| biogeom {biogeom} | R Documentation |
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, 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.
Details
The DESCRIPTION file:
| Package: | biogeom |
| Type: | Package |
| Title: | Biological Geometries |
| Version: | 1.4.3 |
| Date: | 2024-03-21 |
| Authors@R: | c(person(given="Peijian", family="Shi", email="pjshi@njfu.edu.cn", role=c("aut", "cre")), person(given=c("Johan"), family="Gielis", email="johan.gielis@uantwerpen.be", role=c("aut")), person(given=c("Brady K."), family="Quinn", email="brady.quinn@dfo-mpo.gc.ca", role=c("aut"))) |
| Author: | Peijian Shi [aut, cre], Johan Gielis [aut], Brady K. Quinn [aut] |
| Maintainer: | Peijian Shi <pjshi@njfu.edu.cn> |
| Imports: | spatstat.geom (>= 2.4-0) |
| 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) <doi:10.3732/ajb.90.3.333>; Shi et al. (2020) <doi:10.3390/sym12040645>), 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) <doi:10.1016/j.ecolmodel.2017.01.012>; Shi et al. (2021) <doi:10.3390/sym13081524>). The optimization method proposed by Nelder and Mead (1965) <doi:10.1093/comjnl/7.4.308> 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) <doi:10.1111/nyas.14862> for details. |
| Depends: | R (>= 4.3.0) |
| License: | GPL (>= 2) |
| NeedsCompilation: | no |
Index of help topics:
DEPE Calculation of the First-Order Derivative of
the Explicit Preston Equation
DETE Calculation of the First-Order Derivative of
the Explicit Troscianko Equation
DNRGE Calculation of the First-Order Derivative of
the Narushin-Romanov-Griffin Equation
DSGE Calculation of the First-Order Derivative of
the Simplified Gielis Equation
EPE Calculation of the Ordinate For an Arbitrary
Point on the Preston Curve in the Plane
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
LeafSizeDist Leaf size distribution of _Shibataea chinensis_
MBriereE Modified Briere Equation
MLRFE Modified Lobry-Rosso-Flandrois (LRF) Equation
MPerformanceE Modified Performance Equation
MbetaE Modified Beta Equation
NRGE The Narushin-Romanov-Griffin Equation (NRGE)
Neocinnamomum Leaf Boundary Data of Seven Species of
_Neocinnamomum_
PE Calculation of the Abscissa, Ordinate and
Distance From the Origin For an Arbitrary Point
on the Preston Curve
SCSE Sarabia-Castillo-Slottje Equation (SCSE)
SHE Sitthiyot-Holasut Equation
SarabiaE Sarabia Equation
SurfaceAreaEPE Calculation of the Surface Area of An Egg Based
on the Explicit Preston Equation
SurfaceAreaETE Calculation of the Surface Area of An Egg Based
on the Explicit Troscianko Equation
SurfaceAreaNRGE Calculation of the Surface Area of An Egg Based
on the Narushin-Romanov-Griffin Equation
SurfaceAreaSGE Calculation of the Surface Area of An Egg Based
on the Simplified Gielis Equation
TE The Troscianko Equation (TE)
TGE Calculation of the Polar Radius of the Twin
Gielis Curve
TSE The Todd-Smart Equation (TSE)
VolumeEPE Calculation of the Volume of An Egg Based on
the Explicit Preston Equation
VolumeETE Calculation of the Volume of An Egg Based on
the Explicit Troscianko Equation
VolumeNRGE Calculation of the Volume of An Egg Based on
the Narushin-Romanov-Griffin Equation
VolumeSGE Calculation of the Volume of An Egg Based on
the Simplified Gielis Equation
adjdata Boundary Data Adjustment of A Polygon
areaGE Area Calculation for the Gielis Curve Within
