Extracts model outputs

Function extract() extracts daily or subdaily output and returns it as a tidy data frame.

Usage

extract(
  x,
  level = "forest",
  output = NULL,
  vars = NULL,
  dates = NULL,
  subdaily = FALSE,
  addunits = FALSE
)

Arguments

x

An object returned by simulation functions spwb, aspwb, pwb, growth or fordyn.

level

Level of simulation output, either "forest" (stand-level results), "soillayer" (soil layer-level results), "cohort" (cohort-level results), "sunlitleaf" or "shadeleaf" (leaf-level results)

output

Section of the model output to be explored. See details.

vars

Variables to be extracted (by default, all of them).

dates

A date vector indicating the subset of simulated days for which output is desired.

subdaily

A flag to indicate that subdaily values are desired (see details).

addunits

A flag to indicate that variable units should be added whenever possible.

Value

Function extract() returns a data frame:

• If level = "forest", columns are "date" and variable names.

• If level = "soillayer", columns are "date", "soillayer" and variable names.

• If level = "cohort", level = "sunlitleaf" or level = "shadeleaf", columns are "date", "cohorts", "species" and variable names.

• If subdaily = TRUE, columns are "datetime", "cohorts", "species" and variable names.

Details

When subdaily = FALSE, parameter output is used to restrict the section in x where variables are located. For example output = "Plants" will correspond to variables "LAI", "LAIlive", "Transpiration", "StemPLC",... as returned by a call names(x$Plants).

Option subdaily = TRUE only works when simulations have been carried using control option 'subdailyResults = TRUE' (see defaultControl). When using subdaily = TRUE, parameter output is not taken into account, and options for parameter vars are the following:

• Variables for level = "forest" or level = "soillayer": Not allowed. An error is raised.

• Variables for level = "cohort": "E","Ag","An","dEdP","RootPsi","StemPsi","LeafPsi","StemPLC","StemRWC","LeafRWC","StemSympRWC","LeafSympRWC","PWB".

• Variables for level = "shadeleaf" and level="sunlitleaf": "Abs_SWR","Abs_PAR","Net_LWR","E","Ag","An","Ci","Gsw","VPD","Temp","Psi","iWUE".

See also

summary.spwb

Author

Miquel De Cáceres Ainsa, CREAF

Examples

#Load example daily meteorological data
data(examplemeteo)

#Load example plot plant data
data(exampleforest)

#Default species parameterization
data(SpParamsMED)

#Define soil with default soil params (4 layers)
examplesoil <- defaultSoilParams(4)

#Initialize control parameters
control <- defaultControl("Granier")

#Initialize input
x <- spwbInput(exampleforest,examplesoil, SpParamsMED, control)

#Call simulation function (ten days)
S1<-spwb(x, examplemeteo[1:10, ], latitude = 41.82592, elevation = 100)
#> Initial plant water content (mm): 4.67289
#> Initial soil water content (mm): 290.875
#> Initial snowpack content (mm): 0
#> Performing daily simulations
#> 
#>  [Year 2001]:
#> 
#> Final plant water content (mm): 4.67283
#> Final soil water content (mm): 294.931
#> Final snowpack content (mm): 0
#> Change in plant water content (mm): -5.80248e-05
#> Plant water balance result (mm): -5.80248e-05
#> Change in soil water content (mm): 4.05632
#> Soil water balance result (mm): 4.05632
#> Change in snowpack water content (mm): 0
#> Snowpack water balance result (mm): 0
#> Water balance components:
#>   Precipitation (mm) 39 Rain (mm) 34 Snow (mm) 5
#>   Interception (mm) 7 Net rainfall (mm) 26
#>   Infiltration (mm) 32 Infiltration excess (mm) 0 Saturation excess (mm) 0 Capillarity rise (mm) 0
#>   Soil evaporation (mm) 3  Herbaceous transpiration (mm) 0  Woody plant transpiration (mm) 3  Mistletoe transpiration (mm) 0
#>   Plant extraction from soil (mm) 3  Plant water balance (mm) -0 Hydraulic redistribution (mm) 0
#>   Runoff (mm) 0 Deep drainage (mm) 22

#Extracts daily forest-level output as a data frame
extract(S1, level = "forest", addunits = TRUE)
#> Error in UseMethod("extract"): no applicable method for 'extract' applied to an object of class "c('spwb', 'list')"

#Extracts daily soil layer-level output as a data frame
extract(S1, level = "soillayer", addunits = TRUE)
#> Error in UseMethod("extract"): no applicable method for 'extract' applied to an object of class "c('spwb', 'list')"

#Extracts daily cohort-level output as a data frame
extract(S1, level = "cohort", addunits = TRUE)
#> Error in UseMethod("extract"): no applicable method for 'extract' applied to an object of class "c('spwb', 'list')"

#Select the output tables/variables to be extracted
extract(S1, level ="cohort", output="Plants", vars = c("PlantStress", "StemPLC"))
#> Error in UseMethod("extract"): no applicable method for 'extract' applied to an object of class "c('spwb', 'list')"