Introduction | Building a deme graph | Choosing the neighbourhood | Genetic covariance from biallelic (SNP) data | Pairwise F_ST | Covariance from multivariate or microsatellite data | Microsatellite allele calls | From covariance to distance | Directional edge covariates | Gradient of a scalar potential | Projection of a vector flow field | Quick reference | Summary of key functions | See also | References
Package: landgraph 0.0.1
landgraph: Graphs and Covariance for Landscape Genetics
Shared, dependency-light primitives for landscape-genetic network methods: a lightweight deme/landscape graph (vertex coordinates and an undirected edge list) with constructors from coordinates; genetic covariance and distance from biallelic or multiallelic data (the Yang-style normalized-dosage covariance and the Dyer-style multivariate covariance); and antisymmetric per-edge directional covariate builders (the gradient of a scalar potential, and the projection of a vector flow field). Used by 'terradish' (symmetric resistance) and 'dragonflow' (asymmetric gene flow). No compiled code.
Authors:
landgraph_0.0.1.tar.gz
landgraph_0.0.1.zip(r-4.7)landgraph_0.0.1.zip(r-4.6)landgraph_0.0.1.zip(r-4.5)
landgraph_0.0.1.tgz(r-4.6-any)landgraph_0.0.1.tgz(r-4.5-any)
landgraph_0.0.1.tar.gz(r-4.7-any)landgraph_0.0.1.tar.gz(r-4.6-any)
landgraph_0.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
landgraph/json (API)
| # Install 'landgraph' in R: |
| install.packages('landgraph', repos = c('https://wpeterman.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wpeterman/landgraph/issues
Last updated from:1d2fefd4b0. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 119 | ||
| source / vignettes | OK | 161 | ||
| linux-release-x86_64 | OK | 120 | ||
| macos-release-arm64 | OK | 124 | ||
| macos-oldrel-arm64 | OK | 68 | ||
| windows-devel | OK | 82 | ||
| windows-release | OK | 69 | ||
| windows-oldrel | OK | 74 | ||
| wasm-release | OK | 120 |
Exports:cov_from_bialleliccov_from_genetic_datademe_graphdist_from_biallelicdist_from_covedge_flowedge_gradientfst_from_biallelic
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Genetic covariance from biallelic allele counts | cov_from_biallelic |
| Covariance from multivariate genetic data | cov_from_genetic_data |
| Lightweight deme / landscape graph from coordinates | deme_graph |
| Genetic distance matrix from biallelic allele counts | dist_from_biallelic |
| Squared-distance matrix from a covariance matrix | dist_from_cov |
| Circulation (flow-field) edge covariate from a spatial vector field | edge_flow |
| Directional edge covariates from a spatial layer | edge_gradient |
| F_ST from biallelic allele counts | fst_from_biallelic |
