Package: SIBER 2.1.10

Andrew Jackson

SIBER: Stable Isotope Bayesian Ellipses in R

Fits bi-variate ellipses to stable isotope data using Bayesian inference with the aim being to describe and compare their isotopic niche.

Authors:Andrew Jackson [aut, cre], Andrew Parnell [aut]

SIBER_2.1.10.tar.gz
SIBER_2.1.10.zip(r-4.7-any)SIBER_2.1.10.zip(r-4.6-any)
SIBER_2.1.10.tar.gz(r-4.7-any)SIBER_2.1.10.tar.gz(r-4.6-any)
SIBER_2.1.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SIBER/json (API)

# Install 'SIBER' in R:
install.packages('SIBER', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3
Datasets:
  • allgroups - The entire set of Geese isotope data
  • concdepdemo - A set of concentration dependence values for stable isotope analysis
  • correctionsdemo - A set of trophic discrimination factors for brent geese feeding on their sources.
  • demo.siber.data - Simulated d13C and d15N isotope-space data
  • demo.siber.data.2 - Simulated d13C and d15N isotope-space data
  • geese1demo - A single group of the geese data
  • geese2demo - A single group of the geese data
  • mongoose - A set of isotope observations for mongooses nested within packs
  • sourcesdemo - A set of isotope observations on food sources of brent geese

On CRAN:

Conda:

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

jagscpp

4.48 score 1 stars 1 packages 872 downloads 110 mentions 29 exports 50 dependencies

Last updated from:b9b491c111. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK135
source / vignettesOK311
linux-release-x86_64OK125
windows-devel-x86_64OK88
windows-release-x86_64OK84
wasm-releaseOK751

Exports:addEllipseallCentroidVectorsbayesianLaymanbayesianOverlapcommunityMetricsMLcreateSiberObjectellipseInOutellipsoidTransformextractPosteriorMeansfitEllipsegenerateSiberCommunitygenerateSiberDatagenerateSiberGroupgroupMetricsMLlaymanMetricsmaxLikOverlapplotCommunityHullsplotGroupEllipsesplotGroupHullsplotSiberObjectpointsToEllipsoidposteriorSEAsiberCentroidssiberConvexhullsiberDensityPlotsiberEllipsessiberMVNsigmaSEAspecificCentroidVectors

Dependencies:ashclicodacpp11dplyrfarverFNNgenericsggplot2gluegmpgtablehdrcdeisobandkernlabKernSmoothkslabelinglatticelifecyclelocfitmagrittrMatrixmclustmgcvmnormtmulticoolmvtnormnlmepillarpkgconfigpracmapurrrR6RColorBrewerRcpprjagsrlangS7scalesspatstat.utilsstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Plot Some Posterior Ellipses
Rendered fromPlot-posterior-ellipses.Rmdusingknitr::rmarkdown

Last update: 2026-02-09
Started: 2019-02-24

Comparing communities
Rendered fromsiber-comparing-communities.Rmdusingknitr::rmarkdown

Last update: 2023-10-19
Started: 2021-04-13

Comparing populations
Using Bayesian Inference to calculate uncertainty around ellipses | Comparing the posterior distributions | Overlap Between Ellipses
Rendered fromsiber-comparing-populations.Rmdusingknitr::rmarkdown

Last update: 2023-10-19
Started: 2021-04-13

Customising Plots Manually
Creating a Blank Plot
Rendered fromCustomising-Plots-Manually.Rmdusingknitr::rmarkdown

Last update: 2023-10-19
Started: 2016-08-04

Ellipse Overlap
Calculating the Area of Overlap Between Two Ellipses
Rendered fromEllipse-Overlap.Rmdusingknitr::rmarkdown

Last update: 2023-10-19
Started: 2017-02-22

Introduction to SIBER
SIBER introduction and guide | Setting up our R session for this demonstration | Plotting the raw data | Summary statistics and custom graphic additions | Fitting the Bayesian models to the data | Comparing among groups using the Standard Ellipse Area | Comparison of entire communities using the Layman metrics
Rendered fromIntroduction-to-SIBER.Rmdusingknitr::rmarkdown

