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): 6.27649
#> Initial soil water content (mm): 290.875
#> Initial snowpack content (mm): 0
#> Performing daily simulations
#>
#> [Year 2001]:
#>
#> Final plant water content (mm): 6.27638
#> Final soil water content (mm): 294.384
#> Final snowpack content (mm): 0
#> Change in plant water content (mm): -0.000104731
#> Plant water balance result (mm): -0.000104731
#> Change in soil water content (mm): 3.50949
#> Soil water balance result (mm): 3.50949
#> 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) 9 Net rainfall (mm) 24
#> Infiltration (mm) 30 Infiltration excess (mm) 0 Saturation excess (mm) 0 Capillarity rise (mm) 0
#> Soil evaporation (mm) 2 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) 21
#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] 3.2972315 [L/m^2] 0.0000 [L/m^2] 3.2972315 [L/m^2]
#> 2 0.0000 [L/m^2] 0.9721473 [L/m^2] 0.0000 [L/m^2] 0.9721473 [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] 4.2353558 [L/m^2] 0.0000 [L/m^2] 4.2353558 [L/m^2]
#> 5 0.0000 [L/m^2] 0.7332674 [L/m^2] 0.0000 [L/m^2] 0.7332674 [L/m^2]
#> 6 0.0000 [L/m^2] 11.5940646 [L/m^2] 0.0000 [L/m^2] 11.5940646 [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] 3.5457087 [L/m^2] 5.3774 [L/m^2] 8.9231083 [L/m^2]
#> InfiltrationExcess SaturationExcess Runoff DeepDrainage
#> 1 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 2.6175309 [L/m^2]
#> 2 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 0.1881079 [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] 3.0529310 [L/m^2]
#> 5 0 [L/m^2] 0 [L/m^2] 0 [L/m^2] 0.1206369 [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] 2.3794465 [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] 2.2515780 [L/m^2] 1.571877 [L/m^2] 0.4387811 [L/m^2]
#> 2 0 [L/m^2] 2.4730095 [L/m^2] 1.526144 [L/m^2] 0.5000000 [L/m^2]
#> 3 0 [L/m^2] 0.7182154 [L/m^2] 0.000000 [L/m^2] 0.3630184 [L/m^2]
#> 4 0 [L/m^2] 1.8630006 [L/m^2] 1.561617 [L/m^2] 0.1461396 [L/m^2]
#> 5 0 [L/m^2] 2.1085118 [L/m^2] 1.151134 [L/m^2] 0.5000000 [L/m^2]
#> 6 0 [L/m^2] 2.3578418 [L/m^2] 1.765736 [L/m^2] 0.2625835 [L/m^2]
#> 7 0 [L/m^2] 0.1737800 [L/m^2] 0.000000 [L/m^2] 0.0000000 [L/m^2]
#> 8 0 [L/m^2] 0.2269834 [L/m^2] 0.000000 [L/m^2] 0.0000000 [L/m^2]
#> 9 0 [L/m^2] 0.5408987 [L/m^2] 0.000000 [L/m^2] 0.0000000 [L/m^2]
#> 10 0 [L/m^2] 1.9575383 [L/m^2] 1.572059 [L/m^2] 0.1594079 [L/m^2]
#> HerbTranspiration PlantExtraction Transpiration MistletoeTranspiration
#> 1 0 [L/m^2] 0.2409196 [L/m^2] 0.2409196 [L/m^2] 0 [L/m^2]
