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,growthorfordyn.- 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"orlevel = "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"orlevel = "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"andlevel="sunlitleaf": "Abs_SWR","Abs_PAR","Net_LWR","E","Ag","An","Ci","Gsw","VPD","Temp","Psi","iWUE".
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): 4.69853
#> Initial soil water content (mm): 290.875
#> Initial snowpack content (mm): 0
#> Performing daily simulations
#>
#> [Year 2001]:
#>
#> Final plant water content (mm): 4.69847
#> Final soil water content (mm): 294.834
#> Final snowpack content (mm): 0
#> Change in plant water content (mm): -6.55784e-05
#> Plant water balance result (mm): -6.55784e-05
#> Change in soil water content (mm): 3.95915
#> Soil water balance result (mm): 3.95915
#> 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) 8 Net rainfall (mm) 26
#> Infiltration (mm) 31 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
#> 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)
#> date PET Precipitation Rain
#> 1 2001-01-01 0.8828475 [L/m^2] 4.869109 [L/m^2] 4.869109 [L/m^2]
#> 2 2001-01-02 1.6375337 [L/m^2] 2.498292 [L/m^2] 2.498292 [L/m^2]
#> 3 2001-01-03 1.3017026 [L/m^2] 0.000000 [L/m^2] 0.000000 [L/m^2]
#> 4 2001-01-04 0.5690790 [L/m^2] 5.796973 [L/m^2] 5.796973 [L/m^2]
#> 5 2001-01-05 1.6760567 [L/m^2] 1.884401 [L/m^2] 1.884401 [L/m^2]
#> 6 2001-01-06 1.2077028 [L/m^2] 13.359801 [L/m^2] 13.359801 [L/m^2]
#> 7 2001-01-07 0.6368075 [L/m^2] 5.377400 [L/m^2] 0.000000 [L/m^2]
#> 8 2001-01-08 0.8318207 [L/m^2] 0.000000 [L/m^2] 0.000000 [L/m^2]
#> 9 2001-01-09 1.9823797 [L/m^2] 0.000000 [L/m^2] 0.000000 [L/m^2]
#> 10 2001-01-10 0.8286873 [L/m^2] 5.117768 [L/m^2] 5.117768 [L/m^2]
#> Snow NetRain Snowmelt Infiltration
#> 1 0.0000 [L/m^2] 3.6000026 [L/m^2] 0.0000 [L/m^2] 3.6000026 [L/m^2]
#> 2 0.0000 [L/m^2] 1.2454970 [L/m^2] 0.0000 [L/m^2] 1.2454970 [L/m^2]
#> 3 0.0000 [L/m^2] 0.0000000 [L/m^2] 0.0000 [L/m^2] 0.0000000 [L/m^2]
#> 4 0.0000 [L/m^2] 4.5381440 [L/m^2] 0.0000 [L/m^2] 4.5381440 [L/m^2]
#> 5 0.0000 [L/m^2] 0.8222806 [L/m^2] 0.0000 [L/m^2] 0.8222806 [L/m^2]
#> 6 0.0000 [L/m^2] 11.9109817 [L/m^2] 0.0000 [L/m^2] 11.9109817 [L/m^2]
#> 7 5.3774 [L/m^2] 0.0000000 [L/m^2] 0.0000 [L/m^2] 0.0000000 [L/m^2]
#> 8 0.0000 [L/m^2] 0.0000000 [L/m^2] 0.0000 [L/m^2] 0.0000000 [L/m^2]
#> 9 0.0000 [L/m^2] 0.0000000 [L/m^2] 0.0000 [L/m^2] 0.0000000 [L/m^2]
#> 10 0.0000 [L/m^2] 3.8486340 [L/m^2] 5.3774 [L/m^2] 9.2260336 [L/m^2]
#> InfiltrationExcess SaturationExcess Runoff DeepDrainage
#> 1 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 2.9188167 [L/m^2]
#> 2 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 0.3679634 [L/m^2]
#> 3 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 0.0000000 [L/m^2]
#> 4 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 3.4528705 [L/m^2]
#> 5 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 0.1416065 [L/m^2]
