Summary | Introduction: the crow, the wolf, and the drunkard | Theory | Raster basics | Transition* classes | Correcting transition matrix values | Calculating distances | Dispersal paths | Path overlap and non-overlap | Example 1: Hiking around Maunga Whau | Example 2: Geographical genetics | Future work | Acknowledgements | References
Package: gdistance 1.6.4
Andrew Marx
gdistance: Distances and Routes on Geographical Grids
Provides classes and functions to calculate various distance measures and routes in heterogeneous geographic spaces represented as grids. The package implements measures to model dispersal histories first presented by van Etten and Hijmans (2010) <doi:10.1371/journal.pone.0012060>. Least-cost distances as well as more complex distances based on (constrained) random walks can be calculated. The distances implemented in the package are used in geographical genetics, accessibility indicators, and may also have applications in other fields of geospatial analysis.
Authors:
gdistance_1.6.4.tar.gz
gdistance_1.6.4.zip(r-4.7)gdistance_1.6.4.zip(r-4.6)gdistance_1.6.4.zip(r-4.5)
gdistance_1.6.4.tgz(r-4.6-any)gdistance_1.6.4.tgz(r-4.5-any)
gdistance_1.6.4.tar.gz(r-4.7-any)gdistance_1.6.4.tar.gz(r-4.6-any)
gdistance_1.6.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gdistance/json (API)
| # Install 'gdistance' in R: |
| install.packages('gdistance', repos = c('https://agrdatasci.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/agrdatasci/gdistance/issues
Pkgdown/docs site:https://agrdatasci.github.io
Datasets:
Last updated from:4076198439. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 277 | ||
| source / vignettes | OK | 259 | ||
| linux-release-x86_64 | NOTE | 260 | ||
| macos-release-arm64 | NOTE | 187 | ||
| macos-oldrel-arm64 | NOTE | 260 | ||
| windows-devel | NOTE | 231 | ||
| windows-release | NOTE | 242 | ||
| windows-oldrel | NOTE | 235 | ||
| wasm-release | OK | 131 |
Exports:accCostadjacencyFromTransitionArithcoercecommuteDistanceComparecostDistancegeoCorrectionLogicmatrixValuesmatrixValues<-nlayersnonoverlapnormalizeOpsoverlappassagepathIncrasterrSPDistanceshortestPathshowsummarySummarysumReciprocaltransitiontransitionCellstransitionDatatransitionMatrixtransitionMatrix<-
Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigrasterRcpprlangspterravctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Accumulated Cost Surface | accCost accCost,TransitionLayer,Coords-method accCost,TransitionLayer,RasterLayer-method |
| Adjacent cells | adjacencyFromTransition |
| Arithmetic and mathematical operations with objects of Transition* classes | Arith,ANY,TransitionLayer-method Arith,ANY,TransitionStack-method Arith,TransitionLayer,ANY-method Arith,TransitionLayer,TransitionLayer-method Arith,TransitionLayer,TransitionStack-method Arith,TransitionStack,ANY-method Arith,TransitionStack,TransitionLayer-method Arith-methods ArithMath-methods Math,TransitionLayer-method Math,TransitionStack-method Math-methods |
| Commute-time distance | commuteDistance commuteDistance,TransitionLayer,Coords-method |
| Coords class | Coords class Coords-class |
| Cost distance | costDistance costDistance,TransitionLayer,Coords,Coords-method costDistance,TransitionLayer,Coords,missing-method |
| Distances and Routes on Geographical Grids | gdistance-package gdistance |
| Genetic distances and coordinates of haplogroup R1b1b2 populations in Europe | genDist popCoord |
| Geographic Correction | geoCorrection geoCorrection,TransitionLayer,character-method geoCorrection,TransitionLayer,missing-method |
| Normalize | normalize normalize,TransitionLayer-method |
| Overlap and nonoverlap of trajectories | nonoverlap overlap |
| Probability of passage | passage passage,TransitionLayer,Coords,Coords,missing-method passage,TransitionLayer,Coords,Coords,numeric-method passage,TransitionLayer,RasterLayer,RasterLayer,missing-method passage,TransitionLayer,RasterLayer,RasterLayer,numeric-method |
| Incidence of paths from a common origin: overlap and non-overlap | pathInc pathInc,TransitionLayer,Coords,Coords,Coords,missing,missing-method pathInc,TransitionLayer,Coords,Coords,Coords,missing,Transition-method pathInc,TransitionLayer,Coords,Coords,Coords,numeric,missing-method pathInc,TransitionLayer,Coords,Coords,Coords,numeric,Transition-method pathInc,TransitionLayer,Coords,Coords,missing,missing,missing-method pathInc,TransitionLayer,Coords,Coords,missing,missing,Transition-method pathInc,TransitionLayer,Coords,Coords,missing,numeric,missing-method pathInc,TransitionLayer,Coords,Coords,missing,numeric,Transition-method |
| RasterLayer from TransitionLayer object | raster,TransitionLayer-method |
| Randomized shortest path distance | rSPDistance rSPDistance,TransitionLayer,Coords-method |
| Shortest path | shortestPath shortestPath,TransitionLayer,Coords,Coords-method |
| Summary methods | mean,TransitionStack-method sum,TransitionStack-method Summary,TransitionLayer-method summary,TransitionLayer-method Summary,TransitionStack-method summary,TransitionStack-method Summary-methods |
| Reciprocal of the sum of the reciprocals of conductance values in Transition* objects | sumReciprocal |
| Create an object of the class Transition | transition transition,RasterBrick-method transition,RasterLayer-method |
| Transition classes | ==,TransitionLayer,TransitionLayer-method ==,TransitionStack,TransitionStack-method coerce,RasterLayer,TransitionLayer-method coerce,TransitionData,sparseMatrix-method coerce,TransitionLayer,RasterLayer-method coerce,TransitionLayer,sparseMatrix-method coerce,TransitionLayer,TransitionData-method coerce,TransitionLayer,TransitionStack-method show,TransitionLayer-method show,TransitionStack-method Transition-class Transition-classes TransitionData-class TransitionLayer-class TransitionStack-class |
| Extracting and replacing: class Transition | Transition-extract-replace transitionMatrix<- transitionMatrix<-,TransitionLayer,sparseMatrix-method TransitionStack<- [,TransitionLayer,matrix,missing,missing-method [,TransitionLayer,numeric,numeric,missing-method [<-,TransitionLayer,matrix,missing,ANY-method [<-,TransitionLayer,numeric,numeric,ANY-method [[,TransitionStack,numeric,missing-method [[<-,TransitionStack,numeric,missing,TransitionData-method |
| Extract or change elements of Transition* objects | matrixValues matrixValues,TransitionLayer-method matrixValues,TransitionStack-method matrixValues<- matrixValues<-,TransitionLayer,character-method matrixValues<-,TransitionStack,character-method nlayers,TransitionLayer-method nlayers,TransitionStack-method Transition-slots transitionCells transitionCells,TransitionData-method transitionCells,TransitionLayer-method transitionData transitionData,TransitionLayer-method transitionData,TransitionStack-method transitionMatrix transitionMatrix,TransitionData,missing-method transitionMatrix,TransitionLayer,logical-method transitionMatrix,TransitionLayer,missing-method |