#> 2 0 [L/m^2] 0.4468653 [L/m^2] 0.4468653 [L/m^2] 0 [L/m^2]
#> 3 0 [L/m^2] 0.3551970 [L/m^2] 0.3551970 [L/m^2] 0 [L/m^2]
#> 4 0 [L/m^2] 0.1552438 [L/m^2] 0.1552438 [L/m^2] 0 [L/m^2]
#> 5 0 [L/m^2] 0.4573778 [L/m^2] 0.4573778 [L/m^2] 0 [L/m^2]
#> 6 0 [L/m^2] 0.3295223 [L/m^2] 0.3295223 [L/m^2] 0 [L/m^2]
#> 7 0 [L/m^2] 0.1737800 [L/m^2] 0.1737800 [L/m^2] 0 [L/m^2]
#> 8 0 [L/m^2] 0.2269834 [L/m^2] 0.2269834 [L/m^2] 0 [L/m^2]
#> 9 0 [L/m^2] 0.5408987 [L/m^2] 0.5408987 [L/m^2] 0 [L/m^2]
#> 10 0 [L/m^2] 0.2260713 [L/m^2] 0.2260713 [L/m^2] 0 [L/m^2]
#> HydraulicRedistribution LAI LAIherb LAIlive
#> 1 0.000000000 [L/m^2] 1.826041 [m^2/m^2] 0 [m^2/m^2] 1.826041 [m^2/m^2]
#> 2 0.000000000 [L/m^2] 1.826041 [m^2/m^2] 0 [m^2/m^2] 1.826041 [m^2/m^2]
#> 3 0.000000000 [L/m^2] 1.826041 [m^2/m^2] 0 [m^2/m^2] 1.826041 [m^2/m^2]
#> 4 0.000000000 [L/m^2] 1.826041 [m^2/m^2] 0 [m^2/m^2] 1.826041 [m^2/m^2]
#> 5 0.000000000 [L/m^2] 1.826041 [m^2/m^2] 0 [m^2/m^2] 1.826041 [m^2/m^2]
#> 6 0.000000000 [L/m^2] 1.826041 [m^2/m^2] 0 [m^2/m^2] 1.826041 [m^2/m^2]
#> 7 0.003861640 [L/m^2] 1.826041 [m^2/m^2] 0 [m^2/m^2] 1.826041 [m^2/m^2]
#> 8 0.004609261 [L/m^2] 1.826041 [m^2/m^2] 0 [m^2/m^2] 1.826041 [m^2/m^2]
#> 9 0.000000000 [L/m^2] 1.826041 [m^2/m^2] 0 [m^2/m^2] 1.826041 [m^2/m^2]
#> 10 0.000000000 [L/m^2] 1.826041 [m^2/m^2] 0 [m^2/m^2] 1.826041 [m^2/m^2]
#> LAIexpanded LAIdead LAImistletoe Cm LgroundPAR
#> 1 1.826041 [m^2/m^2] 0 [m^2/m^2] 0 1.517698 [L/m^2] 38.91249 [%]
#> 2 1.826041 [m^2/m^2] 0 [m^2/m^2] 0 1.517698 [L/m^2] 38.91249 [%]
#> 3 1.826041 [m^2/m^2] 0 [m^2/m^2] 0 1.517698 [L/m^2] 38.91249 [%]
#> 4 1.826041 [m^2/m^2] 0 [m^2/m^2] 0 1.517698 [L/m^2] 38.91249 [%]
#> 5 1.826041 [m^2/m^2] 0 [m^2/m^2] 0 1.517698 [L/m^2] 38.91249 [%]
#> 6 1.826041 [m^2/m^2] 0 [m^2/m^2] 0 1.517698 [L/m^2] 38.91249 [%]
#> 7 1.826041 [m^2/m^2] 0 [m^2/m^2] 0 1.517698 [L/m^2] 38.91249 [%]
#> 8 1.826041 [m^2/m^2] 0 [m^2/m^2] 0 1.517698 [L/m^2] 38.91249 [%]
#> 9 1.826041 [m^2/m^2] 0 [m^2/m^2] 0 1.517698 [L/m^2] 38.91249 [%]
#> 10 1.826041 [m^2/m^2] 0 [m^2/m^2] 0 1.517698 [L/m^2] 38.91249 [%]
#> LgroundSWR SWE
#> 1 49.70066 [%] 0.0000 [L/m^2]
#> 2 49.70066 [%] 0.0000 [L/m^2]
#> 3 49.70066 [%] 0.0000 [L/m^2]
#> 4 49.70066 [%] 0.0000 [L/m^2]
#> 5 49.70066 [%] 0.0000 [L/m^2]
#> 6 49.70066 [%] 0.0000 [L/m^2]
#> 7 49.70066 [%] 5.3774 [L/m^2]
#> 8 49.70066 [%] 5.3774 [L/m^2]
#> 9 49.70066 [%] 5.3774 [L/m^2]
#> 10 49.70066 [%] 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 0.3022711 0.9976116 0.9964181 68.01099 [L/m^2]