#> 6 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 4.1214138 [L/m^2]
#> 7 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 4.1214138 [L/m^2]
#> 8 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 2.8178168 [L/m^2]
#> 9 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 0.0000000 [L/m^2]
#> 10 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 4.1214138 [L/m^2]
#> CapillarityRise Evapotranspiration Interception SoilEvaporation
#> 1 0 [L/m^2] 1.9502921 [L/m^2] 1.269106 [L/m^2] 0.4776452 [L/m^2]
#> 2 0 [L/m^2] 2.1303282 [L/m^2] 1.252795 [L/m^2] 0.5000000 [L/m^2]
#> 3 0 [L/m^2] 0.8001077 [L/m^2] 0.000000 [L/m^2] 0.5000000 [L/m^2]
#> 4 0 [L/m^2] 1.5439948 [L/m^2] 1.258829 [L/m^2] 0.1540028 [L/m^2]
#> 5 0 [L/m^2] 1.9485359 [L/m^2] 1.062121 [L/m^2] 0.5000000 [L/m^2]
#> 6 0 [L/m^2] 2.0621670 [L/m^2] 1.448819 [L/m^2] 0.3349340 [L/m^2]
#> 7 0 [L/m^2] 0.1468182 [L/m^2] 0.000000 [L/m^2] 0.0000000 [L/m^2]
#> 8 0 [L/m^2] 0.1917697 [L/m^2] 0.000000 [L/m^2] 0.0000000 [L/m^2]
#> 9 0 [L/m^2] 0.4569924 [L/m^2] 0.000000 [L/m^2] 0.0000000 [L/m^2]
#> 10 0 [L/m^2] 1.6502722 [L/m^2] 1.269134 [L/m^2] 0.1901280 [L/m^2]
#> HerbTranspiration PlantExtraction Transpiration
#> 1 0 [L/m^2] 0.2035406 [L/m^2] 0.2035406 [L/m^2]
#> 2 0 [L/m^2] 0.3775336 [L/m^2] 0.3775336 [L/m^2]
#> 3 0 [L/m^2] 0.3001077 [L/m^2] 0.3001077 [L/m^2]
#> 4 0 [L/m^2] 0.1311630 [L/m^2] 0.1311630 [L/m^2]
#> 5 0 [L/m^2] 0.3864150 [L/m^2] 0.3864150 [L/m^2]
#> 6 0 [L/m^2] 0.2784142 [L/m^2] 0.2784142 [L/m^2]
#> 7 0 [L/m^2] 0.1468182 [L/m^2] 0.1468182 [L/m^2]
#> 8 0 [L/m^2] 0.1917697 [L/m^2] 0.1917697 [L/m^2]
#> 9 0 [L/m^2] 0.4569924 [L/m^2] 0.4569924 [L/m^2]
#> 10 0 [L/m^2] 0.1910105 [L/m^2] 0.1910105 [L/m^2]
#> HydraulicRedistribution LAI LAIherb LAIlive
#> 1 0.000000000 [L/m^2] 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.584948 [m^2/m^2]
#> 2 0.000000000 [L/m^2] 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.584948 [m^2/m^2]
#> 3 0.000000000 [L/m^2] 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.584948 [m^2/m^2]
#> 4 0.000000000 [L/m^2] 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.584948 [m^2/m^2]
#> 5 0.000000000 [L/m^2] 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.584948 [m^2/m^2]
#> 6 0.000000000 [L/m^2] 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.584948 [m^2/m^2]
#> 7 0.002845938 [L/m^2] 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.584948 [m^2/m^2]
#> 8 0.003494689 [L/m^2] 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.584948 [m^2/m^2]
#> 9 0.000000000 [L/m^2] 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.584948 [m^2/m^2]
#> 10 0.000000000 [L/m^2] 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.584948 [m^2/m^2]
#> LAIexpanded LAIdead Cm LgroundPAR LgroundSWR
#> 1 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.216848 [L/m^2] 43.63617 [%] 54.1028 [%]
#> 2 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.216848 [L/m^2] 43.63617 [%] 54.1028 [%]
