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

Parameters definition

Here is a list of all necessary parameters to run XPalm.VPalm:

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	Width of leaf base (m)
`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
`rachis_width_tip`	0.03	Width at tip of rachis (m)
`leaf_base_height`	0.1	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

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