#> 3 2001-01-03 1 0.2995179 0.9885253 0.9827911 67.39154 [L/m^2]
#> 4 2001-01-04 1 0.3029947 1.0000000 1.0000000 68.17381 [L/m^2]
#> 5 2001-01-05 1 0.3014625 0.9949431 0.9924161 67.82907 [L/m^2]
#> 6 2001-01-06 1 0.3029947 1.0000000 1.0000000 68.17381 [L/m^2]
#> 7 2001-01-07 1 0.3023870 0.9979944 0.9969922 68.03709 [L/m^2]
#> 8 2001-01-08 1 0.3015967 0.9953860 0.9930803 67.85926 [L/m^2]
#> 9 2001-01-09 1 0.2998639 0.9896669 0.9845032 67.46937 [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 0.3028143 0.9994046 0.9991070 116.58351 [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 0.3029382 0.9998134 0.9997202 116.63120 [L/m^2]
#> 18 2001-01-08 2 0.3028616 0.9995605 0.9993408 116.60170 [L/m^2]
#> 19 2001-01-09 2 0.3025978 0.9986900 0.9980354 116.50016 [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 0.3029286 0.9997818 0.9996728 75.73215 [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 0.3028843 0.9996355 0.9994533 75.72107 [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 0.3028670 0.9995783 0.9993676 30.28670 [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 0.3683527 1.2157066 1.3235001 36.83527 [L/m^2]
#> 37 2001-01-07 4 0.3269857 1.0791796 1.1187473 32.69857 [L/m^2]
#> 38 2001-01-08 4 0.3029947 1.0000000 1.0000000 30.29947 [L/m^2]
#> 39 2001-01-09 4 0.3027762 0.9992788 0.9989183 30.27762 [L/m^2]
#> 40 2001-01-10 4 0.3380896 1.1158268 1.1737080 33.80896 [L/m^2]
#> 41 2001-01-01 Overall 0.3029947 1.0000000 1.0000000 290.87494 [L/m^2]
#> 42 2001-01-02 Overall 0.3028251 0.9994402 0.9991605 290.71211 [L/m^2]
#> 43 2001-01-03 Overall 0.3020770 0.9969711 0.9954574 289.99390 [L/m^2]
#> 44 2001-01-04 Overall 0.3029947 1.0000000 1.0000000 290.87494 [L/m^2]
#> 45 2001-01-05 Overall 0.3026356 0.9988148 0.9982225 290.53019 [L/m^2]
#> 46 2001-01-06 Overall 0.3098029 1.0224694 1.0336979 297.41074 [L/m^2]
#> 47 2001-01-07 Overall 0.3053287 1.0077030 1.0115523 293.11554 [L/m^2]
#> 48 2001-01-08 Overall 0.3026137 0.9987423 0.9981138 290.50911 [L/m^2]
#> 49 2001-01-09 Overall 0.3020502 0.9968828 0.9953250 289.96822 [L/m^2]
#> 50 2001-01-10 Overall 0.3066504 1.0120653 1.0180946 294.38443 [L/m^2]
#> Psi PlantExt HydraulicInput
#> 1 -0.03300000 [MPa] 0.1983726725 [L/m^2] 0.000000000 [L/m^2]
#> 2 -0.03337552 [MPa] 0.3679479453 [L/m^2] 0.000000000 [L/m^2]
#> 3 -0.03484341 [MPa] 0.2564321880 [L/m^2] 0.000000000 [L/m^2]
#> 4 -0.03300000 [MPa] 0.1112605361 [L/m^2] 0.000000000 [L/m^2]
#> 5 -0.03380010 [MPa] 0.3766039244 [L/m^2] 0.000000000 [L/m^2]