#> 3 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.216848 [L/m^2] 43.63617 [%] 54.1028 [%]
#> 4 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.216848 [L/m^2] 43.63617 [%] 54.1028 [%]
#> 5 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.216848 [L/m^2] 43.63617 [%] 54.1028 [%]
#> 6 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.216848 [L/m^2] 43.63617 [%] 54.1028 [%]
#> 7 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.216848 [L/m^2] 43.63617 [%] 54.1028 [%]
#> 8 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.216848 [L/m^2] 43.63617 [%] 54.1028 [%]
#> 9 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.216848 [L/m^2] 43.63617 [%] 54.1028 [%]
#> 10 1.584948 [m^2/m^2] 0 [m^2/m^2] 1.216848 [L/m^2] 43.63617 [%] 54.1028 [%]
#> SWE
#> 1 0.0000 [L/m^2]
#> 2 0.0000 [L/m^2]
#> 3 0.0000 [L/m^2]
#> 4 0.0000 [L/m^2]
#> 5 0.0000 [L/m^2]
#> 6 0.0000 [L/m^2]
#> 7 5.3774 [L/m^2]
#> 8 5.3774 [L/m^2]
#> 9 5.3774 [L/m^2]
#> 10 0.0000 [L/m^2]
#Extracts daily soil layer-level output as a data frame
extract(S1, level = "soillayer", addunits = TRUE)
#> date soillayer SWC RWC REW ML
#> 1 2001-01-01 1 0.3029947 1.0000000 1.0000000 68.17381 [L/m^2]
#> 2 2001-01-02 1 0.3029947 1.0000000 1.0000000 68.17381 [L/m^2]
#> 3 2001-01-03 1 0.2997295 0.9892235 0.9838383 67.43914 [L/m^2]
#> 4 2001-01-04 1 0.3029947 1.0000000 1.0000000 68.17381 [L/m^2]
#> 5 2001-01-05 1 0.3020803 0.9969821 0.9954740 67.96807 [L/m^2]
#> 6 2001-01-06 1 0.3029947 1.0000000 1.0000000 68.17381 [L/m^2]
#> 7 2001-01-07 1 0.3025091 0.9983973 0.9975964 68.06455 [L/m^2]
#> 8 2001-01-08 1 0.3018756 0.9963065 0.9944607 67.92201 [L/m^2]
#> 9 2001-01-09 1 0.3004952 0.9917507 0.9876283 67.61143 [L/m^2]
#> 10 2001-01-10 1 0.3029947 1.0000000 1.0000000 68.17381 [L/m^2]
#> 11 2001-01-01 2 0.3029947 1.0000000 1.0000000 116.65297 [L/m^2]
#> 12 2001-01-02 2 0.3029947 1.0000000 1.0000000 116.65297 [L/m^2]
#> 13 2001-01-03 2 0.3028403 0.9994903 0.9992356 116.59351 [L/m^2]
#> 14 2001-01-04 2 0.3029947 1.0000000 1.0000000 116.65297 [L/m^2]
#> 15 2001-01-05 2 0.3029947 1.0000000 1.0000000 116.65297 [L/m^2]
#> 16 2001-01-06 2 0.3029947 1.0000000 1.0000000 116.65297 [L/m^2]
#> 17 2001-01-07 2 0.3029332 0.9997968 0.9996953 116.62927 [L/m^2]
#> 18 2001-01-08 2 0.3028505 0.9995239 0.9992860 116.59743 [L/m^2]
#> 19 2001-01-09 2 0.3025873 0.9986553 0.9979833 116.49610 [L/m^2]
#> 20 2001-01-10 2 0.3029947 1.0000000 1.0000000 116.65297 [L/m^2]
#> 21 2001-01-01 3 0.3029947 1.0000000 1.0000000 75.74868 [L/m^2]
#> 22 2001-01-02 3 0.3029947 1.0000000 1.0000000 75.74868 [L/m^2]
#> 23 2001-01-03 3 0.3029748 0.9999341 0.9999012 75.74369 [L/m^2]
#> 24 2001-01-04 3 0.3029947 1.0000000 1.0000000 75.74868 [L/m^2]
#> 25 2001-01-05 3 0.3029947 1.0000000 1.0000000 75.74868 [L/m^2]
#> 26 2001-01-06 3 0.3029947 1.0000000 1.0000000 75.74868 [L/m^2]
#> 27 2001-01-07 3 0.3029947 1.0000000 1.0000000 75.74868 [L/m^2]
#> 28 2001-01-08 3 0.3029947 1.0000000 1.0000000 75.74868 [L/m^2]
#> 29 2001-01-09 3 0.3028922 0.9996617 0.9994927 75.72306 [L/m^2]
