apsimx_soil_profile: Create APSIM-X Soil Profiles

In femiguez/apsimx: Inspect, Read, Edit and Run 'APSIM' "Next Generation" and 'APSIM' Classic

Create APSIM-X Soil Profiles

Description

Generates a soil profile that can then replace the existing one in an ‘.apsimx’ or ‘.apsim’ simulation file

plotting function for a soil profile, it requires ‘ggplot2’

checking an apsimx soil profile for reasonable values

Usage

apsimx_soil_profile(
  nlayers = 10,
  Depth = NULL,
  Thickness = NULL,
  BD = NULL,
  AirDry = NULL,
  LL15 = NULL,
  DUL = NULL,
  SAT = NULL,
  KS = NULL,
  crop.LL = NULL,
  crop.KL = NULL,
  crop.XF = NULL,
  Carbon = NULL,
  SoilCNRatio = NULL,
  FOM = NULL,
  FOM.CN = NULL,
  FBiom = NULL,
  FInert = NULL,
  NO3N = NULL,
  NH4N = NULL,
  PH = NULL,
  ParticleSizeClay = NULL,
  ParticleSizeSilt = NULL,
  ParticleSizeSand = NULL,
  soil.bottom = 150,
  water.table = 200,
  soil.type = 0,
  crops = c("Maize", "Soybean", "Wheat"),
  metadata = NULL,
  soilwat = NA,
  swim = NA,
  initialwater = NA,
  soilorganicmatter = NA,
  dist.parms = list(a = 0, b = 0.2),
  check = TRUE
)

## S3 method for class 'soil_profile'
plot(
  x,
  ...,
  property = c("all", "water", "initialwater", "BD", "AirDry", "LL15", "DUL", "SAT",
    "KS", "Carbon", "SoilCNRatio", "FOM", "FOM.CN", "FBiom", "FInert", "NO3N", "NH4N",
    "PH")
)

check_apsimx_soil_profile(x, particle.density = 2.65)

Arguments

nlayers	Number of soil layers (default = 10)
Depth	specific depths for each soil layer (cm)
Thickness	thickness for each soil layer (mm)
BD	bulk density for each soil layer (g/cc) – ‘cc’ is cubic cm
AirDry	air dry for each soil layer (mm/mm)
LL15	lower limit (15 bar) for each soil layer (mm/mm)
DUL	drainage upper limit (0.33 bar) for each soil layer (mm/mm)
SAT	saturation (0 bar) for each soil layer (mm/mm)
KS	saturated hydraulic conductivity (mm/day)
crop.LL	lower limit for a specific crop
crop.KL	root ability to extract water for a specific crop
crop.XF	soil root exploration for a specific crop
Carbon	organic carbon (percent)
SoilCNRatio	organic carbon C:N ratio
FOM	fresh organic matter (kg/ha)
FOM.CN	fresh organic matter C:N ratio
FBiom	Fraction of microbial biomass (0-1)
FInert	Fraction of inert carbon (0-1)
NO3N	nitrate nitrogen (Chemical) (ppm)
NH4N	ammonium nitrogen (Chemical) (ppm)
PH	soil pH
ParticleSizeClay	particle size clay (in percent)
ParticleSizeSilt	particle size silt (in percent)
ParticleSizeSand	particle size sand (in percent)
soil.bottom	bottom of the soil profile (cm)
water.table	water table level (not used at the moment) (cm)
soil.type	might use it in the future for auto filling missing information
crops	name of crops being grown
metadata	list with soil metadata. For possible parameters and values see an example of inspect_apsimx with soil.child = “Metadata”.
soilwat	optional ‘list’ of class ‘soilwat_parms’
swim	optional ‘list’ of class ‘swim_parms’
initialwater	optional ‘list’ of class ‘initialsoilwater_parms’
soilorganicmatter	optional ‘list’ of class ‘soilorganicmatter_parms’
dist.parms	parameter values for creating a profile. If a == 0 and b == 0 then a constant value of 1 is used. If a == 0 and b != 0, then an exponential decay is used. If a != 0 and b != 0 then the equation is a*soil.layer*exp(-b*soil.layer).
check	whether to check for reasonable values using check_apsimx_soil_profile
x	object of class ‘soil_profile’ or the ‘soil’ component within an object of class ‘soil_profile’.
...	additional plotting arguments (none use at the moment).
property	“all” for plotting all soil properties, “water” for just SAT, DUL and LL15
particle.density	default value for soil particle density (2.65 g/cm3)

Details

Soil Profiles

Real soils might have discontinuities, but for APSIM it might be beneficial to be able to create a soil profile with an arbitrary number of layers and have flexibility in the distribution of soil physical and chemical properties. Steps:

1. apsimx_soil_profile is a function which can create a soil matrix with many layers
2. It allows for creating a smooth distribution for Physical (or Water), Chemical, InitialWater, Analysis, InitialN, Organic or SoilOrganicMatter
3. The distribution can be specified with the ‘a’ and ‘c’ parameter of an exponential decay function, using a list. E.g. DUL = list(0.35, 0, -0.1). This means that the top value for DUL will be 0.35 and it will decay with a rate of -0.1.
4. If an increase and then a decay is needed the Ricker function can be used. See ‘SSricker’ in the ‘nlraa’ package.

The value of soil particle density (2.65 g/cm3) is hard coded in APSIM. https://en.wikipedia.org/wiki/Bulk_density

Value

a soil profile with class ‘soil_profile’ with elements ‘soil’, ‘crops’, ‘metadata’, ‘soilwat’ and ‘swim’.

it produces a plot

It does not produce output unless potential issues are found. Only warnings are produced and it returns an object of class ‘soil_profile’.

Examples

 sp <- apsimx_soil_profile()
 require(ggplot2)
 plot(sp)
 

femiguez/apsimx documentation built on April 13, 2024, 12:04 a.m.