v2.1.9

Full Changelog: v2.1.8...v2.1.9

v2.1.8

• 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.

v2.1.7

A Minor update.

• 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.

v.2.1.6

SIBER 2.1.6

• 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

v2.1.5

SIBER 2.1.5

• 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 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 = ...)

v2.1.4

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.

v2.1.3

• 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.

v2.1.2

Adds new functions to make it easier to calculate overlap of ellipses fitted by either maximum likelihood or Bayesian methods. A new vignette illustrates this.

v2.1.0

NB this release has a bug in bayesianOverlap which has been fixed and will be pushed in a new release in the coming days.

SIBER v2.0.3

New vignette added detailing how to add custom ellipses manually.