#> 30 2001-01-10 3 0.3029947 1.0000000 1.0000000 75.74868 [L/m^2]
#> 31 2001-01-01 4 0.3029947 1.0000000 1.0000000 30.29947 [L/m^2]
#> 32 2001-01-02 4 0.3029947 1.0000000 1.0000000 30.29947 [L/m^2]
#> 33 2001-01-03 4 0.3029849 0.9999675 0.9999512 30.29849 [L/m^2]
#> 34 2001-01-04 4 0.3029947 1.0000000 1.0000000 30.29947 [L/m^2]
#> 35 2001-01-05 4 0.3029947 1.0000000 1.0000000 30.29947 [L/m^2]
#> 36 2001-01-06 4 0.3726995 1.2300528 1.3450154 37.26995 [L/m^2]
#> 37 2001-01-07 4 0.3313468 1.0935729 1.1403333 33.13468 [L/m^2]
#> 38 2001-01-08 4 0.3029947 1.0000000 1.0000000 30.29947 [L/m^2]
#> 39 2001-01-09 4 0.3028002 0.9993580 0.9990372 30.28002 [L/m^2]
#> 40 2001-01-10 4 0.3425862 1.1306673 1.1959646 34.25862 [L/m^2]
#> 41 2001-01-01 Overall 0.3029947 1.0000000 1.0000000 290.87494 [L/m^2]
#> 42 2001-01-02 Overall 0.3029947 1.0000000 1.0000000 290.87494 [L/m^2]
#> 43 2001-01-03 Overall 0.3021613 0.9972493 0.9958747 290.07483 [L/m^2]
#> 44 2001-01-04 Overall 0.3029947 1.0000000 1.0000000 290.87494 [L/m^2]
#> 45 2001-01-05 Overall 0.3027804 0.9992927 0.9989392 290.66920 [L/m^2]
#> 46 2001-01-06 Overall 0.3102556 1.0239638 1.0359391 297.84542 [L/m^2]
#> 47 2001-01-07 Overall 0.3058096 1.0092901 1.0139325 293.57719 [L/m^2]
#> 48 2001-01-08 Overall 0.3026746 0.9989434 0.9984154 290.56760 [L/m^2]
#> 49 2001-01-09 Overall 0.3021985 0.9973723 0.9960592 290.11061 [L/m^2]
#> 50 2001-01-10 Overall 0.3071188 1.0136112 1.0204130 294.83409 [L/m^2]
#> Psi PlantExt HydraulicInput
#> 1 -0.033000000 [MPa] 0.1591605366 [L/m^2] 0.000000000 [L/m^2]
#> 2 -0.033000000 [MPa] 0.2952160280 [L/m^2] 0.000000000 [L/m^2]
#> 3 -0.034728345 [MPa] 0.2346721002 [L/m^2] 0.000000000 [L/m^2]
#> 4 -0.033000000 [MPa] 0.0884748965 [L/m^2] 0.000000000 [L/m^2]
#> 5 -0.033475199 [MPa] 0.3021609879 [L/m^2] 0.000000000 [L/m^2]
#> 6 -0.033000000 [MPa] 0.1892670564 [L/m^2] 0.000000000 [L/m^2]
#> 7 -0.033251521 [MPa] 0.1092607714 [L/m^2] 0.000000000 [L/m^2]
#> 8 -0.033582511 [MPa] 0.1425410406 [L/m^2] 0.000000000 [L/m^2]
#> 9 -0.034315105 [MPa] 0.3105861060 [L/m^2] 0.000000000 [L/m^2]
#> 10 -0.033000000 [MPa] 0.1293034084 [L/m^2] 0.000000000 [L/m^2]
#> 11 -0.033000000 [MPa] 0.0403279820 [L/m^2] 0.000000000 [L/m^2]
#> 12 -0.033000000 [MPa] 0.0748016243 [L/m^2] 0.000000000 [L/m^2]
#> 13 -0.033079791 [MPa] 0.0594610475 [L/m^2] 0.000000000 [L/m^2]
#> 14 -0.033000000 [MPa] 0.0307116363 [L/m^2] 0.000000000 [L/m^2]
#> 15 -0.033000000 [MPa] 0.0765613332 [L/m^2] 0.000000000 [L/m^2]
#> 16 -0.033000000 [MPa] 0.0649916543 [L/m^2] 0.000000000 [L/m^2]
#> 17 -0.033031781 [MPa] 0.0237004976 [L/m^2] 0.000000000 [L/m^2]
#> 18 -0.033074520 [MPa] 0.0318372316 [L/m^2] 0.000000000 [L/m^2]
#> 19 -0.033210913 [MPa] 0.1013300222 [L/m^2] 0.000000000 [L/m^2]
#> 20 -0.033000000 [MPa] 0.0430999978 [L/m^2] 0.000000000 [L/m^2]
#> 21 -0.033000000 [MPa] 0.0033836661 [L/m^2] 0.000000000 [L/m^2]
#> 22 -0.033000000 [MPa] 0.0062761316 [L/m^2] 0.000000000 [L/m^2]
#> 23 -0.033010299 [MPa] 0.0049890007 [L/m^2] 0.000000000 [L/m^2]
