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): 4.67289
#> 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)
#> 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] 3.6578430 [L/m^2] 0.0000 [L/m^2] 3.6578430 [L/m^2]
#> 2 0.0000 [L/m^2] 1.3026155 [L/m^2] 0.0000 [L/m^2] 1.3026155 [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] 4.5956523 [L/m^2] 0.0000 [L/m^2] 4.5956523 [L/m^2]
#> 5 0.0000 [L/m^2] 0.8616218 [L/m^2] 0.0000 [L/m^2] 0.8616218 [L/m^2]
#> 6 0.0000 [L/m^2] 11.9754283 [L/m^2] 0.0000 [L/m^2] 11.9754283 [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] 3.9064839 [L/m^2] 5.3774 [L/m^2] 9.2838835 [L/m^2]
#> InfiltrationExcess SaturationExcess Runoff DeepDrainage
#> 1 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 2.9694516 [L/m^2]
#> 2 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 0.4429239 [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] 3.5291110 [L/m^2]
#> 5 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 0.1585395 [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] 2.9111160 [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] 1.8996573 [L/m^2] 1.211266 [L/m^2] 0.4944700 [L/m^2]
#> 2 0 [L/m^2] 2.0553677 [L/m^2] 1.195676 [L/m^2] 0.5000000 [L/m^2]
#> 3 0 [L/m^2] 0.7859248 [L/m^2] 0.000000 [L/m^2] 0.5000000 [L/m^2]
#> 4 0 [L/m^2] 1.4819371 [L/m^2] 1.201321 [L/m^2] 0.1556520 [L/m^2]
#> 5 0 [L/m^2] 1.8909330 [L/m^2] 1.022780 [L/m^2] 0.5000000 [L/m^2]
#> 6 0 [L/m^2] 2.0111056 [L/m^2] 1.384372 [L/m^2] 0.3614728 [L/m^2]
#> 7 0 [L/m^2] 0.1398797 [L/m^2] 0.000000 [L/m^2] 0.0000000 [L/m^2]
#> 8 0 [L/m^2] 0.1827071 [L/m^2] 0.000000 [L/m^2] 0.0000000 [L/m^2]
#> 9 0 [L/m^2] 0.4353967 [L/m^2] 0.000000 [L/m^2] 0.0000000 [L/m^2]
#> 10 0 [L/m^2] 1.5891273 [L/m^2] 1.211284 [L/m^2] 0.1958587 [L/m^2]
#> HerbTranspiration PlantExtraction Transpiration MistletoeTranspiration
#> 1 0 [L/m^2] 0.1939214 [L/m^2] 0.1939214 [L/m^2] 0 [L/m^2]
#> 2 0 [L/m^2] 0.3596916 [L/m^2] 0.3596916 [L/m^2] 0 [L/m^2]
#> 3 0 [L/m^2] 0.2859248 [L/m^2] 0.2859248 [L/m^2] 0 [L/m^2]
#> 4 0 [L/m^2] 0.1249645 [L/m^2] 0.1249645 [L/m^2] 0 [L/m^2]
#> 5 0 [L/m^2] 0.3681534 [L/m^2] 0.3681534 [L/m^2] 0 [L/m^2]
#> 6 0 [L/m^2] 0.2652605 [L/m^2] 0.2652605 [L/m^2] 0 [L/m^2]
#> 7 0 [L/m^2] 0.1398797 [L/m^2] 0.1398797 [L/m^2] 0 [L/m^2]
#> 8 0 [L/m^2] 0.1827071 [L/m^2] 0.1827071 [L/m^2] 0 [L/m^2]
#> 9 0 [L/m^2] 0.4353967 [L/m^2] 0.4353967 [L/m^2] 0 [L/m^2]
