Biomass data from one harvest
harvest_point.RdThis S3 class is designed to store the information from a crop harvest data
sheet (see access_sheet) in an R data structure. Thus, it
represents biomass and leaf area measurements collected from a single plot at
a single time.
Usage
harvest_point(
crop = NA,
variety = NA,
location = NA,
plot = NA,
year = NA,
doy = NA,
hour = 12,
planting_density = NA,
row_spacing = NA,
plant_spacing = NA,
partitioning_nplants = NA,
partitioning_leaf_area = NA,
partitioning_component_weights = list(),
agb_nplants = NA,
agb_components = character(),
agb_row_length = NA,
agb_weight = NA,
trap_area = NA,
trap_component_weights = list(),
...
)Arguments
- crop
A name for the crop, such as
'soybean'.- variety
A name for the crop variety, such as
'ld11'.- location
A name for the crop's location, such as
'energy farm'.- plot
A name for the plot that was harvested, such as
2.- year
The year the crop was grown, such as
2022.- doy
The day of year when the plot was harvested, such as
180.- hour
The hour of the day when the plot was harvested.
- planting_density
The intended number of plants per unit ground area in
plants / acre; typically this will be different from the actual plant population due to seeds that fail to emerge (reduces actual population) or accidental double-planting (increases actual population).- row_spacing
The spacing between rows in the plot (in
m).- plant_spacing
The spacing between plants along a row (in
m).- partitioning_nplants
The number of plants chosen for partitioning.
- partitioning_leaf_area
The total leaf area from the partitioned plants (in
cm^2).- partitioning_component_weights
A list of named numeric elements, where the name of each element indicates a plant component (such as
'leaf') and the value of each element indicates its dry weight as measured from the partitioned plants (ing).- agb_nplants
The number of plants harvested for above-ground biomass.
- agb_components
A character vector indicating the partitioned components that should be added together to determine the above-ground biomass of the partitioned plants.
- agb_row_length
The length of row harvested for above-ground biomass (in
m).- agb_weight
The weight of the row section harvested for above-ground biomass (in
g).- trap_area
The area of the litter trap (in
m^2).- trap_component_weights
A list of named numeric elements, where the name of each element indicates a plant litter component (such as
'leaf_litter') and the value of each element indicates its dry weight as measured from the litter trap contents (ing).- ...
Any additional arguments (such as comments) to include in the
harvest_pointobject.
Details
From a technical point of view, a harvest_point object is simply an R
list with a particular set of named elements, so it can be viewed and modified
using any standard R commands that apply to lists. All of its input arguments
are optional, so a user only needs to enter information that was actually
measured. Typically, a harvest_point object is passed to
process to convert the raw measurements into more useful
quantities like the mass per unit area and leaf area index.
Note about planting density: seed and/or plant densities can be
specified in various ways. When planting by hand, it is convenient to specify
the row spacing and the spacing between plants along each row. When using a
precision planter, it is more typical to specify the row spacing and the plant
population. In either case, the row spacing, plant spacing, and plant
population are related to each other according to
planting_density * row_spacing * plant_spacing = 4047; this equation
assumes that the row and plant spacings are expressed in m and the
density is expressed in plants per acre. If a used specified all three
of these inputs (planting_density, row_spacing, and
plant_spacing), the harvest_point function will check to make
sure the values are consistent with each other. If any two of the inputs are
provided, the value of the third will automatically be calculated.
Examples
# Example 1: Creating a harvest_point object that includes (optional) comments
# about the stem and the leaf litter.
hp <- harvest_point(
crop = 'soybean',
variety = 'ld11',
location = 'energy farm',
plot = 1,
year = 2023,
doy = 186,
planting_density = 140000,
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'
)
str(hp)
#> List of 20
#> $ crop : chr "soybean"
#> $ variety : chr "ld11"
#> $ location : chr "energy farm"
#> $ plot : num 1
#> $ year : num 2023
#> $ doy : num 186
#> $ hour : num 12
#> $ planting_density : num 140000
#> $ row_spacing : num 0.7
#> $ plant_spacing : num 0.0413
#> $ partitioning_nplants : num 6
#> $ partitioning_leaf_area : num 500
#> $ partitioning_component_weights:List of 4
#> ..$ leaf : num 2.5
#> ..$ stem : num 1.5
#> ..$ root : num 1.4
#> ..$ leaf_litter: num 0.2
#> $ agb_components : chr [1:2] "leaf" "stem"
#> $ agb_nplants : num 50
#> $ agb_row_length : num 2
#> $ agb_weight : num 50
#> $ trap_area : num 0.185
#> $ trap_component_weights :List of 2
#> ..$ leaf_litter: num 0.4
#> ..$ stem_litter: num 0.5
#> $ additional_arguments :List of 3
#> ..$ stem_comment : chr "The stem weight includes petioles"
#> ..$ stem_litter_comment: chr "The stem litter is entirely petioles"
#> ..$ leaf_litter_comment: chr "Senesced leaves were present on the plants and in the trap"
#> - attr(*, "class")= chr [1:2] "harvest_point" "list"
# Example 2: Determining the planting density (in plants per acre) from the row
# and plant spacings (in m)
harvest_point(row_spacing = 0.75, plant_spacing = 0.2)$planting_density
#> [1] 26980