#> 24 -0.033000000 [MPa] 0.0068644515 [L/m^2] 0.000000000 [L/m^2]
#> 25 -0.033000000 [MPa] 0.0064237776 [L/m^2] 0.000000000 [L/m^2]
#> 26 -0.033000000 [MPa] 0.0139521534 [L/m^2] 0.000000000 [L/m^2]
#> 27 -0.033000000 [MPa] -0.0024989659 [L/m^2] 0.002845938 [L/m^2]
#> 28 -0.033000000 [MPa] -0.0028441253 [L/m^2] 0.003494689 [L/m^2]
#> 29 -0.033052933 [MPa] 0.0256247240 [L/m^2] 0.000000000 [L/m^2]
#> 30 -0.033000000 [MPa] 0.0111373271 [L/m^2] 0.000000000 [L/m^2]
#> 31 -0.033000000 [MPa] 0.0006684070 [L/m^2] 0.000000000 [L/m^2]
#> 32 -0.033000000 [MPa] 0.0012397826 [L/m^2] 0.000000000 [L/m^2]
#> 33 -0.033005086 [MPa] 0.0009855236 [L/m^2] 0.000000000 [L/m^2]
#> 34 -0.033000000 [MPa] 0.0051120624 [L/m^2] 0.000000000 [L/m^2]
#> 35 -0.033000000 [MPa] 0.0012689485 [L/m^2] 0.000000000 [L/m^2]
#> 36 -0.009879594 [MPa] 0.0102033070 [L/m^2] 0.000000000 [L/m^2]
#> 37 -0.021042183 [MPa] 0.0163558775 [L/m^2] 0.000000000 [L/m^2]
#> 38 -0.033000000 [MPa] 0.0202355136 [L/m^2] 0.000000000 [L/m^2]
#> 39 -0.033100524 [MPa] 0.0194515574 [L/m^2] 0.000000000 [L/m^2]
#> 40 -0.017449592 [MPa] 0.0074697552 [L/m^2] 0.000000000 [L/m^2]
#> 41 -0.033000000 [MPa] 0.2035405917 [L/m^2] 0.000000000 [L/m^2]
#> 42 -0.033000000 [MPa] 0.3775335664 [L/m^2] 0.000000000 [L/m^2]
#> 43 -0.033440292 [MPa] 0.3001076721 [L/m^2] 0.000000000 [L/m^2]
#> 44 -0.033000000 [MPa] 0.1311630467 [L/m^2] 0.000000000 [L/m^2]
#> 45 -0.033111375 [MPa] 0.3864150472 [L/m^2] 0.000000000 [L/m^2]
#> 46 -0.030591624 [MPa] 0.2784141711 [L/m^2] 0.000000000 [L/m^2]
#> 47 -0.031826090 [MPa] 0.1468181805 [L/m^2] 0.002845938 [L/m^2]
#> 48 -0.033166412 [MPa] 0.1917696605 [L/m^2] 0.003494689 [L/m^2]
#> 49 -0.033417068 [MPa] 0.4569924096 [L/m^2] 0.000000000 [L/m^2]
#> 50 -0.031380166 [MPa] 0.1910104885 [L/m^2] 0.000000000 [L/m^2]
#Extracts daily cohort-level output as a data frame
extract(S1, level = "cohort", addunits = TRUE)
#> date cohort species LAI
#> 1 2001-01-01 T1_148 Pinus halepensis 0.84874773 [m^2/m^2]
#> 2 2001-01-02 T1_148 Pinus halepensis 0.84874773 [m^2/m^2]
#> 3 2001-01-03 T1_148 Pinus halepensis 0.84874773 [m^2/m^2]
#> 4 2001-01-04 T1_148 Pinus halepensis 0.84874773 [m^2/m^2]
#> 5 2001-01-05 T1_148 Pinus halepensis 0.84874773 [m^2/m^2]
#> 6 2001-01-06 T1_148 Pinus halepensis 0.84874773 [m^2/m^2]
#> 7 2001-01-07 T1_148 Pinus halepensis 0.84874773 [m^2/m^2]
#> 8 2001-01-08 T1_148 Pinus halepensis 0.84874773 [m^2/m^2]
#> 9 2001-01-09 T1_148 Pinus halepensis 0.84874773 [m^2/m^2]
#> 10 2001-01-10 T1_148 Pinus halepensis 0.84874773 [m^2/m^2]
#> 11 2001-01-01 T2_168 Quercus ilex 0.70557382 [m^2/m^2]
#> 12 2001-01-02 T2_168 Quercus ilex 0.70557382 [m^2/m^2]
#> 13 2001-01-03 T2_168 Quercus ilex 0.70557382 [m^2/m^2]
#> 14 2001-01-04 T2_168 Quercus ilex 0.70557382 [m^2/m^2]
#> 15 2001-01-05 T2_168 Quercus ilex 0.70557382 [m^2/m^2]
#> 16 2001-01-06 T2_168 Quercus ilex 0.70557382 [m^2/m^2]
#> 17 2001-01-07 T2_168 Quercus ilex 0.70557382 [m^2/m^2]
#> 18 2001-01-08 T2_168 Quercus ilex 0.70557382 [m^2/m^2]
