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biogeom (version 1.5.0)

Biological Geometries

Description

Is used to simulate and fit biological geometries. 'biogeom' incorporates several novel universal parametric equations that can generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings (Gielis (2003) ; Shi et al. (2020) ), three growth-rate curves representing the ontogenetic growth trajectories of animals and plants against time, and the axially symmetrical and integral forms of all these functions (Shi et al. (2017) ; Shi et al. (2021) ). The optimization method proposed by Nelder and Mead (1965) was used to estimate model parameters. 'biogeom' includes several real data sets of the boundary coordinates of natural shapes, including avian eggs, fruit, lanceolate and ovate leaves, tree rings, seeds, and sea stars,and can be potentially applied to other natural shapes. 'biogeom' can quantify the conspecific or interspecific similarity of natural outlines, and provides information with important ecological and evolutionary implications for the growth and form of living organisms. Please see Shi et al. (2022) for details.

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Version

Install

install.packages('biogeom')

Monthly Downloads

355

Version

1.5.0

License

GPL (>= 2)

Maintainer

Peijian Shi

Last Published

August 24th, 2025

Functions in biogeom (1.5.0)

LeafSizeDist

Leaf size distribution of Shibataea chinensis
MLRFE

Modified Lobry-Rosso-Flandrois (LRF) Equation
DSGE

Calculation of the First-Order Derivative of the Simplified Gielis Equation
ETE

Calculation of the Ordinate For an Arbitrary Point on the Troscianko Curve in the Plane
GE

Calculation of the Polar Radius of the Gielis Curve
PE

Calculation of the Abscissa, Ordinate and Distance From the Origin For an Arbitrary Point on the Preston Curve
Neocinnamomum

Leaf Boundary Data of Seven Species of Neocinnamomum
MbetaE

Modified Beta Equation
SHE

Sitthiyot-Holasut Equation
PlanCoor

Extracts the Planar Coordinates the 2-D Profiles of Apical Meristems
SAMs

Boundary Data of Shoot Apical Meristems
NRGE

The Narushin-Romanov-Griffin Equation (NRGE)
MPerformanceE

Modified Performance Equation
SarabiaE

Sarabia Equation
SCSE

Sarabia-Castillo-Slottje Equation (SCSE)
SurfaceAreaAM

Calculation of the Lateral Surface Area of an Apical meristem.
TGE

Calculation of the Polar Radius of the Twin Gielis Curve
SurfaceAreaNRGE

Calculation of the Surface Area of An Egg Based on the Narushin-Romanov-Griffin Equation
VolumeAM

Calculation of the Volume of an Apical meristem.
SurfaceAreaSGE

Calculation of the Surface Area of An Egg Based on the Simplified Gielis Equation
TSE

The Todd-Smart Equation (TSE)
TE

The Troscianko Equation (TE)
SurfaceAreaEPE

Calculation of the Surface Area of An Egg Based on the Explicit Preston Equation
VolumeEPE

Calculation of the Volume of An Egg Based on the Explicit Preston Equation
SurfaceAreaETE

Calculation of the Surface Area of An Egg Based on the Explicit Troscianko Equation
curveEPE

Drawing the Preston Curve Produced by the the Explicit Preston Equation
biogeom

Biological Geometries
bambooleaves

Leaf Boundary Data of Phyllostachys incarnata T. H. Wen (Poaceae: Bambusoideae)
VolumeSGE

Calculation of the Volume of An Egg Based on the Simplified Gielis Equation
VolumeETE

Calculation of the Volume of An Egg Based on the Explicit Troscianko Equation
bilat

Measure of the Extent of Bilateral Symmetry of A Polygon
areaovate

Area Calculation for an Ovate Polygon
areaGE

Area Calculation for the Gielis Curve Within \([0, 2\pi)\)
VolumeNRGE

Calculation of the Volume of An Egg Based on the Narushin-Romanov-Griffin Equation
adjdata

Boundary Data Adjustment of A Polygon
fitETE

Data-Fitting Function for the Explicit Troscianko Equation
curveovate

Drawing the Ovate Leaf-Shape Curve
curveGE

Drawing the Gielis Curve
fitAM

Fitting the 2-D Profiles of Apical Meristems
eggs

Egg Boundary Data of Nine Species of Birds
curveNRGE

Drawing the Egg Shape Predicted by the Narushin-Romanov-Griffin Equation
fitGS

Data-Fitting Function for the Geometric Series of Size Distribution Measurements
curveETE

Drawing the Troscianko Curve Produced by the Explicit Troscianko Equation
fitGE

Data-Fitting Function for the Gielis Equation
fitEPE

Data-Fitting Function for the Explicit Preston Equation
fitSuper

Data-Fitting Function for the Superellipse Equation
fitsigmoid

Data-Fitting Function for the Sigmoid Growth Equation
lmPE

Parameter Estimation for the Todd-Smart Equation
fracdim

Calculation of Fractal Dimension of Lef Veins Based on the Box-Counting Method
ginkgoseed

Boundary Data of the Side Projections of Ginkgo biloba Seeds
fitNRGE

Parameter Estimation for the Narushin-Romanov-Griffin Equation
fitLorenz

Data-Fitting Function for the Rotated and Right-Shifted Lorenz Curve
fitovate

Data-Fitting Function for the Ovate Leaf-Shape Equation
kp

Boundary Data of the Vertical Projections of Koelreuteria paniculata Fruit
lmTE

Parameter Estimation for the Troscianko Equation
starfish

Boundary Data of Eight Sea Stars
sigmoid

Sigmoid Growth Equation
whitespruce

Planar Coordinates of Picea glauca Tree Rings
shoots

Height Growth Data of Bamboo Shoots
veins

Leaf Vein Data of Michelia compressa
DNRGE

Calculation of the First-Order Derivative of the Narushin-Romanov-Griffin Equation
DETE

Calculation of the First-Order Derivative of the Explicit Troscianko Equation
MBriereE

Modified Briere Equation
DEPE

Calculation of the First-Order Derivative of the Explicit Preston Equation
EPE

Calculation of the Ordinate For an Arbitrary Point on the Preston Curve in the Plane