SIBER (version 2.1.9)

Stable Isotope Bayesian Ellipses in R

Description

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

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Version

Install

install.packages('SIBER')

Monthly Downloads

1,126

Version

2.1.9

License

GPL (>= 2)

Maintainer

Andrew Jackson

Last Published

October 19th, 2023

Functions in SIBER (2.1.9)

extractPosteriorMeans

Extract posterior means from call to siberMVN

fitEllipse

Fit a multivariate normal distribution to x and y data using jags

demo.siber.data.2

Simulated d13C and d15N isotope-space data

maxLikOverlap

Calculate the overlap between two ellipses based on the maximum likelihood fitted ellipses.

laymanMetrics

Calculates the 6 Layman metrics on a vector of x and y data

geese1demo

A single group of the geese data

groupMetricsML

Calculate maximum likelihood based measures of dispersion of bivariate data

generateSiberGroup

A utility function to simulate a single group of data

genCircle

Create a sequence of points on a circle

generateSiberCommunity

A utility function to simulate a single community comprised of groups

plotGroupEllipses

Adds ellipses to an existing plot for each of your groups

mongoose

A set of isotope observations for mongooses nested within packs

plotCommunityHulls

Adds convex hulls to each community to an existing plot

ellipseInOut

Test whether a set of points are inside or outside a defined circle

generateSiberData

A utility function to simulate isotope data for several communities

siberEllipses

Calculate the Bayesian Standard Ellipse Area for all groups

siberKapow

Calculates the boundary of a union of ellipses

plotGroupHulls

Plots illustrative convex hulls for each group within all communities

hullArea

Calculate the area of a convex hull given its coordinates

plotSiberObject

Creates an isotope scatterplot and provides a wrapper to ellipse and hull plotting

kapow

KAPOW!

posteriorSEA

Calculate the SEA based on a posterior distribution of Sigma

siberCentroids

Calculate the polar form of the vector between pairs of ellipse centroids

demo.siber.data

Simulated d13C and d15N isotope-space data

siberConvexhull

Calculate metrics and plotting information for convex hulls

specificCentroidVectors

Calculate the pairwise distances and angles describing the difference between centroids of paired groups

pointsToEllipsoid

Test whether a set of points are inside or outside a defined ellipse

sourcesdemo

A set of isotope observations on food sources of brent geese

siberMVN

Fit Bayesian bivariate normal distributions to each group in each community

sigmaSEA

Calculate metrics corresponding to the Standard Ellipse based on a covariance matrix

siberDensityPlot

Plot credible intervals as shaded boxplots using hdr.boxplot

allCentroidVectors

Plot the pairwise distances and angles describing the difference between centroids of all groups

bayesianOverlap

Calculate the overlap between two ellipses based on their posterior distributions.

createSiberObject

Read in SIBER format data and generate the SIBER object

bayesianLayman

Calculate Layman metrics on Bayesian posterior samples of a community

communityMetricsML

Calculate the point estimates of the Layman metrics for each community

addEllipse

Adds an ellipse around some data to an existing plot

SIBER-package

SIBER: Stable Isotope Bayesian Ellipses in R

ellipseBackTransform

Back-transform a z-score siber ellipse to original location and scale.

ellipsoidTransform

Apply a normalisation transformation to vectors of data onto ellipsoids

geese2demo

A single group of the geese data

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.