Package: MorphoRegions 0.1.0

Amandine Gillet

MorphoRegions: Analysis of Regionalization Patterns in Serially Homologous Structures

Computes the optimal number of regions (or subdivisions) and their position in serial structures without a priori assumptions and to visualize the results. After reducing data dimensionality with the built-in function for data ordination, regions are fitted as segmented linear regressions along the serial structure. Every region boundary position and increasing number of regions are iteratively fitted and the best model (number of regions and boundary positions) is selected with an information criterion. This package expands on the previous 'regions' package (Jones et al., Science 2018) with improved computation and more fitting and plotting options.

Authors:Amandine Gillet [cre, aut], Katrina Jones [aut], Noah Greifer [aut], Stephanie Pierce [aut]

MorphoRegions_0.1.0.tar.gz
MorphoRegions_0.1.0.tar.gz(r-4.5-noble)MorphoRegions_0.1.0.tar.gz(r-4.4-noble)
MorphoRegions_0.1.0.tgz(r-4.4-emscripten)MorphoRegions_0.1.0.tgz(r-4.3-emscripten)
MorphoRegions.pdf |MorphoRegions.html✨
MorphoRegions/json (API)

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

Peer review:

Bug tracker:https://github.com/aagillet/morphoregions/issues

Datasets:
  • alligator - Measurements from the vertebral column of an alligator
  • dolphin - Measurements from the vertebral column of a dolphin
  • musm - Measurements from the vertebral column of a mouse
  • porpoise1 - Measurements from the vertebral column of three porpoises
  • porpoise2 - Measurements from the vertebral column of three porpoises
  • porpoise3 - Measurements from the vertebral column of three porpoises

16 exports 0.09 score 31 dependencies 4 scripts

Last updated 27 days agofrom:cfb8293643. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 22 2024
R-4.5-linuxOKAug 22 2024

Exports:addregionscalcBPvarcalcmodelcalcregionsmodelperfmodelselectmodelsupportncombosPCOloadPCOselectplotsegregplotvertmapprocess_measurementssimregionssubsamplesvdPCO

Dependencies:chkcliclustercolorspacefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepbapplypillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

MorphoRegions

Rendered fromMorphoRegions.Rmdusingknitr::rmarkdown_notangleon Aug 22 2024.

Last update: 2024-08-22
Started: 2024-08-22

Readme and manuals

Help Manual

Help pageTopics
Measurements from the vertebral column of an alligatoralligator
Calculate variability of breakpointscalcBPvar
Calculate results of a single segmented regression modelcalcmodel
Fit segmented regression models for all combinations of breakpointsaddregions calcregions ncombos summary.regions_results
Measurements from the vertebral column of a dolphindolphin
Assess model performancemodelperf modelperf.regions_pco modelperf.regions_results_single modelperf.regions_sim
Select the best modelsmodelselect
Evaluate model supportmodelsupport
Measurements from the vertebral column of a mousemusm
Calculate PCO loadingsPCOload plot.regions_pco_load
Select PCO scoresPCOselect plot.regions_pco_select summary.regions_pco_select
Plot PCO axesplot.regions_pco
Plot a segmented regression modelplotsegreg plotsegreg.regions_pco plotsegreg.regions_results_single plotsegreg.regions_sim
Plot a vertebra mapplotvertmap
Measurements from the vertebral column of three porpoisesporpoise porpoise1 porpoise2 porpoise3
Process vertebra measurementsprocess_measurements
Simulate regions dataplot.regions_sim simregions
Subsample a datasetsubsample
Calculate PCO (principal co-ordinates analysis) based on SVDsvdPCO