Improved functions, vignettes, and more

With this release we are:

• Expanding the vignettes initially available.
• The crossplot function is more flexible and now accepts as input both trace files on disk as well as data frames. As a consequence, the arguments logPath1 and logPath2 are renamed log1 and log2, which is a breaking change with respect to v1.6.1.
• Also, crossplot accepts statistics other than mean for summarising traces. Possible values are mean or median.
• pkgdown is now being used for generating the static website for the documentation of the package, available at https://gaballench.github.io/tbea/

What's Changed

• Several changes for target v1.7.0 by @gaballench in #22
• Extends crossplot by @spreinalesl in #23
• Includes vignettes by @spreinalesl in #24
• Update readme by @spreinalesl in #25

New Contributors

• @spreinalesl made their first contribution in #23

Full Changelog: v1.6.1...v1.7.0

New functionality for conflated distributions.

Added code for calculating quantiles on conflated distributions.

Corrected a couple bugs in documentation and non-standard assignment operators.

Added code for the truncated Cauchy

the function c_truncauchy allows to estimate this value for a fixed p in the truncated Cauchy distribution which is used by MCMCTree's L calibration density.

Version 1.4.2 accepted on CRAN

From now on, the package can be installed using install.packages("tbea") for the stable version on CRAN, or using remotes::install_github("gaballench/tbea") for the development version.

Patch for `xintercept`

This minor release includes a patch for xintercept which needs to be applied. It also removes a dependency of this package which was making the installation process further install other (unnecessary) dependencies.

Methods for stratigraphic intervals now avaliable.

The function stratCI calculates confidence intervals (or brackets on the CI) using the methods by Strauss and Sadler (89) and Marshall (94). A number of bug fixes are also included. The function table2nexus helps to convert a delimited file to nexus format, which is especially useful for morphological matrices. Several improvements in documentation are also included.

New features for matrices and plotting

This release includes fixes to concatNext and the new table2nexus which reads data in plain-text value-delimited format (e.g., tsv, csv, tab) and returns the data in nexus format. It also includes the function crossplot which allows to compare pairs of densities (e.g. prior vs. posterior or independent runs of the same analysis) and plot the median and error bars representing the highest density interval, these around the identity line y = x.

Patch for summaryBrlen

A part in summaryBrlen had incorrectly hard-coded a tip which should be retrieved automatically for summarising branch lengths.

Topological summary and density conflation now available

Added code for summarising trees (e.g. from the posterior of trees in a Bayesian analysis) and for calculating the conflation of arbitrary distributions.

New major version of tbea with breaking changes

The function fasta2nexus has been deprecated and its dependency network updated to remove apex. This change breaks code using tbea up to v5.2.0.