Package: AlleleShift 1.1-2

AlleleShift: Predict and Visualize Population-Level Changes in Allele Frequencies in Response to Climate Change

Methods (<doi:10.7717/peerj.11534>) are provided of calibrating and predicting shifts in allele frequencies through redundancy analysis ('vegan::rda()') and generalized additive models ('mgcv::gam()'). Visualization functions for predicted changes in allele frequencies include 'shift.dot.ggplot()', 'shift.pie.ggplot()', 'shift.moon.ggplot()', 'shift.waffle.ggplot()' and 'shift.surf.ggplot()' that are made with input data sets that are prepared by helper functions for each visualization method. Examples in the documentation show how to prepare animated climate change graphics through a time series with the 'gganimate' package. Function 'amova.rda()' shows how Analysis of Molecular Variance can be directly conducted with the results from redundancy analysis.

Authors:Roeland Kindt [cre, aut]

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AlleleShift/json (API)

# Install 'AlleleShift' in R:
install.packages('AlleleShift', repos = c('https://roelandkindt.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.70 score 1 stars 4 scripts 386 downloads 1 mentions 17 exports 148 dependencies

Last updated 1 years agofrom:1776876287. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 22 2025
R-4.5-winOKMar 22 2025
R-4.5-macOKMar 22 2025
R-4.5-linuxOKFeb 20 2025
R-4.4-winOKMar 22 2025
R-4.4-macOKMar 22 2025
R-4.4-linuxOKMar 22 2025
R-4.3-winOKMar 22 2025
R-4.3-macOKMar 22 2025

Exports:amova.rdacount.modelcount.predenvironmental.novelfreq.ggplotfreq.modelfreq.predmoon.waxerpie.bakerpopulation.shiftshift.dot.ggplotshift.moon.ggplotshift.pie.ggplotshift.surf.ggplotshift.waffle.ggplotVIF.subsetwaffle.baker

Dependencies:abindade4adegenetapebackportsbase64encBiodiversityRbitbit64bootbroombslibcachemcarcarDatacellrangercheckmateclassclicliprclustercolorspacecommonmarkcowplotcpp11crayondata.tableDBIDerivdigestdoBydplyre1071effectsestimabilityevaluatefansifarverfastmapfontawesomeforcatsforeignFormulafsgenericsggplot2gluegridExtragtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvigraphinsightisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamitoolsmodelrmunsellnlmenloptrnnetnortestnumDerivpbkrtestpermutepillarpixmappkgconfigplyrprettyunitsprogresspromisesproxypurrrquantregR6rappdirsrbibutilsRcmdrRcmdrMiscRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreadstata13readxlreformulasrelimprematchreshape2rlangrmarkdownrpartrstudioapisandwichsassscalessegmentedseqinrshinysourcetoolsspSparseMstringistringrsurveysurvivaltcltk2tibbletidyrtidyselecttinytextzdbutf8vctrsveganviridisviridisLitevroomwithrxfunxtableyamlzoo