GCubeR (version 0.1.3)

biomass_calc: Total Biomass, Carbon and CO2 Estimation for Tree Species

Description

Computes total biomass (aboveground + root), carbon content and CO2 equivalent for tree species using CNPF (with multiple trunk volume sources) and Vallet methods.

Usage

biomass_calc(data, na_action = c("error", "omit"), output = NULL)

Value

A data frame with one row per tree, including:

• species_code: species name in uppercase Latin format.

• dagnelie_vc22_1, dagnelie_vc22_1g, dagnelie_vc22_2, vallet_vc22, rondeux_vc22,algan_vc22: optional trunk volume inputs (in m3).

• vallet_vta: optional total aboveground volume (in m3) for Vallet method.

• vc22_dagnelie: selected trunk volume used for CNPF (Dagnelie), based on priority.

• vc22_source: name of the Dagnelie column used to populate vc22.

CNPF method outputs:

• From Dagnelie (priority selection):

  • cnpf_dagnelie_bag, cnpf_dagnelie_bbg, cnpf_dagnelie_btot, cnpf_dagnelie_c, cnpf_dagnelie_co2

• From Vallet trunk volume (vallet_vc22):

  • cnpf_vallet_bag, cnpf_vallet_bbg, cnpf_vallet_btot, cnpf_vallet_c, cnpf_vallet_co2

• From Rondeux trunk volume (rondeux_vc22):

  • cnpf_rondeux_bag, cnpf_rondeux_bbg, cnpf_rondeux_btot, cnpf_rondeux_c, cnpf_rondeux_co2

• From Algan trunk volume (algan_vc22):

  • cnpf_algan_bag, cnpf_algan_bbg, cnpf_algan_btot, cnpf_algan_c, cnpf_algan_co2

Vallet method outputs (if vallet_vta is available and species is compatible):

• vallet_bag, vallet_bbg, vallet_btot, vallet_c, vallet_co2

Arguments

data

A data frame containing volume and species information for each tree. Must include:

• species_code: species name in uppercase Latin format (e.g. "PICEA_ABIES"), matched against a density table.

• At least one volume column:

  • For CNPF method (trunk volume):

    • Dagnelie equations: dagnelie_vc22_2, dagnelie_vc22_1g, dagnelie_vc22_1 (priority order: dagnelie_vc22_2 > dagnelie_vc22_1g > dagnelie_vc22_1)

    • Vallet equation: vallet_vc22

    • Rondeux equation: rondeux_vc22

    • Algan equation: algan_vc22

  • For Vallet method (total aboveground volume): vallet_vta

If multiple trunk volumes are provided, CNPF is computed separately for each source. If only one is available, the corresponding method is applied. All volume columns must be numeric and expressed in cubic meters (m3).

na_action

How to handle missing values. "error" (default) stops if any required value is missing. "omit" removes rows with missing values.

output

Optional file path where the resulting data frame should be exported as a CSV. If NULL (default), no file is written. Export is handled by the utility function export_output() and failures trigger warnings without interrupting execution.

Details

• The density table provides:

  • density: wood density in tonnes of dry matter per cubic meter (t/m3).

  • con_broad: species group, either "conifer" or "broadleaf".

• The expansion factor feb is derived from con_broad:

  • feb = 1.3 for conifers

  • feb = 1.56 for broadleaves

• Dagnelie trunk volume (vc22_dagnelie) is automatically selected from the best available column, in the following priority: dagnelie_vc22_2 > dagnelie_vc22_1g > dagnelie_vc22_1.

• CNPF outputs are computed separately for each trunk volume source (Dagnelie, Vallet, Rondeux, Algan).

• Vallet method is applied only to a predefined list of compatible species using vallet_vta.

• If required columns are missing, the corresponding method is skipped with a warning.

• Warnings are also displayed if trunk volume columns exist but contain missing values (NA).

• All biomass values are expressed in tonnes of dry matter (t), carbon in tonnes of carbon (t C), and CO2 in tonnes of CO2 equivalent (t CO2).

Examples

data <- data.frame(
  species_code = c("PICEA_ABIES", "QUERCUS_ROBUR", "FAGUS_SYLVATICA"),
  dagnelie_vc22_2 = c(1.1, NA, NA),
  dagnelie_vc22_1g = c(NA, NA, NA),
  dagnelie_vc22_1 = c(NA, 0.9, NA),
  vallet_vc22 = c(NA, 1.2, NA),
  rondeux_vc22 = c(NA, NA, 1.0),
  algan_vc22 = c(NA,0.8,NA),
  vallet_vta = c(1.5, NA, 1.3)
)

output_path <- tempfile(fileext = ".csv")
results <- biomass_calc(data, output = output_path)
if (file.exists(output_path)) {
  message("CSV file successfully created.")
} else {
  warning("CSV file was not created.")
}