Package: SIBER 2.1.9

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]

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SIBER.pdf |SIBER.html✨
SIBER/json (API)
NEWS

# Install 'SIBER' in R:

install.packages('SIBER', repos = c('https://andrewljackson.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/andrewljackson/siber/issues

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:

community-ecology ecology niche-modelling stable-isotopes

31 exports 36 stars 6.47 score 57 dependencies 1 dependents 110 mentions 168 scripts 1.2k downloads

Last updated 4 months agofrom:424c76abe5. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 02 2024
R-4.5-win	OK	Sep 02 2024
R-4.5-linux	OK	Sep 02 2024
R-4.4-win	OK	Sep 02 2024
R-4.4-mac	OK	Sep 02 2024
R-4.3-win	OK	Sep 02 2024
R-4.3-mac	OK	Sep 02 2024

Exports:addEllipse allCentroidVectors bayesianLayman bayesianOverlap communityMetricsML createSiberObject ellipseInOut ellipsoidTransform extractPosteriorMeans fitEllipse generateSiberCommunity generateSiberData generateSiberGroup groupMetricsML kapow laymanMetrics maxLikOverlap plotCommunityHulls plotGroupEllipses plotGroupHulls plotSiberObject pointsToEllipsoid posteriorSEA siberCentroids siberConvexhull siberDensityPlot siberEllipses siberKapow siberMVN sigmaSEA specificCentroidVectors

Dependencies:ash cli coda colorspace cpp11 deldir dplyr fansi farver FNN generics ggplot2 glue gtable hdrcde isoband kernlab KernSmooth ks labeling lattice lifecycle locfit magrittr MASS Matrix mclust mgcv mnormt multicool munsell mvtnorm nlme pillar pkgconfig polyclip pracma purrr R6 RColorBrewer Rcpp rjags rlang scales spatstat.data spatstat.geom spatstat.univar spatstat.utils stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr

Comparing communities

Andrew L Jackson

Rendered fromsiber-comparing-communities.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-10-11
Started: 2020-05-12

Comparing populations

Andrew L Jackson

Rendered fromsiber-comparing-populations.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-10-11
Started: 2020-05-12

Customising Plots Manually

Andrew L Jackson

Rendered fromCustomising-Plots-Manually.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-10-11
Started: 2016-08-03

Ellipse Overlap

Andrew L Jackson

Rendered fromEllipse-Overlap.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-10-11
Started: 2016-08-16

Introduction to SIBER

Andrew L Jackson

Rendered fromIntroduction-to-SIBER.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-10-11
Started: 2015-08-09

KAPOW! example

Andrew Jackson

Rendered fromkapow-example.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-02-15
Started: 2021-05-27

Plot Some Posterior Ellipses

Andrew L Jackson

Rendered fromPlot-posterior-ellipses.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-10-11
Started: 2017-06-01

Points Inside or Outside Ellipse

Andrew L Jackson

Rendered fromPoints-Inside-Outside-Ellipse.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-04-17
Started: 2016-08-10

SIA plots using ggplot2

Andrew L Jackson

Rendered fromPlot-SIA-ggplot2.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-10-11
Started: 2020-07-16

Test Convergence

Andrew L Jackson

Rendered fromTest-convergence.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2021-04-13
Started: 2017-06-02

Vector Statistics on Centroids

Andrew L Jackson

Rendered fromCentroid-Vectors.Rmdusingknitr::rmarkdownon Sep 02 2024.

Last update: 2023-10-11
Started: 2017-03-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Adds an ellipse around some data to an existing plot	addEllipse
Plot the pairwise distances and angles describing the difference between centroids of all groups	allCentroidVectors
The entire set of Geese isotope data	allgroups
Calculate Layman metrics on Bayesian posterior samples of a community	bayesianLayman
Calculate the overlap between two ellipses based on their posterior distributions.	bayesianOverlap
Calculate the point estimates of the Layman metrics for each community	communityMetricsML
A set of concentration dependence values for stable isotope analysis	concdepdemo
A set of trophic discrimination factors for brent geese feeding on their sources.	correctionsdemo
Read in SIBER format data and generate the SIBER object	createSiberObject
Simulated d13C and d15N isotope-space data	demo.siber.data
Simulated d13C and d15N isotope-space data	demo.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 circle	ellipseInOut
Apply a normalisation transformation to vectors of data onto ellipsoids	ellipsoidTransform
Extract posterior means from call to 'siberMVN'	extractPosteriorMeans
Fit a multivariate normal distribution to x and y data using jags	fitEllipse
A single group of the geese data	geese1demo
A single group of the geese data	geese2demo
Create a sequence of points on a circle	genCircle
A utility function to simulate a single community comprised of groups	generateSiberCommunity
A utility function to simulate isotope data for several communities	generateSiberData
A utility function to simulate a single group of data	generateSiberGroup
Calculate maximum likelihood based measures of dispersion of bivariate data	groupMetricsML
Calculate the area of a convex hull given its coordinates	hullArea
KAPOW!	kapow
Calculates the 6 Layman metrics on a vector of x and y data	laymanMetrics
Calculate the overlap between two ellipses based on the maximum likelihood fitted ellipses.	maxLikOverlap
A set of isotope observations for mongooses nested within packs	mongoose
Adds convex hulls to each community to an existing plot	plotCommunityHulls
Adds ellipses to an existing plot for each of your groups	plotGroupEllipses
Plots illustrative convex hulls for each group within all communities	plotGroupHulls
Creates an isotope scatterplot and provides a wrapper to ellipse and hull plotting	plotSiberObject
Test whether a set of points are inside or outside a defined ellipse	pointsToEllipsoid
Calculate the SEA based on a posterior distribution of Sigma	posteriorSEA
Calculate the polar form of the vector between pairs of ellipse centroids	siberCentroids
Calculate metrics and plotting information for convex hulls	siberConvexhull
Plot credible intervals as shaded boxplots using 'hdr.boxplot'	siberDensityPlot
Calculate the Bayesian Standard Ellipse Area for all groups	siberEllipses
Calculates the boundary of a union of ellipses	siberKapow
Fit Bayesian bivariate normal distributions to each group in each community	siberMVN
Calculate metrics corresponding to the Standard Ellipse based on a covariance matrix	sigmaSEA
A set of isotope observations on food sources of brent geese	sourcesdemo
Calculate the pairwise distances and angles describing the difference between centroids of paired groups	specificCentroidVectors

Package: SIBER 2.1.9

SIBER: Stable Isotope Bayesian Ellipses in R

Comparing communities

Comparing populations

Customising Plots Manually

Ellipse Overlap

Introduction to SIBER

KAPOW! example

Plot Some Posterior Ellipses

Points Inside or Outside Ellipse

SIA plots using ggplot2

Test Convergence

Vector Statistics on Centroids

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)