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Soil initialization

Source: R/RcppExports.R, R/summary.soil.R
soil.Rd

Initializes soil parameters and state variables for its use in simulations.

Usage

soil(x, VG_PTF = "Toth")

# S3 method for class 'soil'
summary(object, model = "SX", ...)

Arguments

x

A data frame of soil parameters (see an example in defaultSoilParams).

VG_PTF

Pedotransfer functions to obtain parameters for the van Genuchten-Mualem equations. Either "Carsel" (Carsel and Parrish 1988) or "Toth" (Toth et al. 2015).

object

An object of class soil.

model

Either 'SX' or 'VG' for Saxton or Van Genuchten pedotransfer models.

...

Additional parameters to summary.

Value

Function soil returns a data frame of class soil with the following columns:

  • widths: Width of soil layers (in mm).

  • sand: Sand percentage for each layer (in percent volume).

  • clay: Clay percentage for each layer (in percent volume).

  • om: Organic matter percentage for each layer (in percent volume).

  • nitrogen: Sum of total nitrogen (ammonia, organic and reduced nitrogen) for each layer (in g/kg).

  • rfc: Percentage of rock fragment content for each layer.

  • macro: Macroporosity for each layer (estimated using Stolf et al. 2011).

  • Ksat: Saturated soil conductivity for each layer (in mmol·m-1·s-1·MPa-1, estimated using function soil_saturatedConductivitySX.

  • VG_alpha, VG_n, VG_theta_res, VG_theta_sat: Parameters for van Genuchten's pedotransfer functions, for each layer, corresponding to the USDA texture type.

  • W: State variable with relative water content of each layer (in as proportion relative to FC).

  • Temp: State variable with temperature (in ºC) of each layer.

Details

Function summary prompts a description of soil characteristics and state variables (water content and temperature) according to a water retention curve (either Saxton's or Van Genuchten's). Volume at field capacity is calculated assuming a soil water potential equal to -0.033 MPa. Parameter Temp is initialized as missing for all soil layers.

If available, the user can specify columns VG_alpha, VG_n, VG_theta_res, VG_theta_sat and K_sat, to override Van Genuchten parameters an saturated conductivity estimated from pedotransfer functions when calling function soil.

References

Carsel, R.F., and Parrish, R.S. 1988. Developing joint probability distributions of soil water retention characteristics. Water Resources Research 24: 755–769.

Tóth, B., Weynants, M., Nemes, A., Makó, A., Bilas, G., and Tóth, G. 2015. New generation of hydraulic pedotransfer functions for Europe. European Journal of Soil Science 66: 226–238.

Stolf, R., Thurler, A., Oliveira, O., Bacchi, S., Reichardt, K., 2011. Method to estimate soil macroporosity and microporosity based on sand content and bulk density. Rev. Bras. Ciencias do Solo 35, 447–459.

See also

soil_redefineLayers, soil_psi2thetaSX, soil_psi2thetaVG, spwb, defaultSoilParams

Author

Miquel De Cáceres Ainsa, CREAF

Examples

# Default parameters
df_soil <- defaultSoilParams()

# Initializes soil
s = soil(df_soil)
s
#>   widths sand clay      usda om nitrogen  bd rfc  macro     Ksat VG_alpha
#> 1    300   25   25 Silt loam NA       NA 1.5  25 0.0485 5401.471 89.16112
#> 2    700   25   25 Silt loam NA       NA 1.5  45 0.0485 5401.471 89.16112
#> 3   1000   25   25 Silt loam NA       NA 1.5  75 0.0485 5401.471 89.16112
#> 4   2000   25   25 Silt loam NA       NA 1.5  95 0.0485 5401.471 89.16112
#>       VG_n VG_theta_res VG_theta_sat W Temp
#> 1 1.303861        0.041     0.423715 1   NA
#> 2 1.303861        0.041     0.423715 1   NA
#> 3 1.303861        0.041     0.423715 1   NA
#> 4 1.303861        0.041     0.423715 1   NA

