Description of a forest stand
Number of tree and shrub cohorts, respectively.
Number of species in the seed bank.
An object of class forest has the following structure (see details):
treeData: A data frame of tree cohorts (in rows) and the following columns:
Species: String with species (taxon) name or a non-negative integer for tree species identity (i.e., 0,1,2,...) matching SpParams.
Height: Total tree height (in cm).
DBH: Tree diameter at breast height (in cm).
N: Density (number of individuals/hectare) that the measured tree represents.
Z50: Depth (in mm) corresponding to 50% of fine roots.
Z95: Depth (in mm) corresponding to 95% of fine roots.
shrubData: A data frame of shrub cohorts (in rows) and the following columns:
Species: String with species (taxon) name or a non-negative integer for shrub species identity (i.e., 0,1,2,...) matching SpParams.
Height: Average total height of plants (in cm).
Cover: Percent cover.
Z50: Depth (in mm) corresponding to 50% of fine roots.
Z95: Depth (in mm) corresponding to 95% of fine roots.
herbCover: Percent cover of the herb layer (optional).
herbHeight: Mean height (in cm) of the herb layer (optional).
seedBank: A data frame containing seed bank information with the following columns:
Species: String with species (taxon) name or a non-negative integer for tree species identity (i.e., 0,1,2,...) matching SpParams.
Percent: Amount of seeds in relation to full seed bank (in %).
A data frame with species parameters (see SpParamsMED).
The object returned by summary.forest.
Minimal number of significant digits.
Function summary.forest returns a list with several structural attributes, such as the basal area and LAI of the forest.
Function emptyforest returns an empty forest object.
Function summary.forest can be used to summarize a forest object in the console.
Function emptyforest creates an empty forest object.
The structure presented above for forest objects corresponds to the required data elements.
A forest object can contain additional information when this is available. Data frames treeData
and shrubData can contain additional columns:
LAI: Leaf area index (m2/m2)
FoliarBiomass: Standing dry biomass of leaves (kg/m2)
FuelLoading: Fine fuel loading (kg/m2)
CrownRatio: The ratio between crown length and total height (between 0 and 1)
Similarly, one can define forest list elements herbLAI, herbFoliarBiomass or herbFuelLoading.
All these values are used to override allometry-based estimates of those variables when initializing
inputs for functions spwb or spwb_day. Note that leaf area index, foliar biomass and
fuel loading are related entities, and they are treated as such in medfate. Therefore, users are expected to supply
one or the other, and not all of them at the same time.
data(exampleforest)
data(SpParamsMED)
# Prints forest as a list of data items
exampleforest
#> $treeData
#> Species N DBH Height Z50 Z95
#> 1 Pinus halepensis 168 37.55 800 100 600
#> 2 Quercus ilex 384 14.60 660 300 1000
#>
#> $shrubData
#> Species Cover Height Z50 Z95
#> 1 Quercus coccifera 3.75 80 200 1000
#>
#> $herbCover
#> [1] 10
#>
#> $herbHeight
#> [1] 20
#>
#> $seedBank
#> [1] Species Percent
#> <0 rows> (or 0-length row.names)
#>
#> attr(,"class")
#> [1] "forest" "list"
# Summary of example forest
summary(exampleforest, SpParamsMED)
#> Tree BA (m2/ha): 25.0333016 adult trees: 25.0333016 saplings: 0
#> Density (ind/ha) adult trees: 552 saplings: 0 shrubs (estimated): 749.4923076
#> Cover (%) adult trees: 100 saplings: 0 shrubs: 3.75 herbs: 10
#> LAI (m2/m2) total: 1.7585845 adult trees: 1.5543216 saplings: 0 shrubs: 0.030626 herbs: 0.1736369
#> Fuel loading (kg/m2) total: 0.5588728 adult trees: 0.5255004 saplings: 0 shrubs: 0.0140795 herbs: 0.019293
#> PAR ground (%): NA SWR ground (%): NA