Check the format and validity of a tree inventory data.frame

This function checks whether a tree inventory data.frame is correctly formatted to be used as input for the ray-tracing model. It verifies the presence, type, and validity of mandatory and optional variables describing the geometry and attributes of trees within a forest stand.

Usage

check_inventory(trees_inv, verbose = TRUE)

Arguments

trees_inv

A data.frame with one row per tree and the following columns:

id_tree

Unique identifier of the tree (numeric or character, no duplicates).

x

X position of the tree within the stand (numeric, meters, planar coordinates). Optional if lon and lat are provided.

y

Y position of the tree within the stand (numeric, meters, planar coordinates). Optional if lon and lat are provided.

lon

Longitude of the tree location (numeric, decimal degrees). Optional; if provided with lat, coordinates are converted internally to a UTM planar coordinate system in create_sl_stand().

lat

Latitude of the tree location (numeric, decimal degrees). Optional; see lon.

species

Species name (character).

dbh_cm

Diameter at breast height (1.3 m, in cm).

crown_type

Type of crown geometry. One of "E", "P", "2E", "8E", or "4P".

h_m

Total tree height (numeric, meters).

hbase_m

Height of the crown base (numeric, meters).

hmax_m

Height of the maximum crown radius (numeric, meters). Required only if at least one tree has a crown type "2E" or "8E". For other crown types, the column is optional and the value is internally computed.

rn_m

Crown radius toward North (numeric, meters).

rs_m

Crown radius toward South (numeric, meters).

re_m

Crown radius toward East (numeric, meters).

rw_m

Crown radius toward West (numeric, meters).

crown_lad

Leaf Area Density (m2/m3).

crown_openness

Crown openness (unitless), optional if turbid medium interception. Required if the argument turbid_medium = FALSE in the advanced function run_sl_advanced() (for porous envelope interception). Otherwise, the basic function run_sl() will automatically computed interception in a turbid medium using the crown_lad variable.

verbose

Logical; if TRUE, informative messages and warnings are printed.

Value

Invisibly returns TRUE if all checks pass.

Details

The function performs the following checks and validations:

1

Ensures trees_inv is a non-empty data.frame with all required columns.

2

Checks that id_tree values are unique.

3

Checks that either planar coordinates (x, y) or geographic coordinates (lon, lat) are provided. If only lon and lat are supplied, they are converted to planar UTM coordinates in create_sl_stand(). The plot_inventory() function requires planar coordinates and cannot be used before this conversion.

4

Validates numeric columns (dbh_cm, h_m, hbase_m, rn_m, rs_m, re_m, rw_m) are numeric and non-negative.

5

Verifies that crown_type values are one of "E", "P", "2E", "8E", or "4P".

6

Ensures crown radii are present according to crown type.

7

Checks that hmax_m is provided when required and lies between hbase_m and h_m.

8

Ensures hbase_m < h_m.

9

Verifies that each tree has the crown LAD defined.

10

Provides informative error messages and warnings for all invalid conditions.

Examples

if (FALSE) { # \dontrun{
# Using the example dataset from the package
data_prenovel <- SamsaRaLight::data_prenovel
trees <- data_prenovel$trees

# Check the inventory
check_inventory(trees)

# Quiet mode
check_inventory(trees, verbose = FALSE)
} # }