#> 10 0 [L/m^2] 0.1819848 [L/m^2] 0.1819848 [L/m^2] 0 [L/m^2]
#> HydraulicRedistribution LAI LAIherb LAIlive
#> 1 0.000000000 [L/m^2] 1.497716 [m^2/m^2] 0 [m^2/m^2] 1.497716 [m^2/m^2]
#> 2 0.000000000 [L/m^2] 1.497716 [m^2/m^2] 0 [m^2/m^2] 1.497716 [m^2/m^2]
#> 3 0.000000000 [L/m^2] 1.497716 [m^2/m^2] 0 [m^2/m^2] 1.497716 [m^2/m^2]
#> 4 0.000000000 [L/m^2] 1.497716 [m^2/m^2] 0 [m^2/m^2] 1.497716 [m^2/m^2]
#> 5 0.000000000 [L/m^2] 1.497716 [m^2/m^2] 0 [m^2/m^2] 1.497716 [m^2/m^2]
#> 6 0.000000000 [L/m^2] 1.497716 [m^2/m^2] 0 [m^2/m^2] 1.497716 [m^2/m^2]
#> 7 0.002738725 [L/m^2] 1.497716 [m^2/m^2] 0 [m^2/m^2] 1.497716 [m^2/m^2]
#> 8 0.003379257 [L/m^2] 1.497716 [m^2/m^2] 0 [m^2/m^2] 1.497716 [m^2/m^2]
#> 9 0.000000000 [L/m^2] 1.497716 [m^2/m^2] 0 [m^2/m^2] 1.497716 [m^2/m^2]
#> 10 0.000000000 [L/m^2] 1.497716 [m^2/m^2] 0 [m^2/m^2] 1.497716 [m^2/m^2]
#> LAIexpanded LAIdead LAImistletoe Cm LgroundPAR
#> 1 1.497716 [m^2/m^2] 0 [m^2/m^2] 0 1.160807 [L/m^2] 45.7239 [%]
#> 2 1.497716 [m^2/m^2] 0 [m^2/m^2] 0 1.160807 [L/m^2] 45.7239 [%]
#> 3 1.497716 [m^2/m^2] 0 [m^2/m^2] 0 1.160807 [L/m^2] 45.7239 [%]
#> 4 1.497716 [m^2/m^2] 0 [m^2/m^2] 0 1.160807 [L/m^2] 45.7239 [%]
#> 5 1.497716 [m^2/m^2] 0 [m^2/m^2] 0 1.160807 [L/m^2] 45.7239 [%]
#> 6 1.497716 [m^2/m^2] 0 [m^2/m^2] 0 1.160807 [L/m^2] 45.7239 [%]
#> 7 1.497716 [m^2/m^2] 0 [m^2/m^2] 0 1.160807 [L/m^2] 45.7239 [%]
#> 8 1.497716 [m^2/m^2] 0 [m^2/m^2] 0 1.160807 [L/m^2] 45.7239 [%]
#> 9 1.497716 [m^2/m^2] 0 [m^2/m^2] 0 1.160807 [L/m^2] 45.7239 [%]
#> 10 1.497716 [m^2/m^2] 0 [m^2/m^2] 0 1.160807 [L/m^2] 45.7239 [%]
#> LgroundSWR SWE
#> 1 56.00854 [%] 0.0000 [L/m^2]
#> 2 56.00854 [%] 0.0000 [L/m^2]
#> 3 56.00854 [%] 0.0000 [L/m^2]
#> 4 56.00854 [%] 0.0000 [L/m^2]
#> 5 56.00854 [%] 0.0000 [L/m^2]
#> 6 56.00854 [%] 0.0000 [L/m^2]
#> 7 56.00854 [%] 5.3774 [L/m^2]
#> 8 56.00854 [%] 5.3774 [L/m^2]
#> 9 56.00854 [%] 5.3774 [L/m^2]
#> 10 56.00854 [%] 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 0.2997714 0.9893618 0.9840456 67.44857 [L/m^2]
#> 4 2001-01-04 1 0.3029947 1.0000000 1.0000000 68.17381 [L/m^2]
#> 5 2001-01-05 1 0.3022611 0.9975787 0.9963687 68.00874 [L/m^2]
#> 6 2001-01-06 1 0.3029947 1.0000000 1.0000000 68.17381 [L/m^2]
#> 7 2001-01-07 1 0.3025286 0.9984615 0.9976927 68.06893 [L/m^2]
#> 8 2001-01-08 1 0.3019201 0.9964533 0.9946810 67.93202 [L/m^2]