#> 6 -0.03300000 [MPa] 0.2373576762 [L/m^2] 0.000000000 [L/m^2]
#> 7 -0.03331505 [MPa] 0.1367284850 [L/m^2] 0.000000000 [L/m^2]
#> 8 -0.03372926 [MPa] 0.1778246865 [L/m^2] 0.000000000 [L/m^2]
#> 9 -0.03465549 [MPa] 0.3898945850 [L/m^2] 0.000000000 [L/m^2]
#> 10 -0.03300000 [MPa] 0.1622757075 [L/m^2] 0.000000000 [L/m^2]
#> 11 -0.03300000 [MPa] 0.0387602762 [L/m^2] 0.000000000 [L/m^2]
#> 12 -0.03300000 [MPa] 0.0718937937 [L/m^2] 0.000000000 [L/m^2]
#> 13 -0.03309323 [MPa] 0.0694594280 [L/m^2] 0.000000000 [L/m^2]
#> 14 -0.03300000 [MPa] 0.0307368274 [L/m^2] 0.000000000 [L/m^2]
#> 15 -0.03300000 [MPa] 0.0735850959 [L/m^2] 0.000000000 [L/m^2]
#> 16 -0.03300000 [MPa] 0.0649329291 [L/m^2] 0.000000000 [L/m^2]
#> 17 -0.03302919 [MPa] 0.0217662492 [L/m^2] 0.000000000 [L/m^2]
#> 18 -0.03306879 [MPa] 0.0295065465 [L/m^2] 0.000000000 [L/m^2]
#> 19 -0.03320544 [MPa] 0.1015382875 [L/m^2] 0.000000000 [L/m^2]
#> 20 -0.03300000 [MPa] 0.0433759302 [L/m^2] 0.000000000 [L/m^2]
#> 21 -0.03300000 [MPa] 0.0031558555 [L/m^2] 0.000000000 [L/m^2]
#> 22 -0.03300000 [MPa] 0.0058535812 [L/m^2] 0.000000000 [L/m^2]
#> 23 -0.03303413 [MPa] 0.0165283845 [L/m^2] 0.000000000 [L/m^2]
#> 24 -0.03300000 [MPa] 0.0076703051 [L/m^2] 0.000000000 [L/m^2]
#> 25 -0.03300000 [MPa] 0.0059912868 [L/m^2] 0.000000000 [L/m^2]
#> 26 -0.03300000 [MPa] 0.0153708189 [L/m^2] 0.000000000 [L/m^2]
#> 27 -0.03300000 [MPa] -0.0035537249 [L/m^2] 0.003861640 [L/m^2]
#> 28 -0.03300000 [MPa] -0.0039719816 [L/m^2] 0.004609261 [L/m^2]
#> 29 -0.03305704 [MPa] 0.0276124702 [L/m^2] 0.000000000 [L/m^2]
#> 30 -0.03300000 [MPa] 0.0120198008 [L/m^2] 0.000000000 [L/m^2]
#> 31 -0.03300000 [MPa] 0.0006307718 [L/m^2] 0.000000000 [L/m^2]
#> 32 -0.03300000 [MPa] 0.0011699756 [L/m^2] 0.000000000 [L/m^2]
#> 33 -0.03306600 [MPa] 0.0127769910 [L/m^2] 0.000000000 [L/m^2]
#> 34 -0.03300000 [MPa] 0.0055761451 [L/m^2] 0.000000000 [L/m^2]
#> 35 -0.03300000 [MPa] 0.0011974993 [L/m^2] 0.000000000 [L/m^2]
#> 36 -0.01082795 [MPa] 0.0118608435 [L/m^2] 0.000000000 [L/m^2]
#> 37 -0.02258481 [MPa] 0.0188389967 [L/m^2] 0.000000000 [L/m^2]
#> 38 -0.03300000 [MPa] 0.0236241226 [L/m^2] 0.000000000 [L/m^2]
#> 39 -0.03311296 [MPa] 0.0218533541 [L/m^2] 0.000000000 [L/m^2]
#> 40 -0.01882523 [MPa] 0.0083998431 [L/m^2] 0.000000000 [L/m^2]
#> 41 -0.03300000 [MPa] 0.2409195760 [L/m^2] 0.000000000 [L/m^2]
#> 42 -0.03308801 [MPa] 0.4468652958 [L/m^2] 0.000000000 [L/m^2]
#> 43 -0.03348520 [MPa] 0.3551969915 [L/m^2] 0.000000000 [L/m^2]
#> 44 -0.03300000 [MPa] 0.1552438137 [L/m^2] 0.000000000 [L/m^2]
