Clarify `rachis_length_reference`

[VEZY]

Clarify what rachis_length_reference means in stem_diameter, and what value should be passed into it.

VPalm.jl/src/allometries/stem.jl

Lines 60 to 96 in e236f5f

	"""
	stem_diameter(rachis_length_reference, stem_diameter_max, stem_diameter_slope, stem_diameter_inflection, stem_diameter_residual)
	Computes the stem diameter (m) at a given rachis length reference (m).
	# Arguments
	- `rachis_length_reference`: The rachis length reference (m). Taken as the rachis length of the first leaf.
	- `stem_diameter_max`: The maximum stem diameter (m).
	- `stem_diameter_slope`: The slope of the logistic function.
	- `stem_diameter_inflection`: The inflection point of the logistic function.
	- `stem_diameter_residual`: The residual of the stem diameter (m).
	- `stem_diameter_snag`: The diameter estimation due to snags (m).
	# Optional arguments
	- `rng`: The random number generator.
	# Details
	The stem diameter is computed using a logistic function, and then some variability is added to simulate natural variations that might occur in real-world scenarios.
	"""
	function stem_diameter(rachis_length_reference, stem_diameter_max, stem_diameter_slope, stem_diameter_inflection, stem_diameter_residual, stem_diameter_snag; rng=Random.MersenneTwister(1234))
	# Logistic function for stem diameter
	# !!!!!!!
	# The rachis length reference is supposed to be the first value of the rachisLengths vector.
	# Not present yet in the parameters yaml file.
	# !!!!!!!
	stem_diameter = logistic(rachis_length_reference, stem_diameter_max, stem_diameter_slope, stem_diameter_inflection)
	# Add some variability to the stem_diameter, simulating natural variations that might occur in real-world scenarios:
	# Note that we use max(0.3 * stem_diameter,...) to ensure that the stem diamter is always at least 30% of the maximum diameter.
	stem_diameter = max(0.3 * stem_diameter, mean_and_sd(stem_diameter, stem_diameter_residual; rng=rng))
	# Remove extra diameter estimation due to snags
	stem_diameter = stem_diameter - min(stem_diameter_snag, 0.6 * stem_diameter)
	return stem_diameter
	end

[VEZY]

Moved to PalmStudio/XPalm.jl#73