#> 9 2001-01-09 1 0.3005935 0.9920749 0.9881145 67.63353 [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 0.3028517 0.9995278 0.9992919 116.59789 [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 0.3029381 0.9998130 0.9997196 116.63116 [L/m^2]
#> 18 2001-01-08 2 0.3028620 0.9995618 0.9993428 116.60186 [L/m^2]
#> 19 2001-01-09 2 0.3026170 0.9987534 0.9981304 116.50755 [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 0.3029761 0.9999385 0.9999077 75.74402 [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 0.3028981 0.9996810 0.9995216 75.72452 [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 0.3029853 0.9999690 0.9999535 30.29853 [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 0.3736168 1.2330803 1.3495558 37.36168 [L/m^2]
#> 37 2001-01-07 4 0.3322709 1.0966226 1.1449071 33.22709 [L/m^2]
#> 38 2001-01-08 4 0.3029947 1.0000000 1.0000000 30.29947 [L/m^2]
#> 39 2001-01-09 4 0.3028104 0.9993918 0.9990879 30.28104 [L/m^2]
#> 40 2001-01-10 4 0.3435580 1.1338744 1.2007744 34.35580 [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 0.3021761 0.9972981 0.9959478 290.08901 [L/m^2]
#> 44 2001-01-04 Overall 0.3029947 1.0000000 1.0000000 290.87494 [L/m^2]
#> 45 2001-01-05 Overall 0.3028228 0.9994325 0.9991489 290.70987 [L/m^2]
#> 46 2001-01-06 Overall 0.3103512 1.0242792 1.0364121 297.93715 [L/m^2]
#> 47 2001-01-07 Overall 0.3059124 1.0096293 1.0144412 293.67586 [L/m^2]
#> 48 2001-01-08 Overall 0.3026896 0.9989930 0.9984898 290.58203 [L/m^2]
#> 49 2001-01-09 Overall 0.3022361 0.9974962 0.9962449 290.14664 [L/m^2]
#> 50 2001-01-10 Overall 0.3072201 1.0139452 1.0209140 294.93126 [L/m^2]
#> Psi PlantExt HydraulicInput
#> 1 -0.033000000 [MPa] 0.1527687037 [L/m^2] 0.000000000 [L/m^2]
#> 2 -0.033000000 [MPa] 0.2833602530 [L/m^2] 0.000000000 [L/m^2]
#> 3 -0.034705611 [MPa] 0.2252477487 [L/m^2] 0.000000000 [L/m^2]
#> 4 -0.033000000 [MPa] 0.0850441416 [L/m^2] 0.000000000 [L/m^2]
#> 5 -0.033380729 [MPa] 0.2900263057 [L/m^2] 0.000000000 [L/m^2]
#> 6 -0.033000000 [MPa] 0.1819907001 [L/m^2] 0.000000000 [L/m^2]
#> 7 -0.033241415 [MPa] 0.1048864104 [L/m^2] 0.000000000 [L/m^2]
#> 8 -0.033559159 [MPa] 0.1369046184 [L/m^2] 0.000000000 [L/m^2]
#> 9 -0.034262449 [MPa] 0.2984949581 [L/m^2] 0.000000000 [L/m^2]
#> 10 -0.033000000 [MPa] 0.1242970032 [L/m^2] 0.000000000 [L/m^2]
#> 11 -0.033000000 [MPa] 0.0373553928 [L/m^2] 0.000000000 [L/m^2]
#> 12 -0.033000000 [MPa] 0.0692879712 [L/m^2] 0.000000000 [L/m^2]
