marine-biodiversity-conservation-lab. To fix this you can add URL: https://ropensci-staging.r-universe.dev/ocean3d to the package DESCRIPTION file. See also theR-universe documentation.Package: ocean3d 0.1.1.9008

Jay Matsushiba
ocean3d: Three-Dimensional Marine Spatial Analysis
Facilitates the analysis of marine habitat in 3D, enabling descriptions of habitat by depth and area. Provides tools for volume calculation, environmental extraction, and spatial overlap analysis between species ranges, fisheries, and depth-stratified environmental data.
Authors:
ocean3d_0.1.1.9008.tar.gz
ocean3d_0.1.1.9008.zip(r-4.7-any)ocean3d_0.1.1.9008.zip(r-4.6-any)ocean3d_0.1.1.9008.zip(r-4.5-any)
ocean3d_0.1.1.9008.tgz(r-4.6-any)ocean3d_0.1.1.9008.tgz(r-4.5-any)
ocean3d_0.1.1.9008.tar.gz(r-4.7-any)ocean3d_0.1.1.9008.tar.gz(r-4.6-any)
ocean3d_0.1.1.9008.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ocean3d/json (API)
| # Install 'ocean3d' in R: |
| install.packages('ocean3d', repos = c('https://ropensci-staging.r-universe.dev', 'https://cloud.r-project.org')) |
Reviews:rOpenSci Software Review #()
Bug tracker:https://github.com/marine-biodiversity-conservation-lab/ocean3d/issues
Pkgdown/docs site:https://marine-biodiversity-conservation-lab.github.io
Last updated from:681fd10ed4. Checks:7 NOTE, 3 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 314 | ||
| pkgdown docs | OK | 243 | ||
| source / vignettes | OK | 215 | ||
| linux-release | NOTE | 219 | ||
| macos-release | NOTE | 221 | ||
| macos-oldrel | NOTE | 242 | ||
| windows-devel | NOTE | 216 | ||
| windows-release | NOTE | 270 | ||
| windows-oldrel | NOTE | 268 | ||
| wasm-release | OK | 152 |
Exports:as_envelopeas_voxelcalc_volume_overlapcreate_study_rasterdepthsenvelope_to_voxelextract_to_areaextract_to_pointextract2dextract3d_allextract3d_bottomextract3d_nearestextract3d_surfacefetch_species_assessmentsfill_missing_depthsgfw_effort_to_rasterintersectintersect_3dintersects_3dload_gebco_bathymetrymaskoccupiedprofile_equalprofile_flatvect_to_envelopevolumevoxel_to_envelopewoa_cache_clearwoa_cache_dirwoa_downloadwoa_load_nc
Dependencies:classclassIntclicrulcurlDBIdplyre1071genericsgfwrgluehttpcodejsonliteKernSmoothlifecyclemagrittrmimencdf4pillarpkgconfigproxyR6Rcpprlangrredlists2sfstringistringrterratibbletidyselecttriebeardunitsurltoolsutf8vctrswithrwk
Last update: 2026-10-07
Started: 2026-10-01
Last update: 2026-10-01
Started: 2026-10-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Coerce a 2D footprint to a 2.5D min-max envelope | as_envelope |
| Create a voxel object | as_voxel |
| Per-cell 3D volume overlap between two rasterized domains | calc_volume_overlap calc_volume_overlap,SpatEnvelope,SpatEnvelope-method calc_volume_overlap,SpatEnvelope,SpatVoxel-method calc_volume_overlap,SpatRaster,SpatRaster-method calc_volume_overlap,SpatVoxel,SpatEnvelope-method calc_volume_overlap,SpatVoxel,SpatVoxel-method |
| Create a study area raster grid | create_study_raster |
| Depths of a voxel's layers | depths |
| Convert Envelope 2.5D -> Voxel 3D | envelope_to_voxel |
| Extract a 3D raster to an area and a depth band | extract_to_area |
| Extract values from netCDFs to one or more point observations | extract_to_point |
| Extract values from a 2D netCDF variable | extract2d |
| Extract nearest, surface and bottom values from a 3D netCDF variable | extract3d_all |
| Extract the bottom available layer from a 3D netCDF variable | extract3d_bottom |
| Extract the nearest valid depth layer from a 3D netCDF variable | extract3d_nearest |
| Extract the surface layer from a 3D netCDF variable | extract3d_surface |
| Fetch species assessment data from IUCN Red List API | fetch_species_assessments |
| Fill missing depth values | fill_missing_depths |
| Rasterise a GFW effort tibble onto a target grid | gfw_effort_to_raster |
| The 3D space two objects share | intersect,SpatEnvelope,SpatEnvelope-method intersect,SpatEnvelope,SpatRaster-method intersect,SpatEnvelope,SpatVoxel-method intersect,SpatRaster,SpatEnvelope-method intersect,SpatRaster,SpatVoxel-method intersect,SpatVoxel,SpatEnvelope-method intersect,SpatVoxel,SpatRaster-method intersect,SpatVoxel,SpatVoxel-method intersect-guard intersect_3d intersect_3d,ANY,ANY-method intersect_3d,ANY,SpatEnvelope-method intersect_3d,ANY,SpatVoxel-method intersect_3d,SpatEnvelope,ANY-method intersect_3d,SpatEnvelope,SpatEnvelope-method intersect_3d,SpatEnvelope,SpatVoxel-method intersect_3d,SpatVoxel,ANY-method intersect_3d,SpatVoxel,SpatEnvelope-method intersect_3d,SpatVoxel,SpatVoxel-method |
| Do two objects share any 3D space? | intersects_3d intersects_3d,ANY,ANY-method intersects_3d,ANY,SpatEnvelope-method intersects_3d,ANY,SpatVoxel-method intersects_3d,SpatEnvelope,ANY-method intersects_3d,SpatEnvelope,SpatEnvelope-method intersects_3d,SpatEnvelope,SpatVoxel-method intersects_3d,SpatVoxel,ANY-method intersects_3d,SpatVoxel,SpatEnvelope-method intersects_3d,SpatVoxel,SpatVoxel-method |
| Load GEBCO bathymetry raster | load_gebco_bathymetry |
| Keep a raster's values inside a 3D domain | mask,SpatEnvelope,SpatEnvelope-method mask,SpatEnvelope,SpatVoxel-method mask,SpatRaster,SpatEnvelope-method mask,SpatRaster,SpatVoxel-method mask,SpatVoxel,SpatEnvelope-method mask,SpatVoxel,SpatVoxel-method mask-3d |
| Reduce a variable voxel to a presence voxel | occupied |
| 2.5D min-max envelope: exactly depth_min, depth_max | SpatEnvelope-class |
| Union of the package's 3D domain representations | SpatVolume-class |
| 3D voxel model: one layer per standard depth level | SpatVoxel-class |
| Convert SpatVector or sf to SpatEnvelope | vect_to_envelope |
| Total 3D volume of a rasterized domain | volume volume,SpatEnvelope-method volume,SpatRaster-method volume,SpatVoxel-method |
| Vertical profiles for voxel building | profile_equal profile_flat voxel_profiles |
| Collapse Voxel 3D -> Envelope 2.5D | voxel_to_envelope |
| Clear the WOA cache | woa_cache_clear |
| WOA cache directory | woa_cache_dir |
| Download a WOA NetCDF file (with caching) | woa_download |
| Load a WOA NetCDF file | woa_load_nc |