#> 45 -0.03318752 [MPa] 0.4573778063 [L/m^2] 0.000000000 [L/m^2]
#> 46 -0.03069041 [MPa] 0.3295222677 [L/m^2] 0.000000000 [L/m^2]
#> 47 -0.03200063 [MPa] 0.1737800060 [L/m^2] 0.003861640 [L/m^2]
#> 48 -0.03319851 [MPa] 0.2269833740 [L/m^2] 0.004609261 [L/m^2]
#> 49 -0.03349702 [MPa] 0.5408986968 [L/m^2] 0.000000000 [L/m^2]
#> 50 -0.03152346 [MPa] 0.2260712817 [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 1.20935408 [m^2/m^2]
#> 2 2001-01-02 T1_148 Pinus halepensis 1.20935408 [m^2/m^2]
#> 3 2001-01-03 T1_148 Pinus halepensis 1.20935408 [m^2/m^2]
#> 4 2001-01-04 T1_148 Pinus halepensis 1.20935408 [m^2/m^2]
#> 5 2001-01-05 T1_148 Pinus halepensis 1.20935408 [m^2/m^2]
#> 6 2001-01-06 T1_148 Pinus halepensis 1.20935408 [m^2/m^2]
#> 7 2001-01-07 T1_148 Pinus halepensis 1.20935408 [m^2/m^2]
#> 8 2001-01-08 T1_148 Pinus halepensis 1.20935408 [m^2/m^2]
#> 9 2001-01-09 T1_148 Pinus halepensis 1.20935408 [m^2/m^2]
#> 10 2001-01-10 T1_148 Pinus halepensis 1.20935408 [m^2/m^2]
#> 11 2001-01-01 T2_168 Quercus ilex 0.56790878 [m^2/m^2]
#> 12 2001-01-02 T2_168 Quercus ilex 0.56790878 [m^2/m^2]
#> 13 2001-01-03 T2_168 Quercus ilex 0.56790878 [m^2/m^2]
#> 14 2001-01-04 T2_168 Quercus ilex 0.56790878 [m^2/m^2]
#> 15 2001-01-05 T2_168 Quercus ilex 0.56790878 [m^2/m^2]
#> 16 2001-01-06 T2_168 Quercus ilex 0.56790878 [m^2/m^2]
#> 17 2001-01-07 T2_168 Quercus ilex 0.56790878 [m^2/m^2]
#> 18 2001-01-08 T2_168 Quercus ilex 0.56790878 [m^2/m^2]
#> 19 2001-01-09 T2_168 Quercus ilex 0.56790878 [m^2/m^2]
#> 20 2001-01-10 T2_168 Quercus ilex 0.56790878 [m^2/m^2]
#> 21 2001-01-01 S1_165 Quercus coccifera 0.04877848 [m^2/m^2]
#> 22 2001-01-02 S1_165 Quercus coccifera 0.04877848 [m^2/m^2]
#> 23 2001-01-03 S1_165 Quercus coccifera 0.04877848 [m^2/m^2]
#> 24 2001-01-04 S1_165 Quercus coccifera 0.04877848 [m^2/m^2]
#> 25 2001-01-05 S1_165 Quercus coccifera 0.04877848 [m^2/m^2]
#> 26 2001-01-06 S1_165 Quercus coccifera 0.04877848 [m^2/m^2]
#> 27 2001-01-07 S1_165 Quercus coccifera 0.04877848 [m^2/m^2]
#> 28 2001-01-08 S1_165 Quercus coccifera 0.04877848 [m^2/m^2]
#> 29 2001-01-09 S1_165 Quercus coccifera 0.04877848 [m^2/m^2]
#> 30 2001-01-10 S1_165 Quercus coccifera 0.04877848 [m^2/m^2]
#> LAIlive FPAR AbsorbedSWRFraction Transpiration
#> 1 1.20935408 [m^2/m^2] 88.57701 [%] 44.432640 0.169631434 [L/m^2]
#> 2 1.20935408 [m^2/m^2] 88.57701 [%] 44.432640 0.314637782 [L/m^2]
#> 3 1.20935408 [m^2/m^2] 88.57701 [%] 44.432640 0.250091911 [L/m^2]
#> 4 1.20935408 [m^2/m^2] 88.57701 [%] 44.432640 0.109302523 [L/m^2]
