Initial biomass from seed information — add_seed

Adds a new row to a data.frame created by biomass_table that represents the initial seed biomass.

Usage

add_seed_biomass(
    biomass_df,
    year = NA,
    doy = NA,
    hour = 12,
    seed_mass = NA,
    zero_when_missing = character(),
    component_fractions = list(),
    ...
  )

Arguments

biomass_df: A data frame assumed to have been created by biomass_table.
year: The year the crop was grown, such as 2022.
doy: The day of year when the plot was sown, such as 150.
hour: The hour of the day when the plot was sown.
seed_mass: The average mass per seed (in g), typically determined by weighing a known number of seeds (such as one hundred seeds).
zero_when_missing: A character vector indicating any biomass columns whose values should be set to zero when they were not explicitly measured.
component_fractions: A list of named numeric elements whose values must add to 1. For BioCro simulations, it is often necessary to estimate the initial leaf, stem, and root biomass as fractions of the original seed biomass. For example, if we assume that the initial mass is 80 set component_fractions to list(leaf = 0.8, stem = 0.1, root = 0.1).
...: Any additional arguments (such as comments) to include as columns in the new row.

Details

The new row in the data table will be constructed as follows:

The values of the crop, variety, location, planting_density, row_spacing, and plant_spacing will be copied from the first row of biomass_df.
The values of year, doy, and hour will be taken from the inputs; the value of time will be calculated as in process.
The value of all LAI estimates (LAI_from_LMA, LAI_from_planting_density, and LAI_from_measured_population) will be set to 0 since there cannot be any leaf area corresponding to seeds that were just sown.
The initial seed biomass per unit ground area (in Mg / ha) will be stored in a new column called initial_seed. This value is calculated using initial_seed = seed_mass * planting_density * 2.47e-6, where the factor 2.47e-6 converts from g / acre to Mg / ha using 1 g / acre = 2.47e-6 Mg / ha.
If component fractions were specified, the values of those columns will be set to the corresponding fractions of initial_seed.

Value

A data frame as described above.

Examples

# Example: Creating and processing a harvest_point object that includes
# (optional) comments about the stem and the leaf litter, and then adding an
# initial seed biomass (and another comment).
hp <- harvest_point(
  crop = 'soybean',
  variety = 'ld11',
  location = 'energy farm',
  plot = 1,
  year = 2023,
  doy = 186,
  hour = 12,
  planting_density = 125000,
  row_spacing = 0.7,
  partitioning_leaf_area = 500,
  partitioning_component_weights = list(leaf = 2.5, stem = 1.5, root = 1.4, leaf_litter = 0.2),
  agb_components = c('leaf', 'stem'),
  agb_row_length = 2,
  agb_weight = 50,
  trap_area = 0.185,
  trap_component_weights = list(leaf_litter = 0.4, stem_litter = 0.5),
  partitioning_nplants = 6,
  agb_nplants = 50,
  stem_comment = 'The stem weight includes petioles',
  stem_litter_comment = 'The stem litter is entirely petioles',
  leaf_litter_comment = 'Senesced leaves were present on the plants and in the trap'
)

hpp <- process(hp)

biomass <- biomass_table(hpp)

biomass <- add_seed_biomass(
  biomass,
  year = 2023,
  doy = 152,
  hour = 12,
  seed_mass = 0.17,
  component_fractions = list(leaf = 0.8, stem = 0.1, root = 0.1),
  seed_comment = 'Sown with precision planter'
)

str(biomass)
#> 'data.frame':	2 obs. of  29 variables:
#>  $ crop                        : chr  "soybean" "soybean"
#>  $ variety                     : chr  "ld11" "ld11"
#>  $ location                    : chr  "energy farm" "energy farm"
#>  $ plot                        : num  NA 1
#>  $ year                        : num  2023 2023
#>  $ doy                         : num  152 186
#>  $ hour                        : num  12 12
#>  $ time                        : num  152 186
#>  $ leaf                        : num  0.042 0.223
#>  $ stem                        : num  0.00525 0.13393
#>  $ root                        : num  0.00525 0.125
#>  $ leaf_litter                 : num  NA 0.0395
#>  $ stem_litter                 : num  NA 0.027
#>  $ SLA                         : num  NA 2
#>  $ LMA                         : num  NA 50
#>  $ LAI_from_LMA                : num  0 0.446
#>  $ LAI_from_planting_density   : num  0 0.257
#>  $ LAI_from_measured_population: num  0 0.298
#>  $ agb_per_plant_row           : num  NA 1
#>  $ agb_per_plant_partitioning  : num  NA 0.667
#>  $ measured_population         : num  NA 144536
#>  $ row_spacing                 : num  0.7 0.7
#>  $ plant_spacing               : num  0.0463 0.0463
#>  $ planting_density            : num  125000 125000
#>  $ stem_comment                : chr  NA "The stem weight includes petioles"
#>  $ stem_litter_comment         : chr  NA "The stem litter is entirely petioles"
#>  $ leaf_litter_comment         : chr  NA "Senesced leaves were present on the plants and in the trap"
#>  $ initial_seed                : num  0.0525 NA
#>  $ seed_comment                : chr  "Sown with precision planter" NA