add_forests {medfateland}

Add forests

Description

Creates and adds forest data to an sf object by reading from tree and shrub data tables

Usage

add_forests(
  x,
  tree_table = NULL,
  tree_mapping = NULL,
  shrub_table = NULL,
  shrub_mapping = NULL,
  merge_trees = TRUE,
  merge_shrubs = TRUE,
  SpParams = NULL,
  progress = FALSE
)

Arguments

x

An object of class sf with a valid CRS definition, and a column called 'id'.

tree_table

A data frame with tree records in rows and attributes in columns. Tree records can correspond to individual trees or groups of trees with an associated density.

tree_mapping

A named character vector to specify mappings of columns in tree_table into attributes of treeData. Accepted names (and the corresponding specifications for the columns in tree_table) are:

• "id": Forest stand id.

• "Species": Species code (should follow codes in SpParams).

• "Species.name": Species name. In this case, the species code will be drawn by matching names with species names in SpParams.

• "N": Tree density (in ind./ha).

• "DBH": Diameter at breast height (in cm).

• "Height": Tree height (in cm).

• "plot.size": Plot size (in m2) to which each record refers to. This is used to calculate tree density (stems per hectare) when not supplied.

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

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

shrub_table

A data frame with shrub records in rows and attributes in columns. Records can correspond to individual shrubs (with crown dimensions and height) or groups of shrubs with an associated cover estimate.

shrub_mapping

A named character vector to specify mappings of columns in shrub_table into attributes of shrubData. Accepted names (and the corresponding specifications for the columns in shrub_table) are:

• "id": Forest stand id.

• "Species": Species code (should follow codes in SpParams).

• "Species.name": Species name. In this case, the species code will be drawn by matching names with species names in SpParams.

• "Cover": Shrub cover (in percent).

• "D1": Shrub largest crown diameter (in cm).

• "D2": Shrub crown diameter orthogonal to the largest one (in cm).

• "Height": Shrub height (in cm).

• "plot.size": Plot size (in m2) to which each record refers to. This is used to calculate shrub cover when shrub data is given at the individual level.

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

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

merge_trees

A logical flag to simplify tree cohorts by merging tree records in DBH classes (see forest_mergeTrees).

merge_shrubs

A logical flag to simplify shrub cohorts by merging shrub records in height classes (see forest_mergeShrubs).

SpParams

A data frame with species parameters (see SpParamsMED) from which valid species names are drawn.

progress

A logical flag to include a progress bar while processing the data.

Details

The current implementation will replace existing forests of the indicated 'id' values.

Value

A modified object of class sf with column 'forest'.

Author(s)

Miquel De Cáceres Ainsa, CREAF

See Also

impute_forests(), forest_mapWoodyTables, forest_mergeTrees

Examples

# Load tree data
data(poblet_trees)

# Load species parameters
data(SpParamsMED)

# Define sf with three stands
cc <- rbind(c(1.0215, 41.3432),
            c(1.0219, 41.3443), 
            c(1.0219, 41.3443))
d <- data.frame(lon = cc[,1], lat = cc[,2], 
                id = c("POBL_CTL", "POBL_THI_BEF", "POBL_THI_AFT"))
x <- sf::st_as_sf(d, coords = c("lon", "lat"), crs = 4326)
x

# Define tree mapping 
mapping <- c("id" = "Plot.Code", "Species.name" = "Species", "DBH" = "Diameter.cm")

# Read tree data (warnings are raised)
y_1 <- add_forests(x, tree_table = poblet_trees, tree_mapping = mapping, SpParams = SpParamsMED)

# Correct scientific name for downy oak and repeat to avoid losing tree records
poblet_trees$Species[poblet_trees$Species=="Quercus humilis"] <- "Quercus pubescens"
y_1 <- add_forests(x, tree_table = poblet_trees, tree_mapping = mapping, SpParams = SpParamsMED)

# Display summary of first forest
summary(y_1$forest[[1]], SpParamsMED)

# Add sampled plot surface and repeat reading to correct tree density
poblet_trees$PlotSurface <- 706.86
mapping <- c(mapping, "plot.size" = "PlotSurface")

y_2 <- add_forests(x, tree_table = poblet_trees, tree_mapping = mapping, SpParams = SpParamsMED)
summary(y_2$forest[[1]], SpParamsMED)

# Check forests (height is missing!)
check_forests(y_2)

# Estimate tree height using general allometric
poblet_trees$Height.cm <- 100 * 1.806*poblet_trees$Diameter.cm^0.518

#Modify mapping to include height and repeat
mapping <- c(mapping, "Height" = "Height.cm")

y_3 <- add_forests(x, tree_table = poblet_trees, tree_mapping = mapping, SpParams = SpParamsMED)
summary(y_3$forest[[1]], SpParamsMED)

# Final check
check_forests(y_3)