biogeom: Biological Geometries

In biogeom: Biological Geometries

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: This package was not yet installed at build time.
Index: This package was not yet installed at build time.

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 <[e-mail]>

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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3732/ajb.90.3.333")}

Nelder, J.A., Mead, R. (1965). A simplex method for function minimization. Computer Journal 7, 308-313. \Sexpr[results=rd]{tools:::Rd_expr_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. \Sexpr[results=rd]{tools:::Rd_expr_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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/nyas.14862")}

Shi, P., Ratkowsky, D.A., Gielis, J. (2020) The generalized Gielis geometric equation and its application. Symmetry 12, 645. \Sexpr[results=rd]{tools:::Rd_expr_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. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3390/sym13081524")}

biogeom documentation built on May 29, 2024, 8:52 a.m.