#> 13 -0.033073903 [MPa] 0.0550781535 [L/m^2] 0.000000000 [L/m^2]
#> 14 -0.033000000 [MPa] 0.0285837088 [L/m^2] 0.000000000 [L/m^2]
#> 15 -0.033000000 [MPa] 0.0709179714 [L/m^2] 0.000000000 [L/m^2]
#> 16 -0.033000000 [MPa] 0.0603519134 [L/m^2] 0.000000000 [L/m^2]
#> 17 -0.033029247 [MPa] 0.0218117439 [L/m^2] 0.000000000 [L/m^2]
#> 18 -0.033068580 [MPa] 0.0293036930 [L/m^2] 0.000000000 [L/m^2]
#> 19 -0.033195483 [MPa] 0.0943093548 [L/m^2] 0.000000000 [L/m^2]
#> 20 -0.033000000 [MPa] 0.0401102103 [L/m^2] 0.000000000 [L/m^2]
#> 21 -0.033000000 [MPa] 0.0031607370 [L/m^2] 0.000000000 [L/m^2]
#> 22 -0.033000000 [MPa] 0.0058626356 [L/m^2] 0.000000000 [L/m^2]
#> 23 -0.033009621 [MPa] 0.0046603059 [L/m^2] 0.000000000 [L/m^2]
#> 24 -0.033000000 [MPa] 0.0064840818 [L/m^2] 0.000000000 [L/m^2]
#> 25 -0.033000000 [MPa] 0.0060005541 [L/m^2] 0.000000000 [L/m^2]
#> 26 -0.033000000 [MPa] 0.0131984297 [L/m^2] 0.000000000 [L/m^2]
#> 27 -0.033000000 [MPa] -0.0024269768 [L/m^2] 0.002738725 [L/m^2]
#> 28 -0.033000000 [MPa] -0.0027964736 [L/m^2] 0.003379257 [L/m^2]
#> 29 -0.033049914 [MPa] 0.0241643323 [L/m^2] 0.000000000 [L/m^2]
#> 30 -0.033000000 [MPa] 0.0105003107 [L/m^2] 0.000000000 [L/m^2]
#> 31 -0.033000000 [MPa] 0.0006365964 [L/m^2] 0.000000000 [L/m^2]
#> 32 -0.033000000 [MPa] 0.0011807792 [L/m^2] 0.000000000 [L/m^2]
#> 33 -0.033004844 [MPa] 0.0009386209 [L/m^2] 0.000000000 [L/m^2]
#> 34 -0.033000000 [MPa] 0.0048525568 [L/m^2] 0.000000000 [L/m^2]
#> 35 -0.033000000 [MPa] 0.0012085570 [L/m^2] 0.000000000 [L/m^2]
#> 36 -0.009684429 [MPa] 0.0097194536 [L/m^2] 0.000000000 [L/m^2]
#> 37 -0.020726693 [MPa] 0.0156085328 [L/m^2] 0.000000000 [L/m^2]
#> 38 -0.033000000 [MPa] 0.0192952460 [L/m^2] 0.000000000 [L/m^2]
#> 39 -0.033095227 [MPa] 0.0184280288 [L/m^2] 0.000000000 [L/m^2]
#> 40 -0.017162304 [MPa] 0.0070772748 [L/m^2] 0.000000000 [L/m^2]
#> 41 -0.033000000 [MPa] 0.1939214299 [L/m^2] 0.000000000 [L/m^2]
#> 42 -0.033000000 [MPa] 0.3596916389 [L/m^2] 0.000000000 [L/m^2]
#> 43 -0.033432401 [MPa] 0.2859248291 [L/m^2] 0.000000000 [L/m^2]
#> 44 -0.033000000 [MPa] 0.1249644891 [L/m^2] 0.000000000 [L/m^2]
#> 45 -0.033089233 [MPa] 0.3681533882 [L/m^2] 0.000000000 [L/m^2]
#> 46 -0.030571295 [MPa] 0.2652604967 [L/m^2] 0.000000000 [L/m^2]
#> 47 -0.031789841 [MPa] 0.1398797102 [L/m^2] 0.002738725 [L/m^2]
#> 48 -0.033158556 [MPa] 0.1827070838 [L/m^2] 0.003379257 [L/m^2]
