- Added a check that the data object passed to
`createSiberObject`

is of class`data.frame`

only. If this is the case, it will coerce via`as.data.frame(data.in)`

and issue a warning to this effect, recommending the coercion is done before passing to this function. - Updated PACKAGE help file construction per instructions from CRAN.

- removed suggests, depends or imports “tidyverse” and instead import specific packages as advised is best practice
- added doi to DESCRIPTION per CRAN suggestion
- added new vignette illustrating the kapow method and associated new
dataset
`data/mongooseData.rda`

- fixed a bug in
`siberKapow`

which will hopefully pass CRAN checks re undeclared global variables. Will pick this up on next submission.

- added two vignettes illustrating how to compare populations and communities with calculation of probabilities for differences.
- replaced package
`spatstat`

with direct importing from new sub-packages`spatstat.utils`

and`spatstat.geom`

- Fixed bug in
`createSiberObject`

that meant z-scores could end up out of sync with their respective grouping variable. Thanks to Edward Doherty for pointing out this odd behaviour leading to bug discovery 2020/11/5. Ultimately the entire package needs to be recoded fully in`tidyverse`

. - Fixed bug in
`plotSiberObject`

that meant both x.limits and y.limits had to be specified to invoke manual axis setting. Either or can now be specified on their own with the other reverting to the default which is the max and min values of the corresponding data axis +/- the specified`ax.pad`

value which defaults to 1. - Allow users to specify a matrix of colours to define each group and
each confidence boxplot uniquely using
`siberDensityPlot(Y, clr = ...)`

- 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.

- 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.

- added ability to specify custom pch point orders in
`plotSiberObject()`

- added
`...`

to plotGroupHulls

- 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()`

.

- 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.

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

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

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

- 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