VPalm Parameters

VPalm is a submodule of XPalm that provides a set of functions to reconstruct the architecture of palm trees based on a set of parameters and allometric relations.

Parameters are defined in a YAML file and a template is provided:

using XPalm

VPalm = XPalm.load_vpalm!()

file = joinpath(dirname(dirname(pathof(XPalm))), "test", "references", "vpalm-parameter_file.yml")
parameters = VPalm.read_parameters(file)

Parameters definition

The VPalm geometry parameters are listed below:

The optional juvenile parameters below are enabled by default only in the dynamic XPalm–VPalm coupling file. They are intentionally absent from the linked standalone static template, which therefore retains the historical allometries.

Parameter	Value	Description
`seed`	0	Seed for random number generation
`nb_leaves_emitted`	145	Number of leaves emitted since the seed
`nb_internodes_before_planting`	20	Number of internodes before planting (estimation)
`nb_leaves_in_sheath`	8	Number of leaves in the sheath (rank <1)
`phyllotactic_angle_mean`	136.67	Frond phyllotactic angle mean (°)
`phyllotactic_angle_sd`	0.48	Frond phyllotactic angle standard deviation (°)
`initial_stem_height`	0.05	Stem height at planting (m)
`stem_height_coefficient`	0.018	Coefficient used in the computation of stem height
`internode_length_at_maturity`	0.03	Growth in stem height per leaf (~internode length) at adult stage (m)
`stem_growth_start`	120	Number of leaves emitted when stem starts to grow in height
`stem_height_variation`	0.50	Variation in stem height (m, never > 30% of stem height)
`stem_bending_mean`	0	Average stem bending
`stem_bending_sd`	0	Standard deviation around mean stem bending
`stem_diameter_max`	0.77	Maximum stem diameter (m)
`stem_diameter_slope`	0.007	Slope of the logit function for stem diameter
`stem_diameter_inflection`	1.69	Inflection point of the logit function for stem diameter
`stem_diameter_residual`	0.063	Residual of stem diameter (m)
`stem_diameter_snag`	0.3	Diameter of stem considered as snag (m)
`stem_base_shrinkage`	0.1	Shrinkage at stem base (smaller = sharper)
`stem_top_shrinkage`	0.3	Shrinkage at stem top (smaller = sharper)
`internode_rank_no_expansion`	9	Rank of internode where expansion stops
`internode_final_length`	0.01	Length of internode around apical meristem (m)
`leaf_max_angle`	90	Maximum angle of the leaf (°)
`leaf_slope_angle`	0.05	Slope of leaf angle for logistic function
`leaf_inflection_angle`	40	Inflection point of leaf angle for logistic function
`cpoint_decli_intercept`	10.47	Intercept of linear regression of c-point declination
`cpoint_decli_slope`	1.33	Slope of linear regression of c-point declination
`cpoint_angle_SDP`	5.32	Standard deviation of c-point angle
`rachis_twist_initial_angle`	4.0	Initial twist angle of rachis
`rachis_twist_initial_angle_sdp`	0.0	Standard deviation of initial twist angle of rachis
`petiole_rachis_ratio_mean`	0.25	Mean ratio of petiole length to rachis length
`petiole_rachis_ratio_sd`	0.033	Standard deviation of petiole to rachis length ratio
`petiole_nb_segments`	15	Number of segments in the petiole
`rachis_nb_segments`	100	Number of segments in the rachis
`leafLengthIntercept`	351.20	Intercept for leaf length calculation
`leafLengthSlope`	0.058	Slope for leaf length calculation
`rachisLength_SDP`	15.25	Standard deviation of rachis length
`rachis_fresh_weight`	[array]	Fresh weight of rachis (g) for each leaf
`leaf_length_intercept`	0.0	Intercept of the linear relationship between rachis length and biomass (m) (optional, can use `rachis_final_lengths` instead)
`leaf_length_slope`	1.31	Slope of the linear relationship between rachis length and biomass (m/kg) (optional, can use `rachis_final_lengths` instead)
`rachis_final_lengths`	[array]	Final rachis lengths (m) from oldest to rank 1 leaf (optional, can use `leaf_length_intercept` + `leaf_length_slope` instead)
`leaflet_lamina_angle`	140	V-shape angle of leaflet (°)
`leaflets_nb_max`	171.72	Maximum number of leaflets on a leaf
`leaflets_nb_min`	20	Minimum number of leaflets on a leaf
`leaflets_nb_slope`	0.25	Slope of logistic relationship between rachis length and nb leaflets
`leaflets_nb_inflexion`	2.33	Inflection point of logistic relationship (rachis length vs nb leaflets)
`nbLeaflets_SDP`	6	Standard deviation around computed value for given rachis length
`leaflet_position_shape_coefficient`	2.48	Shape coefficient for placing leaflets along rachis
`leaflets_between_to_within_group_ratio`	2.0	Ratio of inter-group to intra-group leaflets spacing
`relative_position_bpoint`	0.66	Relative position of b-point
`relative_position_bpoint_sd`	0.034	Standard deviation of relative position of b-point
`leaflet_length_at_b_intercept`	0.61	Intercept of leaflet length at b-point (m)
`leaflet_length_at_b_slope`	0.054	Slope of leaflet length at b-point
`leaflet_width_at_b_intercept`	0.063	Intercept of leaflet width at b-point
`leaflet_width_at_b_slope`	-0.004	Slope of leaflet width at b-point