#> 49 -0.033397201 [MPa] 0.4353966739 [L/m^2] 0.000000000 [L/m^2]
#> 50 -0.031350240 [MPa] 0.1819847991 [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_158 Pinus halepensis 0.82389823 [m^2/m^2]
#> 2 2001-01-02 T1_158 Pinus halepensis 0.82389823 [m^2/m^2]
#> 3 2001-01-03 T1_158 Pinus halepensis 0.82389823 [m^2/m^2]
#> 4 2001-01-04 T1_158 Pinus halepensis 0.82389823 [m^2/m^2]
#> 5 2001-01-05 T1_158 Pinus halepensis 0.82389823 [m^2/m^2]
#> 6 2001-01-06 T1_158 Pinus halepensis 0.82389823 [m^2/m^2]
#> 7 2001-01-07 T1_158 Pinus halepensis 0.82389823 [m^2/m^2]
#> 8 2001-01-08 T1_158 Pinus halepensis 0.82389823 [m^2/m^2]
#> 9 2001-01-09 T1_158 Pinus halepensis 0.82389823 [m^2/m^2]
#> 10 2001-01-10 T1_158 Pinus halepensis 0.82389823 [m^2/m^2]
#> 11 2001-01-01 T2_179 Quercus ilex 0.62107792 [m^2/m^2]
#> 12 2001-01-02 T2_179 Quercus ilex 0.62107792 [m^2/m^2]
#> 13 2001-01-03 T2_179 Quercus ilex 0.62107792 [m^2/m^2]
#> 14 2001-01-04 T2_179 Quercus ilex 0.62107792 [m^2/m^2]
#> 15 2001-01-05 T2_179 Quercus ilex 0.62107792 [m^2/m^2]
#> 16 2001-01-06 T2_179 Quercus ilex 0.62107792 [m^2/m^2]
#> 17 2001-01-07 T2_179 Quercus ilex 0.62107792 [m^2/m^2]
#> 18 2001-01-08 T2_179 Quercus ilex 0.62107792 [m^2/m^2]
#> 19 2001-01-09 T2_179 Quercus ilex 0.62107792 [m^2/m^2]
#> 20 2001-01-10 T2_179 Quercus ilex 0.62107792 [m^2/m^2]
#> 21 2001-01-01 S1_176 Quercus coccifera 0.05274013 [m^2/m^2]
#> 22 2001-01-02 S1_176 Quercus coccifera 0.05274013 [m^2/m^2]
#> 23 2001-01-03 S1_176 Quercus coccifera 0.05274013 [m^2/m^2]
#> 24 2001-01-04 S1_176 Quercus coccifera 0.05274013 [m^2/m^2]
#> 25 2001-01-05 S1_176 Quercus coccifera 0.05274013 [m^2/m^2]
#> 26 2001-01-06 S1_176 Quercus coccifera 0.05274013 [m^2/m^2]
#> 27 2001-01-07 S1_176 Quercus coccifera 0.05274013 [m^2/m^2]
#> 28 2001-01-08 S1_176 Quercus coccifera 0.05274013 [m^2/m^2]
#> 29 2001-01-09 S1_176 Quercus coccifera 0.05274013 [m^2/m^2]
#> 30 2001-01-10 S1_176 Quercus coccifera 0.05274013 [m^2/m^2]
#> LAIlive FPAR AbsorbedSWRFraction Transpiration
#> 1 0.82389823 [m^2/m^2] 92.06855 [%] 34.81224 0.120304166 [L/m^2]
#> 2 0.82389823 [m^2/m^2] 92.06855 [%] 34.81224 0.223143996 [L/m^2]
#> 3 0.82389823 [m^2/m^2] 92.06855 [%] 34.81224 0.177380851 [L/m^2]
#> 4 0.82389823 [m^2/m^2] 92.06855 [%] 34.81224 0.077520563 [L/m^2]
#> 5 0.82389823 [m^2/m^2] 92.06855 [%] 34.81224 0.228393461 [L/m^2]
#> 6 0.82389823 [m^2/m^2] 92.06855 [%] 34.81224 0.164559074 [L/m^2]
