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.


News

SIBER 2.1.4

  • fixed "vignettes with duplicate titles" warning
  • added new vignette Plot-posterior-ellipses that shows how to plot multiple posterior ellipse draws on top of data using ggplot2.
  • fixed fitEllipse so that it now correctly inherits parms$n.chains and parms$n.thin from input
  • added ability to save the raw jags output to *.RData file to enable convergence diagnostics for each ellipse within fitEllipse. This option is set in the higher level user-specified object parms$save.output.
  • added new vignette Test-convergence to illustrate this new functionality of saving the raw jags output and testing using Gelman diagnostics.

SIBER 2.1.3

  • Contains a hotfix owing to a change to 'spatstat' detailed below
  • swapped package spatstat for spatstat.utils as per instructions from their package maintainers 23/03/2017
  • New functions siberCentroids, specificCentroidVectors and allCentoidVectors added to allow pairwise comparison of the locations of two groups using vectors. Illustrated in an accompanying vignette.

SIBER 2.1.2

  • added ability to specify custom pch point orders in plotSiberObject()
  • added ... to plotGroupHulls

SIBER 2.1.1

  • N.B. an error during uploading to CRAN meant a release was never lodged. I have moved on to v2.1.2 for the next release as above.
  • hotfix for bug in bayesianOverlap - thanks Mark Nowak for spotting this.
  • Important: install from github if you want to use bayesianOverlap for now until I can push a hotfix to CRAN. devtools::install_github("andrewljackson/SIBER", build_vingettes = TRUE)
  • examples added to maxLikOverlap() and pointsToEllipsoid().

SIBER 2.1.0

  • Added functions to calculate whether arbitrary points are inside or outside ellipses or higher dimensional ellipsoids along with illustrative vignettes.
  • Changed method of calculation of angle of ellipse with x-axis to using atan in place of asin which is a more elegant way of ensuring the sign of the returned angle is correct.
  • Small sample size correction for drawing ellipses can now be toggled using addEllipse(small.sample = TRUE, m = m) effectively meaning SEAc or SEA can be illustrated.
  • New vignette added illustrating how to calculate overlap between two ellipses. Two new functions detailed below greatly improve the ease with which this can be applied.
  • Fixed three bugs in the ellipse overlap vignette. Thanks to Sarina for pointing this out. These are no longer an issue as the new functions detailed below replace this code in the vignette, but it was helpful for me during the creation of these functions. Thanks.
  • Added a new function bayesianOverlap() that calculates the posterior overlap between ellipses fitted to two groups. Thanks to Josh Stewart for forcing my hand on this long-overdue feature.
  • Added a new function maxLikOverlap() to ease the calculation of overlap between ellipses using the ML estimated ellipses which previously required more manually coding than was ideal. Thanks Mark Nowak and SarinaJ for spotting some bugs and helping work them out.
  • added new functions ellipseInOut() and pointsToEllipsoid to enable testing of whether points lie inside or outside an n-dimensional ellipsoid, including the bivariate ellipse. These are useful for testing that the quantile prediction ellipses do indeed contain the expected number of data points from a sample. It might also be useful for assignment, identification of outliers, or measures of overlap of individual data points with other ellipses.

SIBER 2.0.3

  • Added a new vignette illustrating how to add custom ellipses to each group manually using the function addEllipse

SIBER 2.0.2

  • Bug in Group labels as character strings fixed
  • Community labels as character strings now implemented

SIBER 2.0.1

  • Group labels can now be strings and do not have to be sequential integers (#14)

SIBER 2.0

  • Major overhaul of all code and underlying fitting algorithms
  • Fitting is now via JAGS
  • Data are z-score transformed prior to fitting to improve convergence
  • Data structures have now changed from previous versions embedded within SIAR so you will have to reformat your data and write new scripts to interface with the new code

Reference manual

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install.packages("SIBER")

2.1.4 by Andrew Jackson, 7 months ago


Browse source code at https://github.com/cran/SIBER


Authors: Andrew Jackson and Andrew Parnell


Documentation:   PDF Manual  


GPL (>= 2) license


Imports coda, ellipse, hdrcde, graphics, grDevices, mnormt, rjags, spatstat, spatstat.utils, stats, viridis, tidyr, dplyr, ggplot2, magrittr, purrr

Suggests knitr, rmarkdown

System requirements: JAGS (>= 4.1)


See at CRAN