Package: biogeom 1.4.3

Peijian Shi

biogeom: Biological Geometries

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.

Authors:Peijian Shi [aut, cre], Johan Gielis [aut], Brady K. Quinn [aut]

biogeom_1.4.3.tar.gz
biogeom_1.4.3.tar.gz(r-4.5-noble)biogeom_1.4.3.tar.gz(r-4.4-noble)
biogeom_1.4.3.tgz(r-4.4-emscripten)biogeom_1.4.3.tgz(r-4.3-emscripten)
biogeom.pdf |biogeom.html
biogeom/json (API)

# Install 'biogeom' in R:
install.packages('biogeom', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • LeafSizeDist - Leaf size distribution of _Shibataea chinensis_
  • Neocinnamomum - Leaf Boundary Data of Seven Species of _Neocinnamomum_
  • bambooleaves - Leaf Boundary Data of _Phyllostachys incarnata_ T. H. Wen
  • eggs - Egg Boundary Data of Nine Species of Birds
  • ginkgoseed - Boundary Data of the Side Projections of _Ginkgo biloba_ Seeds
  • kp - Boundary Data of the Vertical Projections of _Koelreuteria paniculata_ Fruit
  • shoots - Height Growth Data of Bamboo Shoots
  • starfish - Boundary Data of Eight Sea Stars
  • veins - Leaf Vein Data of _Michelia compressa_
  • whitespruce - Planar Coordinates of _Picea glauca_ Tree Rings

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.48 score 1 stars 1 scripts 330 downloads 48 exports 8 dependencies

Last updated 7 months agofrom:eaabb894c0. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-linuxNOTEOct 27 2024

Exports:adjdataareaGEareaovatebilatcurveEPEcurveETEcurveGEcurveNRGEcurveovateDEPEDETEDNRGEDSGEEPEETEfitEPEfitETEfitGEfitLorenzfitNRGEfitovatefitsigmoidfitSuperfracdimGElmPElmTEMbetaEMBriereEMLRFEMPerformanceENRGEPESarabiaESCSESHEsigmoidSurfaceAreaEPESurfaceAreaETESurfaceAreaNRGESurfaceAreaSGETETGETSEVolumeEPEVolumeETEVolumeNRGEVolumeSGE

Dependencies:deldirlatticeMatrixpolyclipspatstat.dataspatstat.geomspatstat.univarspatstat.utils

Readme and manuals

Help Manual

Help pageTopics
Boundary Data Adjustment of A Polygonadjdata
Area Calculation for the Gielis Curve Within [0, 2pi)areaGE
Area Calculation for an Ovate Polygonareaovate
Leaf Boundary Data of _Phyllostachys incarnata_ T. H. Wen (Poaceae: Bambusoideae)bambooleaves
Measure of the Extent of Bilateral Symmetry of A Polygonbilat
Biological Geometriesbiogeom
Drawing the Preston Curve Produced by the the Explicit Preston EquationcurveEPE
Drawing the Troscianko Curve Produced by the Explicit Troscianko EquationcurveETE
Drawing the Gielis CurvecurveGE
Drawing the Egg Shape Predicted by the Narushin-Romanov-Griffin EquationcurveNRGE
Drawing the Ovate Leaf-Shape Curvecurveovate
Calculation of the First-Order Derivative of the Explicit Preston EquationDEPE
Calculation of the First-Order Derivative of the Explicit Troscianko EquationDETE
Calculation of the First-Order Derivative of the Narushin-Romanov-Griffin EquationDNRGE
Calculation of the First-Order Derivative of the Simplified Gielis EquationDSGE
Egg Boundary Data of Nine Species of Birdseggs
Calculation of the Ordinate For an Arbitrary Point on the Preston Curve in the PlaneEPE
Calculation of the Ordinate For an Arbitrary Point on the Troscianko Curve in the PlaneETE
Data-Fitting Function for the Explicit Preston EquationfitEPE
Data-Fitting Function for the Explicit Troscianko EquationfitETE
Data-Fitting Function for the Gielis EquationfitGE
Data-Fitting Function for the Rotated and Right-Shifted Lorenz CurvefitLorenz
Parameter Estimation for the Narushin-Romanov-Griffin EquationfitNRGE
Data-Fitting Function for the Ovate Leaf-Shape Equationfitovate
Data-Fitting Function for the Sigmoid Growth Equationfitsigmoid
Data-Fitting Function for the Superellipse EquationfitSuper
Calculation of Fractal Dimension of Lef Veins Based on the Box-Counting Methodfracdim
Calculation of the Polar Radius of the Gielis CurveGE
Boundary Data of the Side Projections of _Ginkgo biloba_ Seedsginkgoseed
Boundary Data of the Vertical Projections of _Koelreuteria paniculata_ Fruitkp
Leaf size distribution of _Shibataea chinensis_LeafSizeDist
Parameter Estimation for the Todd-Smart EquationlmPE
Parameter Estimation for the Troscianko EquationlmTE
Modified Beta EquationMbetaE
Modified Briere EquationMBriereE
Modified Lobry-Rosso-Flandrois (LRF) EquationMLRFE
Modified Performance EquationMPerformanceE
Leaf Boundary Data of Seven Species of _Neocinnamomum_Neocinnamomum
The Narushin-Romanov-Griffin Equation (NRGE)NRGE
Calculation of the Abscissa, Ordinate and Distance From the Origin For an Arbitrary Point on the Preston CurvePE
Sarabia EquationSarabiaE
Sarabia-Castillo-Slottje Equation (SCSE)SCSE
Sitthiyot-Holasut EquationSHE
Height Growth Data of Bamboo Shootsshoots
Sigmoid Growth Equationsigmoid
Boundary Data of Eight Sea Starsstarfish
Calculation of the Surface Area of An Egg Based on the Explicit Preston EquationSurfaceAreaEPE
Calculation of the Surface Area of An Egg Based on the Explicit Troscianko EquationSurfaceAreaETE
Calculation of the Surface Area of An Egg Based on the Narushin-Romanov-Griffin EquationSurfaceAreaNRGE
Calculation of the Surface Area of An Egg Based on the Simplified Gielis EquationSurfaceAreaSGE
The Troscianko Equation (TE)TE
Calculation of the Polar Radius of the Twin Gielis CurveTGE
The Todd-Smart Equation (TSE)TSE
Leaf Vein Data of _Michelia compressa_veins
Calculation of the Volume of An Egg Based on the Explicit Preston EquationVolumeEPE
Calculation of the Volume of An Egg Based on the Explicit Troscianko EquationVolumeETE
Calculation of the Volume of An Egg Based on the Narushin-Romanov-Griffin EquationVolumeNRGE
Calculation of the Volume of An Egg Based on the Simplified Gielis EquationVolumeSGE
Planar Coordinates of _Picea glauca_ Tree Ringswhitespruce