#> 7 0.82389823 [m^2/m^2] 92.06855 [%] 34.81224 0.086776787 [L/m^2]
#> 8 0.82389823 [m^2/m^2] 92.06855 [%] 34.81224 0.113345372 [L/m^2]
#> 9 0.82389823 [m^2/m^2] 92.06855 [%] 34.81224 0.270105015 [L/m^2]
#> 10 0.82389823 [m^2/m^2] 92.06855 [%] 34.81224 0.112894793 [L/m^2]
#> 11 0.62107792 [m^2/m^2] 75.49574 [%] 27.96302 0.064545279 [L/m^2]
#> 12 0.62107792 [m^2/m^2] 75.49574 [%] 27.96302 0.119720638 [L/m^2]
#> 13 0.62107792 [m^2/m^2] 75.49574 [%] 27.96302 0.095167914 [L/m^2]
#> 14 0.62107792 [m^2/m^2] 75.49574 [%] 27.96302 0.041597419 [L/m^2]
#> 15 0.62107792 [m^2/m^2] 75.49574 [%] 27.96302 0.122537067 [L/m^2]
#> 16 0.62107792 [m^2/m^2] 75.49574 [%] 27.96302 0.088291861 [L/m^2]
#> 17 0.62107792 [m^2/m^2] 75.49574 [%] 27.96302 0.046558953 [L/m^2]
#> 18 0.62107792 [m^2/m^2] 75.49574 [%] 27.96302 0.060814148 [L/m^2]
#> 19 0.62107792 [m^2/m^2] 75.49574 [%] 27.96302 0.144922539 [L/m^2]
#> 20 0.62107792 [m^2/m^2] 75.49574 [%] 27.96302 0.060575967 [L/m^2]
#> 21 0.05274013 [m^2/m^2] 46.97224 [%] 3.66289 0.009071984 [L/m^2]
#> 22 0.05274013 [m^2/m^2] 46.97224 [%] 3.66289 0.016827005 [L/m^2]
#> 23 0.05274013 [m^2/m^2] 46.97224 [%] 3.66289 0.013376065 [L/m^2]
#> 24 0.05274013 [m^2/m^2] 46.97224 [%] 3.66289 0.005846507 [L/m^2]
#> 25 0.05274013 [m^2/m^2] 46.97224 [%] 3.66289 0.017222861 [L/m^2]
#> 26 0.05274013 [m^2/m^2] 46.97224 [%] 3.66289 0.012409562 [L/m^2]
#> 27 0.05274013 [m^2/m^2] 46.97224 [%] 3.66289 0.006543971 [L/m^2]
#> 28 0.05274013 [m^2/m^2] 46.97224 [%] 3.66289 0.008547564 [L/m^2]
#> 29 0.05274013 [m^2/m^2] 46.97224 [%] 3.66289 0.020369120 [L/m^2]
#> 30 0.05274013 [m^2/m^2] 46.97224 [%] 3.66289 0.008514039 [L/m^2]
#> GrossPhotosynthesis PlantPsi LeafPLC StemPLC PlantWaterBalance
#> 1 1.16694360 [L/m^2] -0.03300000 [MPa] 0 0 0.000000e+00 [L/m^2]
#> 2 2.02349191 [L/m^2] -0.03300000 [MPa] 0 0 0.000000e+00 [L/m^2]
#> 3 1.70651396 [L/m^2] -0.03300000 [MPa] 0 0 0.000000e+00 [L/m^2]
#> 4 0.78213563 [L/m^2] -0.03462455 [MPa] 0 0 -6.068589e-05 [L/m^2]
#> 5 2.10061235 [L/m^2] -0.03300000 [MPa] 0 0 6.068589e-05 [L/m^2]
#> 6 1.72263008 [L/m^2] -0.03336168 [MPa] 0 0 -1.351101e-05 [L/m^2]
#> 7 0.98837489 [L/m^2] -0.03299485 [MPa] 0 0 1.370326e-05 [L/m^2]
#> 8 1.17078977 [L/m^2] -0.03322767 [MPa] 0 0 -8.696912e-06 [L/m^2]
#> 9 2.00921705 [L/m^2] -0.03353450 [MPa] 0 0 -1.146192e-05 [L/m^2]
#> 10 1.11639225 [L/m^2] -0.03420904 [MPa] 0 0 -2.519803e-05 [L/m^2]