#> 19 2001-01-09 T2_168 Quercus ilex 0.70557382 [m^2/m^2]
#> 20 2001-01-10 T2_168 Quercus ilex 0.70557382 [m^2/m^2]
#> 21 2001-01-01 S1_165 Quercus coccifera 0.03062604 [m^2/m^2]
#> 22 2001-01-02 S1_165 Quercus coccifera 0.03062604 [m^2/m^2]
#> 23 2001-01-03 S1_165 Quercus coccifera 0.03062604 [m^2/m^2]
#> 24 2001-01-04 S1_165 Quercus coccifera 0.03062604 [m^2/m^2]
#> 25 2001-01-05 S1_165 Quercus coccifera 0.03062604 [m^2/m^2]
#> 26 2001-01-06 S1_165 Quercus coccifera 0.03062604 [m^2/m^2]
#> 27 2001-01-07 S1_165 Quercus coccifera 0.03062604 [m^2/m^2]
#> 28 2001-01-08 S1_165 Quercus coccifera 0.03062604 [m^2/m^2]
#> 29 2001-01-09 S1_165 Quercus coccifera 0.03062604 [m^2/m^2]
#> 30 2001-01-10 S1_165 Quercus coccifera 0.03062604 [m^2/m^2]
#> LAIlive FPAR AbsorbedSWRFraction Transpiration
#> 1 0.84874773 [m^2/m^2] 92.18285 [%] 35.076344 0.125013855 [L/m^2]
#> 2 0.84874773 [m^2/m^2] 92.18285 [%] 35.076344 0.231879677 [L/m^2]
#> 3 0.84874773 [m^2/m^2] 92.18285 [%] 35.076344 0.184324988 [L/m^2]
#> 4 0.84874773 [m^2/m^2] 92.18285 [%] 35.076344 0.080554970 [L/m^2]
#> 5 0.84874773 [m^2/m^2] 92.18285 [%] 35.076344 0.237334648 [L/m^2]
#> 6 0.84874773 [m^2/m^2] 92.18285 [%] 35.076344 0.170998005 [L/m^2]
#> 7 0.84874773 [m^2/m^2] 92.18285 [%] 35.076344 0.090173939 [L/m^2]
#> 8 0.84874773 [m^2/m^2] 92.18285 [%] 35.076344 0.117782393 [L/m^2]
#> 9 0.84874773 [m^2/m^2] 92.18285 [%] 35.076344 0.280677793 [L/m^2]
#> 10 0.84874773 [m^2/m^2] 92.18285 [%] 35.076344 0.117313138 [L/m^2]
#> 11 0.70557382 [m^2/m^2] 72.36365 [%] 30.444383 0.072474080 [L/m^2]
#> 12 0.70557382 [m^2/m^2] 72.36365 [%] 30.444383 0.134427230 [L/m^2]
#> 13 0.70557382 [m^2/m^2] 72.36365 [%] 30.444383 0.106858427 [L/m^2]
#> 14 0.70557382 [m^2/m^2] 72.36365 [%] 30.444383 0.046707139 [L/m^2]
#> 15 0.70557382 [m^2/m^2] 72.36365 [%] 30.444383 0.137589632 [L/m^2]
#> 16 0.70557382 [m^2/m^2] 72.36365 [%] 30.444383 0.099136682 [L/m^2]
#> 17 0.70557382 [m^2/m^2] 72.36365 [%] 30.444383 0.052278282 [L/m^2]
#> 18 0.70557382 [m^2/m^2] 72.36365 [%] 30.444383 0.068284485 [L/m^2]
#> 19 0.70557382 [m^2/m^2] 72.36365 [%] 30.444383 0.162724441 [L/m^2]
#> 20 0.70557382 [m^2/m^2] 72.36365 [%] 30.444383 0.068016672 [L/m^2]
#> 21 0.03062604 [m^2/m^2] 44.32407 [%] 2.366131 0.006052657 [L/m^2]
#> 22 0.03062604 [m^2/m^2] 44.32407 [%] 2.366131 0.011226660 [L/m^2]
#> 23 0.03062604 [m^2/m^2] 44.32407 [%] 2.366131 0.008924258 [L/m^2]
#> 24 0.03062604 [m^2/m^2] 44.32407 [%] 2.366131 0.003900938 [L/m^2]
#> 25 0.03062604 [m^2/m^2] 44.32407 [%] 2.366131 0.011490767 [L/m^2]
#> 26 0.03062604 [m^2/m^2] 44.32407 [%] 2.366131 0.008279484 [L/m^2]
#> 27 0.03062604 [m^2/m^2] 44.32407 [%] 2.366131 0.004365959 [L/m^2]
#> 28 0.03062604 [m^2/m^2] 44.32407 [%] 2.366131 0.005702782 [L/m^2]
#> 29 0.03062604 [m^2/m^2] 44.32407 [%] 2.366131 0.013590175 [L/m^2]
#> 30 0.03062604 [m^2/m^2] 44.32407 [%] 2.366131 0.005680678 [L/m^2]
#> GrossPhotosynthesis PlantPsi LeafPLC StemPLC
