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Description of a forest stand.

Source: R/dataset_documentation.R
forest.Rd

exampleforest is an example of forest stand description, whereas exampleforest2 is an alternative forest description where leaf area index and crown ratio are supplied instead of structural (density, DBH and cover) parameters.

Format

An object of class forest contains the description of the woody (tree or shrub) cohorts of a forest patch. It has the following structure (see additional columns in 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.

Additionally, it can contain information about the herbaceous layer, seedling/sapling bank and seed bank:

  • herbData: A data frame of herbaceous cohorts (in rows) and the following columns (see an alternative way of defining the herbaceous layer in details):

    • Species: String with species (taxon) name or a non-negative integer for herbaceous 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.

  • seedlingBank: An optional data frame containing seedling/sapling 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 seedling in relation to full seedling bank (in %).

    • Age: A numeric vector indicating age of seedlings/saplings in years.

    • Z50: Depth (in mm) corresponding to 50% of fine roots.

    • Z95: Depth (in mm) corresponding to 95% of fine roots.

  • seedBank: An optional 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 %).

Source

DGCN (2005). Tercer Inventario Forestal Nacional (1997-2007): Catalunya. Dirección General de Conservación de la Naturaleza, Ministerio de Medio Ambiente, Madrid.

Details

The structure presented above for forest objects corresponds to the main (required and optional) data elements and their required columns. A forest object can contain additional information when this is available. Data frames treeData, shrubData and herbData can contain additional columns (Z100 is also commonly used for data frame seedlingBank):

  • Z100: Depth (in mm) corresponding to 100% of fine roots (to specify a truncated root distribution).

  • Age: A numeric vector indicating age of cohorts in years. Used to track cohort age in simulations with fordyn.

  • 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)

  • ObsID: A string identifying plant cohorts at the stage of forest sampling. Used to track the fate of particular plant cohorts through simulations. In fordyn, the use of these identifiers can be combined with the control option keepCohortsWithObsID so that these cohorts are not merged or removed during simulations.

Leaf area index (LAI), foliar biomass (FoliarBiomass), fuel loading (FuelLoading) and CrownRatio are used to override allometry-based estimates of those variables when initializing inputs for functions spwb or spwb_day, but they will have no effect in simulations of growth, growth_day or fordyn. 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.

Instead of defining herbData, the herbaceous layer can be defined collectively (avoiding the need to specify species parameters for herbaceous species), using the following list items:

  • herbCover: Percent cover of the herb layer.

  • herbHeight: Mean height (in cm) of the herb layer.

  • herbLAI: Leaf area index (m2/m2) of the herb layer.

  • herbFoliarBiomass: Dry biomass (kg/m2) of the herb layer.

  • herbFuelLoading: Fine fuel loading (kg/m2) of the herb layer.

See also

forest, spwb, spwbInput

summary.forest, emptyforest, plot.forest

Examples

data(exampleforest)
exampleforest
#> $treeData
#>            Species   DBH Height   N Z50  Z95
#> 1 Pinus halepensis 37.55    800 168 100  300
#> 2     Quercus ilex 14.60    660 384 300 1000
#> 
#> $shrubData
#>             Species Height Cover Z50  Z95
#> 1 Quercus coccifera     80  3.75 200 1000
#> 
#> attr(,"class")
#> [1] "forest" "list"  

data(exampleforest2)
exampleforest2
#> $treeData
#>            Species DBH Height  N Z50  Z95 LAI CrownRatio
#> 1 Pinus halepensis  NA    800 NA 100  300 0.8       0.66
#> 2     Quercus ilex  NA    660 NA 300 1000 0.5       0.60
#> 
#> $shrubData
#>             Species Height Cover Z50  Z95  LAI CrownRatio
#> 1 Quercus coccifera     80    NA 200 1000 0.03        0.8
#> 
#> $herbLAI
#> [1] 0.25
#> 
#> attr(,"class")
#> [1] "forest" "list"