#> 11 0.78228374 [L/m^2] -0.03300000 [MPa] 0 0 0.000000e+00 [L/m^2]
#> 12 1.42874621 [L/m^2] -0.03300000 [MPa] 0 0 0.000000e+00 [L/m^2]
#> 13 1.15120639 [L/m^2] -0.03300000 [MPa] 0 0 0.000000e+00 [L/m^2]
#> 14 0.50892440 [L/m^2] -0.03388946 [MPa] 0 0 -1.481840e-05 [L/m^2]
#> 15 1.46701747 [L/m^2] -0.03300000 [MPa] 0 0 1.481840e-05 [L/m^2]
#> 16 1.09004861 [L/m^2] -0.03319078 [MPa] 0 0 -3.178435e-06 [L/m^2]
#> 17 0.58744269 [L/m^2] -0.03282893 [MPa] 0 0 6.028481e-06 [L/m^2]
#> 18 0.74832663 [L/m^2] -0.03304056 [MPa] 0 0 -3.525820e-06 [L/m^2]
#> 19 1.65870682 [L/m^2] -0.03331111 [MPa] 0 0 -4.507366e-06 [L/m^2]
#> 20 0.73754199 [L/m^2] -0.03372383 [MPa] 0 0 -6.875828e-06 [L/m^2]
#> 21 0.07662789 [L/m^2] -0.03300000 [MPa] 0 0 0.000000e+00 [L/m^2]
#> 22 0.13754284 [L/m^2] -0.03300000 [MPa] 0 0 0.000000e+00 [L/m^2]
#> 23 0.11252499 [L/m^2] -0.03300000 [MPa] 0 0 0.000000e+00 [L/m^2]
#> 24 0.05036618 [L/m^2] -0.03418295 [MPa] 0 0 -1.034878e-06 [L/m^2]
#> 25 0.14173928 [L/m^2] -0.03300000 [MPa] 0 0 1.034878e-06 [L/m^2]
#> 26 0.10893396 [L/m^2] -0.03325903 [MPa] 0 0 -2.266077e-07 [L/m^2]
#> 27 0.06004781 [L/m^2] -0.03278612 [MPa] 0 0 4.137207e-07 [L/m^2]
#> 28 0.07452055 [L/m^2] -0.03305076 [MPa] 0 0 -2.315200e-07 [L/m^2]
#> 29 0.15208855 [L/m^2] -0.03339924 [MPa] 0 0 -3.048585e-07 [L/m^2]
#> 30 0.07260908 [L/m^2] -0.03391588 [MPa] 0 0 -4.519669e-07 [L/m^2]
#> LeafRWC StemRWC LFMC PlantStress
#> 1 0.9981628 [%] 0.9998346 [%] 122.02311 [%] 0.004613739
#> 2 0.9981628 [%] 0.9998346 [%] 122.02311 [%] 0.004613739
#> 3 0.9981628 [%] 0.9998346 [%] 122.02311 [%] 0.004613739
#> 4 0.9980724 [%] 0.9998265 [%] 122.01616 [%] 0.004958814
#> 5 0.9981628 [%] 0.9998346 [%] 122.02311 [%] 0.004613739
#> 6 0.9981427 [%] 0.9998328 [%] 122.02156 [%] 0.004689850
#> 7 0.9981631 [%] 0.9998347 [%] 122.02314 [%] 0.004612659
#> 8 0.9981501 [%] 0.9998335 [%] 122.02214 [%] 0.004661600
#> 9 0.9981330 [%] 0.9998320 [%] 122.02083 [%] 0.004726361
#> 10 0.9980955 [%] 0.9998286 [%] 122.01794 [%] 0.004869772
#> 11 0.9991208 [%] 0.9997405 [%] 109.14738 [%] 0.006282261
#> 12 0.9991208 [%] 0.9997405 [%] 109.14738 [%] 0.006282261
#> 13 0.9991208 [%] 0.9997405 [%] 109.14738 [%] 0.006282261
#> 14 0.9990971 [%] 0.9997335 [%] 109.14514 [%] 0.006476584
#> 15 0.9991208 [%] 0.9997405 [%] 109.14738 [%] 0.006282261
#> 16 0.9991157 [%] 0.9997390 [%] 109.14690 [%] 0.006323880
#> 17 0.9991254 [%] 0.9997418 [%] 109.14781 [%] 0.006244971