#> 1 1.21341578 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 2 2.10407515 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 3 1.77447392 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 4 0.81327944 [L/m^2] -0.03464644 [MPa] 0.0000000000 0
#> 5 2.18426681 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 6 1.79119773 [L/m^2] -0.03345144 [MPa] 0.0000000000 0
#> 7 1.02773578 [L/m^2] -0.03299488 [MPa] 0.0000000000 0
#> 8 1.21741260 [L/m^2] -0.03323746 [MPa] 0.0000000000 0
#> 9 2.08922183 [L/m^2] -0.03355697 [MPa] 0.0000000000 0
#> 10 1.16083862 [L/m^2] -0.03425983 [MPa] 0.0000000000 0
#> 11 0.87313959 [L/m^2] -0.03300000 [MPa] 0.0009945146 0
#> 12 1.59468338 [L/m^2] -0.03300000 [MPa] 0.0009945146 0
#> 13 1.28490959 [L/m^2] -0.03300000 [MPa] 0.0009945146 0
#> 14 0.56803003 [L/m^2] -0.03390356 [MPa] 0.0011025914 0
#> 15 1.63739954 [L/m^2] -0.03300000 [MPa] 0.0009945146 0
#> 16 1.21663617 [L/m^2] -0.03323815 [MPa] 0.0010229055 0
#> 17 0.65566916 [L/m^2] -0.03283022 [MPa] 0.0009743149 0
#> 18 0.83523708 [L/m^2] -0.03304909 [MPa] 0.0010003618 0
#> 19 1.85134619 [L/m^2] -0.03332550 [MPa] 0.0010333362 0
#> 20 0.82319538 [L/m^2] -0.03375737 [MPa] 0.0010850391 0
#> 21 0.05005525 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 22 0.08984642 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 23 0.07350414 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 24 0.03290263 [L/m^2] -0.03420012 [MPa] 0.0000000000 0
#> 25 0.09258764 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 26 0.07115889 [L/m^2] -0.03332335 [MPa] 0.0000000000 0
#> 27 0.03922424 [L/m^2] -0.03278767 [MPa] 0.0000000000 0
#> 28 0.04867876 [L/m^2] -0.03306128 [MPa] 0.0000000000 0
#> 29 0.09935011 [L/m^2] -0.03341676 [MPa] 0.0000000000 0
#> 30 0.04743233 [L/m^2] -0.03395616 [MPa] 0.0000000000 0
#> PlantWaterBalance LeafRWC StemRWC LFMC PlantStress
#> 1 0.000000e+00 [L/m^2] 0.9979679 [%] 0.9998350 [%] 125.86544 [%] 0.004613739
#> 2 0.000000e+00 [L/m^2] 0.9979679 [%] 0.9998350 [%] 125.86544 [%] 0.004613739
#> 3 0.000000e+00 [L/m^2] 0.9979679 [%] 0.9998350 [%] 125.86544 [%] 0.004613739
#> 4 -7.410286e-05 [L/m^2] 0.9978666 [%] 0.9998267 [%] 125.85720 [%] 0.004963522
#> 5 7.410286e-05 [L/m^2] 0.9979679 [%] 0.9998350 [%] 125.86544 [%] 0.004613739
#> 6 -2.031870e-05 [L/m^2] 0.9979401 [%] 0.9998327 [%] 125.86318 [%] 0.004708802
#> 7 2.054901e-05 [L/m^2] 0.9979682 [%] 0.9998350 [%] 125.86546 [%] 0.004612665
#> 8 -1.091793e-05 [L/m^2] 0.9979533 [%] 0.9998338 [%] 125.86425 [%] 0.004663662
#> 9 -1.438064e-05 [L/m^2] 0.9979336 [%] 0.9998322 [%] 125.86265 [%] 0.004731116
#> 10 -3.163438e-05 [L/m^2] 0.9978904 [%] 0.9998287 [%] 125.85914 [%] 0.004880628
#> 11 0.000000e+00 [L/m^2] 0.9986797 [%] 0.9997500 [%] 93.05186 [%] 0.006282261
#> 12 0.000000e+00 [L/m^2] 0.9986797 [%] 0.9997500 [%] 93.05186 [%] 0.006282261
#> 13 0.000000e+00 [L/m^2] 0.9986797 [%] 0.9997500 [%] 93.05186 [%] 0.006282261
#> 14 -9.503885e-06 [L/m^2] 0.9986436 [%] 0.9997431 [%] 93.04909 [%] 0.006479670
#> 15 9.503885e-06 [L/m^2] 0.9986797 [%] 0.9997500 [%] 93.05186 [%] 0.006282261
