions from researchers and experts in various fields of science worldwide. However, the packages destined for soil science are scarce (Omuto and Gumbe, 2009) and there is still no package that can deal with LLWR, IWC, and EI for the users of the R software.

In this paper, a computer program is presented which is available as an R package called soilphysics. With soilphysics, it is possible to determine the LLWR, IWC and EI by two simple functions, respectively. In addition to limiting factors used by Groenevelt et al. (2001) and Asgarzadeh et al. (2014) for calculation of the IWC, we included salinity effect (i.e. salinity weighting function) proposed by Groenevelt et al. (2004) as an option for users. The package produces graphics with high quality, included as outputs, when soilphysics is run. This package is a new interface for the calculations of plant available water quantities using R language. The package soilphysics is distribution-free and is available at CRAN (http://cran.r-project.org/).

Section snippets

Least limiting water range (LLWR)

The LLWR concept was introduced by Silva et al. (1994) as the integration of three main plant growth-limiting factors (i.e. soil penetration resistance, aeration and water potential) into a single parameter. The changes in the LLWR as a function of bulk density are considered (Guedes Filho et al., 2013). According to Silva et al. (1994), the LLWR can be described as follows:

  • (i)

    The soil water retention curve is determined as the relationship between the volumetric water content and matric head, as

The R package soilphysics

soilphysics is an easy-to-use R package which contains several functions relating to soil physics. The theory of LLWR and IWC was implemented into two functions: llwr() and iwc(), respectively. Users are required to pass simple input arguments. The outputs were designed to be concise and both functions provide didactic graphical solutions.

Function llwr()

The function llwr() needs the inputs required by the LLWR theory (Silva et al., 1994), which are essentially soil physical quantities, as follows:

llwr(theta, h, Bd, Pr,
 particle.density, air,
 critical.PR, h.FC, h.WP,
 water.model = c(“Silva”, “Ross”),
 Pr.model = c(“Busscher”, “noBd”),
 pars.water = NULL, pars.Pr = NULL,
 graph = TRUE, graph2 = TRUE,
 xlab = expression(Bulk∼Density∼(Mg∼m^{-3})),
 ylab = expression(theta∼(m^{3}∼m^{-3})),
 main = “Least Limiting Water Range”, …)
The user has two main options to

Determining llwr()

soilphysics uses Eqs. (1), (2), (3), (4), (5), (6), (7), (8), (9) for determining LLWR. Parameters are estimated using a self-start Newton–Raphson algorithm for non-linear fitting. After convergence, soilphysics outputs the summary and the statistical significance of the estimates for the water retention and penetration resistance curves. If convergence is not achieved, a warning message is printed on console.

The statistical significance for coefficients of both the water retention (Eqs. (1) or

Illustrating LLWR

As an example, we used a data set also used by Leão and da Silva (2004) (Table 1). They used a simplified Excel® algorithm for determining LLWR of a silt loam soil. This data set is available in soilphysics under the name skp1994. The columns BD, W, PR and h correspond to the values of dry bulk density, soil water content, soil penetration resistance and matric head, numeric vectors to be passed for the arguments Bb, theta, Pr and h, respectively. According to Leão and da Silva (2004), the

LLWR by llwr()

We compared the results calculated by llwr() function with those obtained using the Excel® algorithm presented by Leão and da Silva (2004). Results are shown in Table 2. Both algorithms have promoted the same values, with negligible differences.

IWC by iwc()

We also compared the results calculated by iwc() function with those obtained through SAWCal (Asgarzadeh et al., 2014) for the examples without considering salinity effect (Table 3). The results of both software (SAWCal and soilphysics) are essentially

Availability of soilphysics

soilphysics is freely available as an R (R Core Team, 2015) package from the Comprehensive R Archive Network (http://CRAN.R-project.org/package=soilphysics). Thus, users first need to download a recent version of R, which is also available from CRAN.

Conclusions

We have developed a user-friendly R package, called soilphysics, which has two functions related to available soil water, llwr() and iwc(), for determination of the least limiting water range (LLWR), the integral water capacity (IWC) and the integral energy (EI). In addition, we included an option for the user to calculate IWC by considering salinity effect on the soil available water.

We compared the LLWR, IWC and EI calculations by soilphysics with those obtained using a published MS Excel®

Acknowledgements

We thank the Coordination for Improvement of Higher Level Personnel (CAPES, Brazil) for granting scholarships, and the Goiano Federal Institute (Brazil) for the financial support, as well as to the referees of this paper for their thoughtful reviews.

References (21)

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