#> 18 0.9991197 [%] 0.9997402 [%] 109.14728 [%] 0.006291107
#> 19 0.9991125 [%] 0.9997380 [%] 109.14660 [%] 0.006350147
#> 20 0.9991015 [%] 0.9997348 [%] 109.14556 [%] 0.006440342
#> 21 0.9987742 [%] 0.9995054 [%] 98.30066 [%] 0.004541797
#> 22 0.9987742 [%] 0.9995054 [%] 98.30066 [%] 0.004541797
#> 23 0.9987742 [%] 0.9995054 [%] 98.30066 [%] 0.004541797
#> 24 0.9987303 [%] 0.9994876 [%] 98.29739 [%] 0.004754072
#> 25 0.9987742 [%] 0.9995054 [%] 98.30066 [%] 0.004541797
#> 26 0.9987646 [%] 0.9995015 [%] 98.29994 [%] 0.004588090
#> 27 0.9987821 [%] 0.9995086 [%] 98.30125 [%] 0.004503652
#> 28 0.9987723 [%] 0.9995046 [%] 98.30052 [%] 0.004550860
#> 29 0.9987594 [%] 0.9994994 [%] 98.29955 [%] 0.004613192
#> 30 0.9987402 [%] 0.9994916 [%] 98.29813 [%] 0.004705955
#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_158 Pinus halepensis 0.004613739 0
#> 2 2001-01-02 T1_158 Pinus halepensis 0.004613739 0
#> 3 2001-01-03 T1_158 Pinus halepensis 0.004613739 0
#> 4 2001-01-04 T1_158 Pinus halepensis 0.004958814 0
#> 5 2001-01-05 T1_158 Pinus halepensis 0.004613739 0
#> 6 2001-01-06 T1_158 Pinus halepensis 0.004689850 0
#> 7 2001-01-07 T1_158 Pinus halepensis 0.004612659 0
#> 8 2001-01-08 T1_158 Pinus halepensis 0.004661600 0
#> 9 2001-01-09 T1_158 Pinus halepensis 0.004726361 0
#> 10 2001-01-10 T1_158 Pinus halepensis 0.004869772 0
#> 11 2001-01-01 T2_179 Quercus ilex 0.006282261 0
#> 12 2001-01-02 T2_179 Quercus ilex 0.006282261 0
#> 13 2001-01-03 T2_179 Quercus ilex 0.006282261 0
#> 14 2001-01-04 T2_179 Quercus ilex 0.006476584 0
#> 15 2001-01-05 T2_179 Quercus ilex 0.006282261 0
#> 16 2001-01-06 T2_179 Quercus ilex 0.006323880 0
#> 17 2001-01-07 T2_179 Quercus ilex 0.006244971 0
#> 18 2001-01-08 T2_179 Quercus ilex 0.006291107 0
#> 19 2001-01-09 T2_179 Quercus ilex 0.006350147 0
#> 20 2001-01-10 T2_179 Quercus ilex 0.006440342 0
#> 21 2001-01-01 S1_176 Quercus coccifera 0.004541797 0
#> 22 2001-01-02 S1_176 Quercus coccifera 0.004541797 0
#> 23 2001-01-03 S1_176 Quercus coccifera 0.004541797 0
#> 24 2001-01-04 S1_176 Quercus coccifera 0.004754072 0
#> 25 2001-01-05 S1_176 Quercus coccifera 0.004541797 0
#> 26 2001-01-06 S1_176 Quercus coccifera 0.004588090 0
#> 27 2001-01-07 S1_176 Quercus coccifera 0.004503652 0
#> 28 2001-01-08 S1_176 Quercus coccifera 0.004550860 0
#> 29 2001-01-09 S1_176 Quercus coccifera 0.004613192 0
#> 30 2001-01-10 S1_176 Quercus coccifera 0.004705955 0