Package: ashapesampler 1.0.0

Emily Winn-Nunez

ashapesampler: Generating Alpha Shapes

Understanding morphological variation is an important task in many applications. Recent studies in computational biology have focused on developing computational tools for the task of sub-image selection which aims at identifying structural features that best describe the variation between classes of shapes. A major part in assessing the utility of these approaches is to demonstrate their performance on both simulated and real datasets. However, when creating a model for shape statistics, real data can be difficult to access and the sample sizes for these data are often small due to them being expensive to collect. Meanwhile, the landscape of current shape simulation methods has been mostly limited to approaches that use black-box inference---making it difficult to systematically assess the power and calibration of sub-image models. In this R package, we introduce the alpha-shape sampler: a probabilistic framework for simulating realistic 2D and 3D shapes based on probability distributions which can be learned from real data or explicitly stated by the user. The 'ashapesampler' package supports two mechanisms for sampling shapes in two and three dimensions. The first, empirically sampling based on an existing data set, was highlighted in the original main text of the paper. The second, probabilistic sampling from a known distribution, is the computational implementation of the theory derived in that paper. Work based on Winn-Nunez et al. (2024) <doi:10.1101/2024.01.09.574919>.

Authors:Emily Winn-Nunez [aut, cre], Lorin Crawford [aut]

ashapesampler_1.0.0.tar.gz
ashapesampler_1.0.0.tar.gz(r-4.5-noble)ashapesampler_1.0.0.tar.gz(r-4.4-noble)
ashapesampler_1.0.0.tgz(r-4.4-emscripten)ashapesampler_1.0.0.tgz(r-4.3-emscripten)
ashapesampler.pdf |ashapesampler.html
ashapesampler/json (API)
NEWS

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

Peer review:

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

3.30 score 8 scripts 221 downloads 28 exports 92 dependencies

Last updated 11 months agofrom:1c423b30ed. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 26 2024
R-4.5-linuxOKNov 26 2024

Exports:calc_overlap_2Dcalc_overlap_3Dcount_neighborseuclid_dists_point_cloud_2Deuclid_dists_point_cloud_3Dextract_complex_edgesextract_complex_facesextract_complex_tetextreme_ptsgenerate_ashape2dgenerate_ashape3dget_alpha_complexn_bound_connect_2Dn_bound_connect_3Dn_bound_homology_2Dn_bound_homology_3Dread_alpha_txtreadOFFrunif_annulusrunif_ball_3Drunif_cuberunif_diskrunif_shell_3Drunif_squaresampling2Dashapesampling3Dashapetau_boundwrite_alpha_txt

Dependencies:abindalphahullalphashape3dbase64encBHbslibcachemclicodetoolscolorspacecpp11deldirdigestdoParalleldplyrevaluatefansifarverfastmapFNNfontawesomeforeachfsgenericsgeometryggplot2gluegtablehighrhtmltoolshtmlwidgetsigraphinterpisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclelinproglpSolvemagicmagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigpolyclippracmaR.methodsS3R.ooR.utilsR6RANNrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppProgressrglrlangrmarkdownRvcgsassscalessgeostatspspatstat.dataspatstat.geomspatstat.randomspatstat.univarspatstat.utilssplancsTDAtibbletidyselecttinytextruncnormutf8vctrsviridisLitewithrxfunyaml

annulus_demo

Rendered fromannulus_demo.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2024-01-31
Started: 2024-01-31

probability_demo_2D

Rendered fromprobability_demo_2D.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2024-01-31
Started: 2024-01-31

probability_demo_3D

Rendered fromprobability_demo_3D.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2024-01-31
Started: 2024-01-31

torus_demo

Rendered fromtorus_demo.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2024-01-31
Started: 2024-01-31

Readme and manuals

Help Manual

Help pageTopics
Calculate Overlap 2Dcalc_overlap_2D
calculate overlap in three dimensions (calc_overlap_3D)calc_overlap_3D
Intersection of spherescap_intersect_vol
Circumcenter face - three points in 2D Given 3 sets of coordinates, calculates the circumcentercirc_face_2D
Circumcenter face - three points in 3D Given 3 sets of coordinates, calculates the circumcentercirc_face_3D
Circumcenter tetrahedron - 4 points in 3D Given 3D coordinates of 4 points, calculates circumcentercirc_tet_3D
Circle Overlap Centered on Circumferencecircle_overlap_cc
Circle Overlap Inner Annuluscircle_overlap_ia
circumcenter Facecircumcenter_face
circumcenter Tetrahedracircumcenter_tet
Neighbors function - finds number of neighbors for each point in point cloud.count_neighbors
Euclidean Distance Point Cloud 2Deuclid_dists_point_cloud_2D
Euclidean Distance Point Cloud 3Deuclid_dists_point_cloud_3D
Returns the edges of complex.extract_complex_edges
Returns faces of complex.extract_complex_faces
Returns tetrahedra of complex (3 dimensions)extract_complex_tet
Extreme points Finds the boundary points of a simplicial complexextreme_pts
Generate 2D alpha shapegenerate_ashape2d
Generate 3D alpha shapegenerate_ashape3d
Get alpha complexget_alpha_complex
Get areaget_area
Get volumeget_volume
n Bound Connect 2Dn_bound_connect_2D
N Bound Connect 3Dn_bound_connect_3D
n Bound Homology 2Dn_bound_homology_2D
n Bound Homology 3Dn_bound_homology_3D
Read alpha text fileread_alpha_txt
Read OFF FilereadOFF
Uniform Sampling from Annulusrunif_annulus
Uniform Ball 3Drunif_ball_3D
r Uniform Cuberunif_cube
Uniform sampling from diskrunif_disk
Uniform Shell 3Drunif_shell_3D
Uniform Sampling from Squarerunif_square
Sampling 2D alpha shapessampling2Dashape
Sample 3D alpha shapessampling3Dashape
sphere overlap when one is centered on circumference of the othersphere_overlap_cs
sphere overlap inner shellsphere_overlap_is
Spherical capspherical_cap
tau_boundtau_bound
Write Alpha Text filewrite_alpha_txt