#> 5 1.20935408 [m^2/m^2] 88.57701 [%] 44.432640 0.322039638 [L/m^2]
#> 6 1.20935408 [m^2/m^2] 88.57701 [%] 44.432640 0.232012134 [L/m^2]
#> 7 1.20935408 [m^2/m^2] 88.57701 [%] 44.432640 0.122357110 [L/m^2]
#> 8 1.20935408 [m^2/m^2] 88.57701 [%] 44.432640 0.159817006 [L/m^2]
#> 9 1.20935408 [m^2/m^2] 88.57701 [%] 44.432640 0.380840716 [L/m^2]
#> 10 1.20935408 [m^2/m^2] 88.57701 [%] 44.432640 0.159171238 [L/m^2]
#> 11 0.56790878 [m^2/m^2] 69.05317 [%] 24.578915 0.062675617 [L/m^2]
#> 12 0.56790878 [m^2/m^2] 69.05317 [%] 24.578915 0.116252729 [L/m^2]
#> 13 0.56790878 [m^2/m^2] 69.05317 [%] 24.578915 0.092407399 [L/m^2]
#> 14 0.56790878 [m^2/m^2] 69.05317 [%] 24.578915 0.040391773 [L/m^2]
#> 15 0.56790878 [m^2/m^2] 69.05317 [%] 24.578915 0.118987576 [L/m^2]
#> 16 0.56790878 [m^2/m^2] 69.05317 [%] 24.578915 0.085730377 [L/m^2]
#> 17 0.56790878 [m^2/m^2] 69.05317 [%] 24.578915 0.045210220 [L/m^2]
#> 18 0.56790878 [m^2/m^2] 69.05317 [%] 24.578915 0.059051908 [L/m^2]
#> 19 0.56790878 [m^2/m^2] 69.05317 [%] 24.578915 0.140721974 [L/m^2]
#> 20 0.56790878 [m^2/m^2] 69.05317 [%] 24.578915 0.058818662 [L/m^2]
#> 21 0.04877848 [m^2/m^2] 39.89406 [%] 3.156504 0.008612525 [L/m^2]
#> 22 0.04877848 [m^2/m^2] 39.89406 [%] 3.156504 0.015974785 [L/m^2]
#> 23 0.04877848 [m^2/m^2] 39.89406 [%] 3.156504 0.012697682 [L/m^2]
#> 24 0.04877848 [m^2/m^2] 39.89406 [%] 3.156504 0.005549517 [L/m^2]
#> 25 0.04877848 [m^2/m^2] 39.89406 [%] 3.156504 0.016350592 [L/m^2]
#> 26 0.04877848 [m^2/m^2] 39.89406 [%] 3.156504 0.011779757 [L/m^2]
#> 27 0.04877848 [m^2/m^2] 39.89406 [%] 3.156504 0.006212676 [L/m^2]
#> 28 0.04877848 [m^2/m^2] 39.89406 [%] 3.156504 0.008114461 [L/m^2]
#> 29 0.04877848 [m^2/m^2] 39.89406 [%] 3.156504 0.019336007 [L/m^2]
#> 30 0.04877848 [m^2/m^2] 39.89406 [%] 3.156504 0.008081382 [L/m^2]
#> GrossPhotosynthesis PlantPsi LeafPLC StemPLC
#> 1 1.61242254 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 2 2.79595687 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 3 2.35779525 [L/m^2] -0.03335674 [MPa] 0.0000000000 0
#> 4 1.08068388 [L/m^2] -0.03475656 [MPa] 0.0000000000 0
#> 5 2.90251792 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 6 2.38003980 [L/m^2] -0.03376019 [MPa] 0.0000000000 0
#> 7 1.36568545 [L/m^2] -0.03299503 [MPa] 0.0000000000 0
#> 8 1.61771289 [L/m^2] -0.03329804 [MPa] 0.0000000000 0
#> 9 2.77613711 [L/m^2] -0.03369614 [MPa] 0.0000000000 0
#> 10 1.54244904 [L/m^2] -0.03458319 [MPa] 0.0000000000 0
#> 11 0.75011437 [L/m^2] -0.03300000 [MPa] 0.0009945146 0
