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:
AlleleShift_1.1-2.tar.gz
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AlleleShift_1.1-2.tgz(r-4.4-any)AlleleShift_1.1-2.tgz(r-4.3-any)
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AlleleShift.pdf |AlleleShift.html✨
AlleleShift/json (API)
| # Install 'AlleleShift' in R: |
| install.packages('AlleleShift', repos = c('https://roelandkindt.r-universe.dev', 'https://cloud.r-project.org')) |
- Poptri.1985to2085 - Example data sets for Populus trichocarpa.
- Poptri.baseline.env - Example data sets for Populus trichocarpa.
- Poptri.freq.baseline - Example data sets for Populus trichocarpa.
- Poptri.freq.future - Example data sets for Populus trichocarpa.
- Poptri.future.env - Example data sets for Populus trichocarpa.
- Poptri.genind - Example data sets for Populus trichocarpa.
- Poptri.loc - Example data sets for Populus trichocarpa.
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 11 months agofrom:1776876287. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 24 2024 |
| R-4.5-win | OK | Aug 24 2024 |
| R-4.5-linux | OK | Aug 24 2024 |
| R-4.4-win | OK | Aug 24 2024 |
| R-4.4-mac | OK | Aug 24 2024 |
| R-4.3-win | OK | Aug 24 2024 |
| R-4.3-mac | OK | Aug 24 2024 |
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.tableDBIDerivdigestdoBydplyre1071effectsestimabilityevaluatefansifarverfastmapfontawesomeforcatsforeignFormulafsgenericsggplot2gluegridExtragtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvigraphinsightisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamitoolsmodelrmunsellnlmenloptrnnetnortestnumDerivpbkrtestpermutepillarpixmappkgconfigplyrprettyunitsprogresspromisesproxypurrrquantregR6rappdirsRcmdrRcmdrMiscRColorBrewerRcppRcppArmadilloRcppEigenreadrreadstata13readxlrelimprematchreshape2rlangrmarkdownrpartrstudioapisandwichsassscalessegmentedseqinrshinysourcetoolsspSparseMstringistringrsurveysurvivaltcltk2tibbletidyrtidyselecttinytextzdbutf8vctrsveganviridisviridisLitevroomwithrxfunxtableyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Analysis of Molecular Variance (AMOVA) via Redundancy Analysis | amova.rda |
| Calibration and Prediction Functions for Changes in Allele Frequencies | count.model count.pred freq.ggplot freq.model freq.pred |
| Example data sets for Populus trichocarpa. | Poptri.1985to2085 Poptri.baseline.env Poptri.freq.baseline Poptri.freq.future Poptri.future.env Poptri.genind Poptri.loc |
| Shifts of Populations in Environmental Space as Response to Climate Change | environmental.novel population.shift |
| Shifts of Allele Frequencies as Response to Climate Change | shift.dot.ggplot |
| Shifts of Allele Frequencies as Response to Climate Change | moon.waxer shift.moon.ggplot |
| Shifts of Allele Frequencies as Response to Climate Change | pie.baker shift.pie.ggplot |
| Shifts of Allele Frequencies as Response to Climate Change | shift.surf.ggplot |
| Shifts of Allele Frequencies as Response to Climate Change | shift.waffle.ggplot waffle.baker |
| Reduce the Climate Data based on Variance Inflation Factor Analysis. | VIF.subset |
