Input data | The workflow | Import the pedigree | [example] get_colony() & kinship2 | Animal timespan | Organize families | Pedigree | Families | Plotting table | Temporal plot | Spatial files | [example] Drawing maps in R | ggplot2 | leaflet | GIS output | Outside of the workflow
Package: wpeR 0.2.0
wpeR: Streamlined Analysis of Wild Pedigree Data
Analyzing pedigree data of wild populations. While primarily designed to process outputs from the 'COLONY' (Jones & Wang (2010) <doi:10.1111/j.1755-0998.2009.02787.x>) pedigree reconstruction software, it can also accommodate data from other sources. By linking reconstructed pedigrees with genetic sample metadata, 'wpeR' produces spatial and temporal visualizations as well as tabular summaries that support interpretation of family structures and dynamics. The main goal of the package is to provide a solution for the analysis of complex wild pedigree data and to help the user to gain insights into genetic relationships within wild animal populations.
Authors:
wpeR_0.2.0.tar.gz
wpeR_0.2.0.zip(r-4.7)wpeR_0.2.0.zip(r-4.6)wpeR_0.2.0.zip(r-4.5)
wpeR_0.2.0.tgz(r-4.6-any)wpeR_0.2.0.tgz(r-4.5-any)
wpeR_0.2.0.tar.gz(r-4.7-any)wpeR_0.2.0.tar.gz(r-4.6-any)
wpeR_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
wpeR/json (API)
| # Install 'wpeR' in R: |
| install.packages('wpeR', repos = c('https://gr3602.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gr3602/wper/issues
Pkgdown/docs site:https://gr3602.github.io
Datasets:
- wolf_samples - Wolf monitoring genetic samples metadata
Last updated from:3479cfab58. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 185 | ||
| source / vignettes | OK | 263 | ||
| linux-release-x86_64 | OK | 183 | ||
| macos-release-arm64 | OK | 188 | ||
| macos-oldrel-arm64 | OK | 207 | ||
| windows-devel | OK | 120 | ||
| windows-release | OK | 118 | ||
| windows-oldrel | OK | 116 | ||
| wasm-release | OK | 142 |
Exports:anim_timespancheck_sampledatadyn_matrixget_colonyget_pednbtw_seasonsorg_famsped_satplotped_spatialplot_table
Dependencies:classclassIntclicpp11DBIdplyre1071farvergenericsggplot2gluegtableisobandKernSmoothlabelinglifecyclemagrittrMASSpillarpkgconfigproxyR6RColorBrewerRcpprlangs2S7scalessftibbletidyselectunitsutf8vctrsviridisLitewithrwk
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get dates of individuals first and last sample | anim_timespan |
| Check and prepare genetic sample metadata | check_sampledata |
| Get matrix of apparent survival | dyn_matrix |
| Organizes COLONY output | get_colony |
| Organizes pedigree data | get_ped |
| Number of detected animals between two sampling seasons | nbtw_seasons |
| Organize animals into families and expand pedigree data | org_fams |
| Temporal plot of pedigree | ped_satplot |
| Get files for spatial representation of pedigree | ped_spatial |
| Prepares pedigree data for plotting and spatial representation | plot_table |
| Wolf monitoring genetic samples metadata | wolf_samples |