#> 16 -2.504870e-06 [L/m^2] 0.9986702 [%] 0.9997482 [%] 93.05113 [%] 0.006334217
#> 17 4.290706e-06 [L/m^2] 0.9986865 [%] 0.9997513 [%] 93.05238 [%] 0.006245252
#> 18 -2.302214e-06 [L/m^2] 0.9986778 [%] 0.9997496 [%] 93.05171 [%] 0.006292967
#> 19 -2.907280e-06 [L/m^2] 0.9986667 [%] 0.9997475 [%] 93.05086 [%] 0.006353288
#> 20 -4.542506e-06 [L/m^2] 0.9986494 [%] 0.9997442 [%] 93.04953 [%] 0.006447678
#> 21 3.469447e-18 [L/m^2] 0.9987207 [%] 0.9983684 [%] 96.38420 [%] 0.003088161
#> 22 0.000000e+00 [L/m^2] 0.9987207 [%] 0.9983684 [%] 96.38420 [%] 0.003088161
#> 23 0.000000e+00 [L/m^2] 0.9987207 [%] 0.9983684 [%] 96.38420 [%] 0.003088161
#> 24 -1.141669e-06 [L/m^2] 0.9986741 [%] 0.9983091 [%] 96.37874 [%] 0.003234714
#> 25 1.141669e-06 [L/m^2] 0.9987207 [%] 0.9983684 [%] 96.38420 [%] 0.003088161
#> 26 -3.076025e-07 [L/m^2] 0.9987081 [%] 0.9983524 [%] 96.38273 [%] 0.003127494
#> 27 5.095914e-07 [L/m^2] 0.9987289 [%] 0.9983789 [%] 96.38517 [%] 0.003062395
#> 28 -2.602870e-07 [L/m^2] 0.9987183 [%] 0.9983654 [%] 96.38392 [%] 0.003095607
#> 29 -3.381711e-07 [L/m^2] 0.9987045 [%] 0.9983478 [%] 96.38231 [%] 0.003138878
#> 30 -5.131216e-07 [L/m^2] 0.9986836 [%] 0.9983212 [%] 96.37985 [%] 0.003204797
#Select the output tables/variables to be extracted
extract(S1, level ="cohort", output="Plants", vars = c("PlantStress", "StemPLC"))
#> date cohort species PlantStress StemPLC
#> 1 2001-01-01 T1_148 Pinus halepensis 0.004613739 0
#> 2 2001-01-02 T1_148 Pinus halepensis 0.004613739 0
#> 3 2001-01-03 T1_148 Pinus halepensis 0.004613739 0
#> 4 2001-01-04 T1_148 Pinus halepensis 0.004963522 0
#> 5 2001-01-05 T1_148 Pinus halepensis 0.004613739 0
#> 6 2001-01-06 T1_148 Pinus halepensis 0.004708802 0
#> 7 2001-01-07 T1_148 Pinus halepensis 0.004612665 0
#> 8 2001-01-08 T1_148 Pinus halepensis 0.004663662 0
#> 9 2001-01-09 T1_148 Pinus halepensis 0.004731116 0
#> 10 2001-01-10 T1_148 Pinus halepensis 0.004880628 0
#> 11 2001-01-01 T2_168 Quercus ilex 0.006282261 0
#> 12 2001-01-02 T2_168 Quercus ilex 0.006282261 0
#> 13 2001-01-03 T2_168 Quercus ilex 0.006282261 0
#> 14 2001-01-04 T2_168 Quercus ilex 0.006479670 0
#> 15 2001-01-05 T2_168 Quercus ilex 0.006282261 0
#> 16 2001-01-06 T2_168 Quercus ilex 0.006334217 0
#> 17 2001-01-07 T2_168 Quercus ilex 0.006245252 0
#> 18 2001-01-08 T2_168 Quercus ilex 0.006292967 0
#> 19 2001-01-09 T2_168 Quercus ilex 0.006353288 0
#> 20 2001-01-10 T2_168 Quercus ilex 0.006447678 0
#> 21 2001-01-01 S1_165 Quercus coccifera 0.003088161 0
#> 22 2001-01-02 S1_165 Quercus coccifera 0.003088161 0
#> 23 2001-01-03 S1_165 Quercus coccifera 0.003088161 0
#> 24 2001-01-04 S1_165 Quercus coccifera 0.003234714 0
#> 25 2001-01-05 S1_165 Quercus coccifera 0.003088161 0
#> 26 2001-01-06 S1_165 Quercus coccifera 0.003127494 0
#> 27 2001-01-07 S1_165 Quercus coccifera 0.003062395 0
#> 28 2001-01-08 S1_165 Quercus coccifera 0.003095607 0
#> 29 2001-01-09 S1_165 Quercus coccifera 0.003138878 0
#> 30 2001-01-10 S1_165 Quercus coccifera 0.003204797 0