Package: wingen 2.2.0

wingen: Continuous Mapping of Genetic Diversity

Generate continuous maps of genetic diversity using moving windows with options for rarefaction, interpolation, and masking as described in Bishop et al. (2023) <doi:10.1111/2041-210X.14090>.

Authors:Anusha Bishop [aut, cre], Anne Chambers [aut], Ian Wang [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
wingen/json (API)

# Install 'wingen' in R:

install.packages('wingen', repos = c('https://anushapb.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/anushapb/wingen/issues

Datasets:

lotr_coords - Middle earth example coordinates
lotr_lyr - Middle earth example raster
lotr_range - Middle earth example range polygon
lotr_vcf - Middle earth example vcf
mini_coords - Mini middle earth example coordinates
mini_lyr - Mini middle earth example raster
mini_vcf - Mini middle earth example vcf
mini_vcf_NA - Mini middle earth example vcf with NA values

On CRAN:

6.88 score 18 stars 47 scripts 560 downloads 20 exports 112 dependencies

Last updated from:c2cfd25b0a. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	368
source / vignettes	OK	351
linux-release-x86_64	OK	363
macos-release-arm64	OK	405
macos-oldrel-arm64	OK	531
windows-devel	OK	337
windows-release	OK	334
windows-oldrel	OK	320
wasm-release	OK	169

Exports:circle_gd circle_general coords_to_raster get_geodist get_resdist ggplot_count ggplot_gd krig_gd load_middle_earth_ex load_mini_ex mask_gd plot_count plot_gd preview_gd resist_gd resist_general vcf_to_dosage window_gd window_general wkrig_gd

Dependencies:abind ade4 adegenet ape base64enc boot bslib cachem class classInt cli cluster codetools commonmark cpp11 crayon DBI digest dplyr e1071 farver fastmap FNN fontawesome fs furrr future gaston gdistance generics ggplot2 globals glue gridExtra gstat gtable gtools hierfstat htmltools httpuv igraph intervals isoband jquerylib jsonlite KernSmooth labeling later lattice lifecycle listenv magrittr MASS Matrix memoise memuse mgcv mime nlme otel parallelly pegas permute pillar pinfsc50 pixmap pkgconfig plyr promises proxy purrr R6 rappdirs raster RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel reshape2 rlang s2 S7 sass scales segmented seqinr sf sftime shiny sourcetools sp spacetime stars stringi stringr terra tibble tidyr tidyselect units utf8 vcfR vctrs vegan viridis viridisLite withr wk xtable xts zoo

wingen-vignette

Rendered fromwingen-vignette.Rmdusingknitr::rmarkdown

Last update: 2025-08-05
Started: 2022-06-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Create a moving window map of genetic diversity using a circle window	circle_gd
General function for making circular moving window maps	circle_general
Create a raster from coordinates	coords_to_raster
Get a matrix of geographic distances for circle_gd	get_geodist
Get a matrix of resistance distances for resist_gd	get_resdist
Plot moving window map of sample counts	ggplot_count
Plot moving window map of genetic diversity	ggplot_gd
Superseded: Krige moving window maps	krig_gd
Middle earth example	load_middle_earth_ex
Mini middle earth example	load_mini_ex
Middle earth example coordinates	lotr_coords
Middle earth example raster	lotr_lyr
Middle earth example range polygon	lotr_range
Middle earth example vcf	lotr_vcf
Mask moving window maps	mask_gd
Mini middle earth example coordinates	mini_coords
Mini middle earth example raster	mini_lyr
Mini middle earth example vcf	mini_vcf
Mini middle earth example vcf with NA values	mini_vcf_NA
Plot moving window map of sample counts	plot_count
Plot moving window map of genetic diversity	plot_gd
Preview moving window and sample counts	preview_gd
Create a moving window map of genetic diversity based on resistance	resist_gd
General function for making resistance-based maps	resist_general
Convert a vcf to a dosage matrix	vcf_to_dosage
Create a moving window map of genetic diversity	window_gd
General function for making moving window maps	window_general
Krige moving window maps with variogram selection	wkrig_gd