#> 12 1.36999277 [L/m^2] -0.03300000 [MPa] 0.0009945146 0
#> 13 1.10382046 [L/m^2] -0.03318817 [MPa] 0.0010169423 0
#> 14 0.48798768 [L/m^2] -0.03396887 [MPa] 0.0011104407 0
#> 15 1.40669023 [L/m^2] -0.03300000 [MPa] 0.0009945146 0
#> 16 1.04517492 [L/m^2] -0.03340110 [MPa] 0.0010423718 0
#> 17 0.56328471 [L/m^2] -0.03283652 [MPa] 0.0009750646 0
#> 18 0.71754569 [L/m^2] -0.03309120 [MPa] 0.0010053793 0
#> 19 1.59046701 [L/m^2] -0.03339652 [MPa] 0.0010418233 0
#> 20 0.70718101 [L/m^2] -0.03392612 [MPa] 0.0011053024 0
#> 21 0.06854474 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 22 0.12303404 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 23 0.10064778 [L/m^2] -0.03325548 [MPa] 0.0000000000 0
#> 24 0.04504606 [L/m^2] -0.03428379 [MPa] 0.0000000000 0
#> 25 0.12678781 [L/m^2] -0.03300000 [MPa] 0.0000000000 0
#> 26 0.09743214 [L/m^2] -0.03354466 [MPa] 0.0000000000 0
#> 27 0.05371475 [L/m^2] -0.03279444 [MPa] 0.0000000000 0
#> 28 0.06665803 [L/m^2] -0.03311813 [MPa] 0.0000000000 0
#> 29 0.13603484 [L/m^2] -0.03351515 [MPa] 0.0000000000 0
#> 30 0.06493816 [L/m^2] -0.03418719 [MPa] 0.0000000000 0
#> PlantWaterBalance LeafRWC StemRWC LFMC PlantStress
#> 1 -8.881784e-16 [L/m^2] 0.9981628 [%] 0.9998346 [%] 122.02311 [%] 0.004613739
#> 2 0.000000e+00 [L/m^2] 0.9981628 [%] 0.9998346 [%] 122.02311 [%] 0.004613739
#> 3 -2.218448e-05 [L/m^2] 0.9981429 [%] 0.9998329 [%] 122.02159 [%] 0.004688806
#> 4 -8.705002e-05 [L/m^2] 0.9980650 [%] 0.9998258 [%] 122.01559 [%] 0.004987215
#> 5 1.092345e-04 [L/m^2] 0.9981628 [%] 0.9998346 [%] 122.02311 [%] 0.004613739
#> 6 -4.727401e-05 [L/m^2] 0.9981205 [%] 0.9998308 [%] 122.01986 [%] 0.004774186
#> 7 4.758305e-05 [L/m^2] 0.9981631 [%] 0.9998347 [%] 122.02313 [%] 0.004612696
#> 8 -1.884324e-05 [L/m^2] 0.9981462 [%] 0.9998332 [%] 122.02184 [%] 0.004676427
#> 9 -2.475704e-05 [L/m^2] 0.9981240 [%] 0.9998312 [%] 122.02013 [%] 0.004760599
#> 10 -5.516260e-05 [L/m^2] 0.9980747 [%] 0.9998267 [%] 122.01634 [%] 0.004949928
#> 11 0.000000e+00 [L/m^2] 0.9991208 [%] 0.9997405 [%] 109.14738 [%] 0.006282261
#> 12 0.000000e+00 [L/m^2] 0.9991208 [%] 0.9997405 [%] 109.14738 [%] 0.006282261
#> 13 -1.072842e-06 [L/m^2] 0.9991158 [%] 0.9997390 [%] 109.14691 [%] 0.006323310
#> 14 -4.451059e-06 [L/m^2] 0.9990950 [%] 0.9997329 [%] 109.14494 [%] 0.006493968
#> 15 5.523901e-06 [L/m^2] 0.9991208 [%] 0.9997405 [%] 109.14738 [%] 0.006282261
#> 16 -2.286844e-06 [L/m^2] 0.9991101 [%] 0.9997373 [%] 109.14637 [%] 0.006369800
#> 17 3.218894e-06 [L/m^2] 0.9991251 [%] 0.9997418 [%] 109.14779 [%] 0.006246626