Last update: 2023-10-19
Started: 2015-08-13

SIA plots using ggplot2
Errorbar scatterplots | Ellipses instead of errorbars | Trouble shooting
Rendered fromPlot-SIA-ggplot2.Rmdusingknitr::rmarkdown

Last update: 2023-10-19
Started: 2021-04-13

Vector Statistics on Centroids
Load up some data to illustrate the vector-based metrics | Introducing the vector-based statistics. | Polar density plots
Rendered fromCentroid-Vectors.Rmdusingknitr::rmarkdown

Last update: 2023-10-19
Started: 2017-04-28

Points Inside or Outside Ellipse
Creating some test data | Determine whether points are inside or outside ellipse | Large simulation across sample size | 3 and more dimensions
Rendered fromPoints-Inside-Outside-Ellipse.Rmdusingknitr::rmarkdown

Last update: 2023-08-22
Started: 2017-02-22

Test Convergence
Rendered fromTest-convergence.Rmdusingknitr::rmarkdown

Last update: 2021-04-13
Started: 2019-02-24

Readme and manuals

Help Manual

Help pageTopics
Adds an ellipse around some data to an existing plotaddEllipse
Plot the pairwise distances and angles describing the difference between centroids of all groupsallCentroidVectors
The entire set of Geese isotope dataallgroups
Calculate Layman metrics on Bayesian posterior samples of a communitybayesianLayman
Calculate the overlap between two ellipses based on their posterior distributions.bayesianOverlap
Calculate the point estimates of the Layman metrics for each communitycommunityMetricsML
A set of concentration dependence values for stable isotope analysisconcdepdemo
A set of trophic discrimination factors for brent geese feeding on their sources.correctionsdemo
Read in SIBER format data and generate the SIBER objectcreateSiberObject
Simulated d13C and d15N isotope-space datademo.siber.data
Simulated d13C and d15N isotope-space datademo.siber.data.2
Back-transform a z-score siber ellipse to original location and scale.ellipseBackTransform
Test whether a set of points are inside or outside a defined circleellipseInOut
Apply a normalisation transformation to vectors of data onto ellipsoidsellipsoidTransform
Extract posterior means from call to 'siberMVN'extractPosteriorMeans
Fit a multivariate normal distribution to x and y data using jagsfitEllipse
A single group of the geese datageese1demo
A single group of the geese datageese2demo
Create a sequence of points on a circlegenCircle
A utility function to simulate a single community comprised of groupsgenerateSiberCommunity
A utility function to simulate isotope data for several communitiesgenerateSiberData
A utility function to simulate a single group of datagenerateSiberGroup
Calculate maximum likelihood based measures of dispersion of bivariate datagroupMetricsML
Calculate the area of a convex hull given its coordinateshullArea
Calculates the 6 Layman metrics on a vector of x and y datalaymanMetrics
Calculate the overlap between two ellipses based on the maximum likelihood fitted ellipses.maxLikOverlap
A set of isotope observations for mongooses nested within packsmongoose
Adds convex hulls to each community to an existing plotplotCommunityHulls
Adds ellipses to an existing plot for each of your groupsplotGroupEllipses
Plots illustrative convex hulls for each group within all communitiesplotGroupHulls
Creates an isotope scatterplot and provides a wrapper to ellipse and hull plottingplotSiberObject
Test whether a set of points are inside or outside a defined ellipsepointsToEllipsoid
Calculate the SEA based on a posterior distribution of SigmaposteriorSEA
Calculate the polar form of the vector between pairs of ellipse centroidssiberCentroids
Calculate metrics and plotting information for convex hullssiberConvexhull
Plot credible intervals as shaded boxplots using 'hdr.boxplot'siberDensityPlot
Calculate the Bayesian Standard Ellipse Area for all groupssiberEllipses
Fit Bayesian bivariate normal distributions to each group in each communitysiberMVN
Calculate metrics corresponding to the Standard Ellipse based on a covariance matrixsigmaSEA
A set of isotope observations on food sources of brent geesesourcesdemo
Calculate the pairwise distances and angles describing the difference between centroids of paired groupsspecificCentroidVectors