v1.1.0: Incorporated CVD risk analysis, Bland-Altman alnalysis, time series u…

…tilities, epoch length extraction, REE calculation enhancements, and residual adjustment. Also fixed an annoying bug with factor/non-atomic input to index_runs.

Skirting Debian unit test issue

Release of v1.0.0 was prevented due to a Debian error traced to the following (from a dependency) inside a unit test:

WARNING: Initial Java 12 release has broken JNI support and does NOT work. Use stable Java 11 (or watch for 12u if avaiable).
ERROR: Java exception occurred during rJava bootstrap - see stderr for Java stack trace. Exception in thread "main"

Rcpp, Dependencies, and More

Here's what's new in PAutilities 1.0.0:

• Added a function (weight_status) to classify body mass index for adults
  using CDC cutoffs. (This can also be used as a wrapper for the existing
  function get_BMI_percentile that classifies youth BMI based on CDC percentiles.)

• Added Rcpp functions related to rolling windows (get_indices to extract
  indices for rolling windows; rolling_groups to extract rolling
  subsequences of raw data).

• Removed dependency on orphaned clues package (resulting in changes to
  unit test cache)

TPM Vignette

In this release, a vignette was introduced for the transition pairing method (TPM).

New and Improved Utilities

Here's what's new in PAutilities 0.3.0:

• Added paired equivalence testing functionality, including plot method
• Added a function to classify activity intensity from metabolic equivalents and
  (if available) posture
• Added a wrapper for base::rle that gives a data frame with original rle
  information, plus start/stop indices for each run
• Added various performance indicators to summary.transition
• Converted summary.transition output to an S4 framework, and added
  addition/subraction methods
• Added spurious curve generation functions
• Adjusted Transition Pairing Method to make it more robust (e.g. to deal with
  missing values)

New and Improved Utilities

Here's what's new in this release:

• Removed unused dependency on package AGread
• Added support for calculation of RMR via sliding window analysis
• Added process management utility for easy messaging and timekeeping
• Added tools to compare objects more specifically than via all.equal
• Added na.rm = TRUE to the mean bias line on Bland-Altman plots
• Added shape control as an option for Bland-Altman plots
• Cleaned up TPM summary method
• Added rejection of non-consecutive pairings to the TPM

Initial release

v0.1.2

Tweak cran-comments