[0, 2pi)
areaovate Area Calculation for an Ovate Polygon
bambooleaves Leaf Boundary Data of _Phyllostachys incarnata_
T. H. Wen (Poaceae: Bambusoideae)
bilat Measure of the Extent of Bilateral Symmetry of
A Polygon
biogeom Biological Geometries
curveEPE Drawing the Preston Curve Produced by the the
Explicit Preston Equation
curveETE Drawing the Troscianko Curve Produced by the
Explicit Troscianko Equation
curveGE Drawing the Gielis Curve
curveNRGE Drawing the Egg Shape Predicted by the
Narushin-Romanov-Griffin Equation
curveovate Drawing the Ovate Leaf-Shape Curve
eggs Egg Boundary Data of Nine Species of Birds
fitEPE Data-Fitting Function for the Explicit Preston
Equation
fitETE Data-Fitting Function for the Explicit
Troscianko Equation
fitGE Data-Fitting Function for the Gielis Equation
fitLorenz Data-Fitting Function for the Rotated and
Right-Shifted Lorenz Curve
fitNRGE Parameter Estimation for the
Narushin-Romanov-Griffin Equation
fitSuper Data-Fitting Function for the Superellipse
Equation
fitovate Data-Fitting Function for the Ovate Leaf-Shape
Equation
fitsigmoid Data-Fitting Function for the Sigmoid Growth
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
kp Boundary Data of the Vertical Projections of
_Koelreuteria paniculata_ Fruit
lmPE Parameter Estimation for the Todd-Smart
Equation
lmTE Parameter Estimation for the Troscianko
Equation
shoots Height Growth Data of Bamboo Shoots
sigmoid Sigmoid Growth Equation
starfish Boundary Data of Eight Sea Stars
veins Leaf Vein Data of _Michelia compressa_
whitespruce Planar Coordinates of _Picea glauca_ Tree Rings
Note
We are deeply thankful to Cang Hui, Yang Li, Uwe Ligges, Valeriy G. Narushin, Ülo Niinemets, Karl J. Nikas, Honghua Ruan, David A. Ratkowsky, Julian Schrader, Rolf Turner, Lin Wang, and Victoria Wimmer for their valuable help during creating this package. This work was supported by the National Key Research and Development Program of China (Grant No. 2021YFD02200403) and Simon Stevin Institute for Geometry (Antwerpen, Belguim).
Author(s)
Peijian Shi [aut, cre], Johan Gielis [aut], Brady K. Quinn [aut]
Maintainer: Peijian Shi <pjshi@njfu.edu.cn>
References
Gielis, J. (2003) A generic geometric transformation that unifies a wide range of natural
and abstract shapes. American Journal of Botany 90, 333-338. doi:10.3732/ajb.90.3.333
Nelder, J.A., Mead, R. (1965). A simplex method for function minimization.
Computer Journal 7, 308-313. doi:10.1093/comjnl/7.4.308
Shi, P., Fan, M., Ratkowsky, D.A., Huang, J., Wu, H., Chen, L., Fang, S.,
Zhang, C. (2017) Comparison of two ontogenetic growth equations for animals and plants.
Ecological Modelling 349, 1-10. doi:10.1016/j.ecolmodel.2017.01.012
Shi, P., Gielis, J., Quinn, B.K., Niklas, K.J., Ratkowsky, D.A., Schrader, J., Ruan, H.,
Wang, L., Niinemets, Ü. (2022) 'biogeom': An R package for simulating and fitting natural
shapes. Annals of the New York Academy of Sciences 1516, 123-134. doi:10.1111/nyas.14862
Shi, P., Ratkowsky, D.A., Gielis, J. (2020) The generalized Gielis geometric equation and its application. Symmetry 12, 645. doi:10.3390/sym12040645
Shi, P., Yu, K., Niklas, K.J., Schrader, J., Song, Y., Zhu, R., Li, Y., Wei, H., Ratkowsky, D.A. (2021) A general model for describing the ovate leaf shape. Symmetry, 13, 1524. doi:10.3390/sym13081524