sarp.snowprofile.alignment 2.0.0

Improved computation speeds of profile alignments by
- making bottlenecks more efficient
- adding functionality for parallel computations in distanceSP, averageSP and clusterSP
Added extended functionality to cluster snow profiles, see clusterSP, plot.clusterSP
Added the vignette Clustering snow profiles
Consolidated existing distance functions
- distMatSP is now distanceSPlayers
- distanceSP now works on both profile pairs and entire snowprofileSets to compute pairwise distance matrices

sarp.snowprofile.alignment 1.2.2

Fixed a seldom bug in the averageSPalongSeason rescaling routine that would cause the function to fail without recovery
Make averageSPalongSeason more user-friendly wrt providing precomputed averages as initial condition
Add concat_avgSP_timeseries to combine two return objects from averageSPalongSeason where one holds the season history and the other holds the recent average. This is useful if the routine is applied in an operational setting where the average timeseries is update day-by-day.

Added the vignette Averaging of profiles and retrieval of distributions –> browseVignettes(package = "sarp.snowprofile.alignment")

Added density and optical grain size (ogs) as warping variables for alignment
Averaging of profiles:
- include slab_rhogs, p_unstable, bdate, scalingFactor, ppu_all in warpSP and all dba routines
- fix minor bugs for averaging shallow profiles and backtracking layers
- add more detailed documentation (also for future developers)
Robustify medoidSP

Implemented functionality to align profiles without the requirement to re-scale them first! see examples in ?dtwSP
simSP
- includes several different approaches of computing snow profile similarities
- can handle variable similarity values for non-matched layers
- can apply penalty based on thickness of non-matched layers
Implementation of Dynamic Time Warping Barycenter Averaging (dbaSP) enables to
- average snow profiles. see also averageSP and averageSPalongSeason
- connect layers within a profile set (backtrackLayers) to conveniently compute summary statistics and distributions of layers
Minor scale changes:
- Implemented ability to configure the absolute warping window (instead of relative one only)
- Included first systematic tests (of various different alignment scenarios)
- Fix bug in warpSP, which was introduced due to changes in the sarp.snowprofile::snowprofile data class (i.e., introduction of unobservedBasalLayers)
- package shiny is not imported anymore, but only suggested –> enhances usability on clusters

Updated license (GPL >= 3)
Two new vignettes
Adjust to upstream changes in sarp.snowprofile: new class (incl. methods) snowprofileSet
(i.e., not backwards-compatible)
Bug fixes:
- rename remaining deprecated field names (e.g., grain_type to gtype, deposition_date to ddate, etc.)
- make documentation available
- interactive alignment shiny app is fixed
- ‘globalAlignment’ has been made directional (i.e., bottom-up, top-down)