# Prints soil characteristics according to Saxton's water retention curve
summary(s, model="SX")
#> Soil depth (mm): 4000 
#> 
#> Layer  1  [ 0  to  300 mm ] 
#>     clay (%): 25 silt (%): 50 sand (%): 25 organic matter (%): NA [ Silt loam ]
#>     Rock fragment content (%): 25 Macroporosity (%): 5 
#>     Theta WP (%): 14 Theta FC (%): 30 Theta SAT (%): 49 Theta current (%) 30 
#>     Vol. WP (mm): 32 Vol. FC (mm): 68 Vol. SAT (mm): 111 Vol. current (mm): 68 
#>     Temperature (Celsius): NA 
#> 
#> Layer  2  [ 300  to  1000 mm ] 
#>     clay (%): 25 silt (%): 50 sand (%): 25 organic matter (%): NA [ Silt loam ]
#>     Rock fragment content (%): 45 Macroporosity (%): 5 
#>     Theta WP (%): 14 Theta FC (%): 30 Theta SAT (%): 49 Theta current (%) 30 
#>     Vol. WP (mm): 55 Vol. FC (mm): 117 Vol. SAT (mm): 190 Vol. current (mm): 117 
#>     Temperature (Celsius): NA 
#> 
#> Layer  3  [ 1000  to  2000 mm ] 
#>     clay (%): 25 silt (%): 50 sand (%): 25 organic matter (%): NA [ Silt loam ]
#>     Rock fragment content (%): 75 Macroporosity (%): 5 
#>     Theta WP (%): 14 Theta FC (%): 30 Theta SAT (%): 49 Theta current (%) 30 
#>     Vol. WP (mm): 36 Vol. FC (mm): 76 Vol. SAT (mm): 123 Vol. current (mm): 76 
#>     Temperature (Celsius): NA 
#> 
#> Layer  4  [ 2000  to  4000 mm ] 
#>     clay (%): 25 silt (%): 50 sand (%): 25 organic matter (%): NA [ Silt loam ]
#>     Rock fragment content (%): 95 Macroporosity (%): 5 
#>     Theta WP (%): 14 Theta FC (%): 30 Theta SAT (%): 49 Theta current (%) 30 
#>     Vol. WP (mm): 14 Vol. FC (mm): 30 Vol. SAT (mm): 49 Vol. current (mm): 30 
#>     Temperature (Celsius): NA 
#> 
#> Total soil saturated capacity (mm): 473 
#> Total soil water holding capacity (mm): 291 
#> Total soil extractable water (mm): 183 
#> Total soil current Volume (mm): 291 
#> Saturated water depth (mm): NA 
#> 

# Prints soil characteristics according to Van Genuchten's water retention curve
summary(s, model="VG")
#> Soil depth (mm): 4000 
#> 
#> Layer  1  [ 0  to  300 mm ] 
#>     clay (%): 25 silt (%): 50 sand (%): 25 organic matter (%): NA [ Silt loam ]
#>     Rock fragment content (%): 25 Macroporosity (%): 5 
#>     Theta WP (%): 13 Theta FC (%): 30 Theta SAT (%): 42 Theta current (%) 30 
#>     Vol. WP (mm): 29 Vol. FC (mm): 68 Vol. SAT (mm): 95 Vol. current (mm): 68 
#>     Temperature (Celsius): NA 
#> 
#> Layer  2  [ 300  to  1000 mm ] 
#>     clay (%): 25 silt (%): 50 sand (%): 25 organic matter (%): NA [ Silt loam ]
#>     Rock fragment content (%): 45 Macroporosity (%): 5 
#>     Theta WP (%): 13 Theta FC (%): 30 Theta SAT (%): 42 Theta current (%) 30 
#>     Vol. WP (mm): 49 Vol. FC (mm): 117 Vol. SAT (mm): 163 Vol. current (mm): 117 
#>     Temperature (Celsius): NA 
#> 
#> Layer  3  [ 1000  to  2000 mm ] 
#>     clay (%): 25 silt (%): 50 sand (%): 25 organic matter (%): NA [ Silt loam ]
#>     Rock fragment content (%): 75 Macroporosity (%): 5 
#>     Theta WP (%): 13 Theta FC (%): 30 Theta SAT (%): 42 Theta current (%) 30 
#>     Vol. WP (mm): 32 Vol. FC (mm): 76 Vol. SAT (mm): 106 Vol. current (mm): 76 
#>     Temperature (Celsius): NA 
#> 
#> Layer  4  [ 2000  to  4000 mm ] 
#>     clay (%): 25 silt (%): 50 sand (%): 25 organic matter (%): NA [ Silt loam ]
#>     Rock fragment content (%): 95 Macroporosity (%): 5 
#>     Theta WP (%): 13 Theta FC (%): 30 Theta SAT (%): 42 Theta current (%) 30 
#>     Vol. WP (mm): 13 Vol. FC (mm): 30 Vol. SAT (mm): 42 Vol. current (mm): 30 
#>     Temperature (Celsius): NA 
#> 
#> Total soil saturated capacity (mm): 407 
#> Total soil water holding capacity (mm): 291 
#> Total soil extractable water (mm): 194 
#> Total soil current Volume (mm): 291 
#> Saturated water depth (mm): NA 
#> 