`relative_length_first_leaflet`	0.18	Relative length of first leaflet
`relative_length_last_leaflet`	0.52	Relative length of last leaflet
`relative_position_leaflet_max_length`	0.52	Relative position of leaflet with maximum length
`relative_width_first_leaflet`	0.22	Relative width of first leaflet
`relative_width_last_leaflet`	0.53	Relative width of last leaflet
`relative_position_leaflet_max_width`	0.61	Relative position of leaflet with maximum width
`leaflet_xm_intercept`	0.18	Base value for xm (position of maximum width) for leaflets
`leaflet_xm_slope`	0.08	How much xm changes per unit of relative position along rachis
`leaflet_ym_intercept`	0.51	Base value for relative width at maximum width position
`leaflet_ym_slope`	-0.025	How much relative width changes per unit of position along rachis
`leaflet_axial_angle_c`	78.22	Leaflet axial angle parameter c
`leaflet_axial_angle_a`	10.43	Leaflet axial angle parameter a
`leaflet_axial_angle_slope`	-4.69	Leaflet axial angle slope
`leaflet_axial_angle_sdp`	8.06	Standard deviation of leaflet axial angle
`leaflet_stiffness`	1500	Leaflet stiffness
`leaflet_stiffness_sd`	7000	Standard deviation of leaflet stiffness
`leaflet_frequency_high`	[array]	Frequency of high position leaflets along 10 rachis sub-sections
`leaflet_frequency_low`	[array]	Frequency of low position leaflets along 10 rachis sub-sections
`nbInflorescences`	0	Number of inflorescences
`leaf_base_width`	0.3	Adult width of leaf base (m)
`leaf_base_width_juvenile`	0.01	Optional juvenile width of leaf base (m)
`leaf_base_height_juvenile`	0.001	Optional juvenile height of leaf base (m)
`leaf_base_dimensions_juvenile_max_emitted_leaf`	60	Last emitted leaf at the juvenile base dimensions
`leaf_base_dimensions_adult_min_emitted_leaf`	110	First emitted leaf at the adult base dimensions
`cpoint_width_intercept`	0.01	Rachis width at c-point intercept for linear interpolation (m)
`cpoint_width_slope`	0.012	Rachis width at c-point slope for linear interpolation
`cpoint_width_juvenile_coefficient`	0.0167	Optional juvenile width at a 1 m rachis (m)
`cpoint_width_juvenile_exponent`	0.5381	Optional juvenile width power exponent
`cpoint_height_juvenile_coefficient`	0.0106	Optional juvenile height at a 1 m rachis (m)
`cpoint_height_juvenile_exponent`	0.5125	Optional juvenile height power exponent
`cpoint_dimensions_juvenile_max_rachis_length`	1.71	End of the juvenile section allometry (m)
`cpoint_dimensions_adult_min_rachis_length`	2.45	Start of the adult section allometry (m)
`rachis_width_tip`	0.003	Width at tip of rachis (m)
`leaf_base_height`	0.1	Adult height of leaf base (m)
`cpoint_height_width_ratio`	0.57	Height to width ratio at c-point
`height_rachis_tappering`	-0.93	Tapering factor for rachis height
`leaflet_radial_high_a0_sup`	26.30	Upper bound of leaflet angle at position 0 for high position leaflets
`leaflet_radial_high_amax_sup`	60.49	Upper bound of maximum angle for high position leaflets
`leaflet_radial_high_a0_inf`	16.66	Lower bound of angle at position 0 for high position leaflets
`leaflet_radial_high_amax_inf`	9.08	Lower bound of maximum angle for high position leaflets
`leaflet_radial_low_a0_sup`	-7.91	Upper bound of angle at position 0 for low position leaflets
`leaflet_radial_low_amax_sup`	-4.83	Upper bound of maximum angle for low position leaflets
`leaflet_radial_low_a0_inf`	-12.29	Lower bound of angle at position 0 for low position leaflets
`leaflet_radial_low_amax_inf`	-34.33	Lower bound of maximum angle for low position leaflets
`elastic_modulus`	2221.67	Elastic modulus for biomechanical calculations
`shear_modulus`	68.20	Shear modulus for biomechanical calculations

Juvenile rachis sections

The six cpoint_*_juvenile_* and cpoint_dimensions_* parameters are an optional, indivisible set. Their power laws were fitted to 14 EKA1 rachises measured between 0.60 and 1.71 m. The measurement position was not written explicitly in the JPCE workbook and is assumed to be the C point from its context. A smooth transition from 1.71 to 2.45 m reconnects the juvenile fits to the historical adult VPalm allometry. If the six parameters are omitted, VPalm uses the historical allometry at every rachis length.

Provisional juvenile petiole base

The four optional leaf_base_*_juvenile and leaf_base_dimensions_*_emitted_leaf parameters reuse the 1 cm × 1 mm setting from the JPCE EKA1 reconstruction script. JPCE did not measure these dimensions, so they are a visual ontogenetic hypothesis rather than a calibrated allometry. VPalm interpolates them logarithmically to the adult dimensions between emitted leaves 60 and 110. Omit the complete set to retain the historical fixed adult base dimensions.

Biomechanical Model Parameters

Parameter	Value	Description
`nb_sections`	100	Number of sections for discretizing constant form sections
`angle_max`	21.0	Maximum flexion and torsion angles between sections (°)
`iterations`	15	Number of iterations for recursive computation