#> 18 -1.452022e-06 [L/m^2] 0.9991184 [%] 0.9997398 [%] 109.14715 [%] 0.006302152
#> 19 -1.740712e-06 [L/m^2] 0.9991102 [%] 0.9997374 [%] 109.14638 [%] 0.006368798
#> 20 -3.019489e-06 [L/m^2] 0.9990961 [%] 0.9997332 [%] 109.14505 [%] 0.006484609
#> 21 0.000000e+00 [L/m^2] 0.9987189 [%] 0.9995007 [%] 98.29725 [%] 0.007310922
#> 22 0.000000e+00 [L/m^2] 0.9987189 [%] 0.9995007 [%] 98.29725 [%] 0.007310922
#> 23 -2.144826e-07 [L/m^2] 0.9987089 [%] 0.9994967 [%] 98.29652 [%] 0.007384316
#> 24 -8.634388e-07 [L/m^2] 0.9986689 [%] 0.9994810 [%] 98.29356 [%] 0.007681368
#> 25 1.077921e-06 [L/m^2] 0.9987189 [%] 0.9995007 [%] 98.29725 [%] 0.007310922
#> 26 -4.572688e-07 [L/m^2] 0.9986977 [%] 0.9994923 [%] 98.29569 [%] 0.007467586
#> 27 6.298313e-07 [L/m^2] 0.9987268 [%] 0.9995038 [%] 98.29784 [%] 0.007251989
#> 28 -2.717307e-07 [L/m^2] 0.9987143 [%] 0.9994989 [%] 98.29691 [%] 0.007344837
#> 29 -3.333209e-07 [L/m^2] 0.9986988 [%] 0.9994928 [%] 98.29577 [%] 0.007459078
#> 30 -5.643111e-07 [L/m^2] 0.9986727 [%] 0.9994825 [%] 98.29384 [%] 0.007653352
#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 0.004688806 0
#> 4 2001-01-04 T1_148 Pinus halepensis 0.004987215 0
#> 5 2001-01-05 T1_148 Pinus halepensis 0.004613739 0
#> 6 2001-01-06 T1_148 Pinus halepensis 0.004774186 0
#> 7 2001-01-07 T1_148 Pinus halepensis 0.004612696 0
#> 8 2001-01-08 T1_148 Pinus halepensis 0.004676427 0
#> 9 2001-01-09 T1_148 Pinus halepensis 0.004760599 0
#> 10 2001-01-10 T1_148 Pinus halepensis 0.004949928 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 0.006323310 0
#> 14 2001-01-04 T2_168 Quercus ilex 0.006493968 0
#> 15 2001-01-05 T2_168 Quercus ilex 0.006282261 0
#> 16 2001-01-06 T2_168 Quercus ilex 0.006369800 0
#> 17 2001-01-07 T2_168 Quercus ilex 0.006246626 0
#> 18 2001-01-08 T2_168 Quercus ilex 0.006302152 0
#> 19 2001-01-09 T2_168 Quercus ilex 0.006368798 0
#> 20 2001-01-10 T2_168 Quercus ilex 0.006484609 0
#> 21 2001-01-01 S1_165 Quercus coccifera 0.007310922 0
#> 22 2001-01-02 S1_165 Quercus coccifera 0.007310922 0
#> 23 2001-01-03 S1_165 Quercus coccifera 0.007384316 0
#> 24 2001-01-04 S1_165 Quercus coccifera 0.007681368 0
#> 25 2001-01-05 S1_165 Quercus coccifera 0.007310922 0
#> 26 2001-01-06 S1_165 Quercus coccifera 0.007467586 0
#> 27 2001-01-07 S1_165 Quercus coccifera 0.007251989 0
#> 28 2001-01-08 S1_165 Quercus coccifera 0.007344837 0
#> 29 2001-01-09 S1_165 Quercus coccifera 0.007459078 0
#> 30 2001-01-10 S1_165 Quercus coccifera 0.007653352 0