# Add columns 'VG_theta_sat' and 'VG_theta_res' with custom values
df_soil$VG_theta_sat <- 0.400 
df_soil$VG_theta_res <- 0.040 

# Reinitialize soil (should override estimations)
s2 = soil(df_soil)
s2
#>   widths sand clay      usda om nitrogen  bd rfc  macro     Ksat VG_alpha
#> 1    300   25   25 Silt loam NA       NA 1.5  25 0.0485 5401.471 89.16112
#> 2    700   25   25 Silt loam NA       NA 1.5  45 0.0485 5401.471 89.16112
#> 3   1000   25   25 Silt loam NA       NA 1.5  75 0.0485 5401.471 89.16112
#> 4   2000   25   25 Silt loam NA       NA 1.5  95 0.0485 5401.471 89.16112
#>       VG_n VG_theta_res VG_theta_sat W Temp
#> 1 1.303861         0.04          0.4 1   NA
#> 2 1.303861         0.04          0.4 1   NA
#> 3 1.303861         0.04          0.4 1   NA
#> 4 1.303861         0.04          0.4 1   NA
summary(s2, model="VG")
#> Soil depth (mm): 4000 
#> 
#> Layer  1  [ 0  to  300 mm ] 
#>     clay (%): 25 silt (%): 50 sand (%): 25 organic matter (%): NA [ Silt loam ]
#>     Rock fragment content (%): 25 Macroporosity (%): 5 
#>     Theta WP (%): 12 Theta FC (%): 29 Theta SAT (%): 40 Theta current (%) 29 
#>     Vol. WP (mm): 27 Vol. FC (mm): 64 Vol. SAT (mm): 90 Vol. current (mm): 64 
#>     Temperature (Celsius): NA 
#> 
#> Layer  2  [ 300  to  1000 mm ] 
#>     clay (%): 25 silt (%): 50 sand (%): 25 organic matter (%): NA [ Silt loam ]
#>     Rock fragment content (%): 45 Macroporosity (%): 5 
#>     Theta WP (%): 12 Theta FC (%): 29 Theta SAT (%): 40 Theta current (%) 29 
#>     Vol. WP (mm): 47 Vol. FC (mm): 110 Vol. SAT (mm): 154 Vol. current (mm): 110 
#>     Temperature (Celsius): NA 
#> 
#> Layer  3  [ 1000  to  2000 mm ] 
#>     clay (%): 25 silt (%): 50 sand (%): 25 organic matter (%): NA [ Silt loam ]
#>     Rock fragment content (%): 75 Macroporosity (%): 5 
#>     Theta WP (%): 12 Theta FC (%): 29 Theta SAT (%): 40 Theta current (%) 29 
#>     Vol. WP (mm): 30 Vol. FC (mm): 72 Vol. SAT (mm): 100 Vol. current (mm): 72 
#>     Temperature (Celsius): NA 
#> 
#> Layer  4  [ 2000  to  4000 mm ] 
#>     clay (%): 25 silt (%): 50 sand (%): 25 organic matter (%): NA [ Silt loam ]
#>     Rock fragment content (%): 95 Macroporosity (%): 5 
#>     Theta WP (%): 12 Theta FC (%): 29 Theta SAT (%): 40 Theta current (%) 29 
#>     Vol. WP (mm): 12 Vol. FC (mm): 29 Vol. SAT (mm): 40 Vol. current (mm): 29 
#>     Temperature (Celsius): NA 
#> 
#> Total soil saturated capacity (mm): 384 
#> Total soil water holding capacity (mm): 275 
#> Total soil extractable water (mm): 182 
#> Total soil current Volume (mm): 275 
#> Saturated water depth (mm): NA 
#>