Swiftpack.co - Package - jjlynch2/OsteoSort

Changes for OsteoSort version : 1.2.5

Minor changes:

Added ByteCompile: yes on install

Adjusted articulation t-test default options

Moderage:

Removed plyr as a dependency

Adjusted population specific Trotter corrections for antemortem stature strength association

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Releases

v1.2.4 - Dec 17, 2017

Changes for OsteoSort version : 1.2.4

Minor:

Added example datasets antemortem_data and postmortem_data

Adjusted plots and removed labels

Moderate changes:

Probability values calculated for PCACCA-Regression with options to use alpha level as cut-off

v1.2.3 - Dec 15, 2017

OsteoSort:

A statistical osteological sorting R package for commingled human remains using metric, 2D, and 3D data.

Changes for OsteoSort version : 1.2.3

Minor changes:

Adjusted print messages for start/finish of functions

Moderate changes:

parLapply implemented on Windows to replace Lapply

Bug fixes:

Fixed directory creation if not present for sessiontempdir

Fixed testagainstzero argument mislabeled as testagainst

Fixed measurement argument being NULL

Fixed typo with Fem_17 mislabeled as Fem_18

Fixed typo with Tib_11 mislabeled as Tib_10

Fixed Factors being introduced by forcing stringsAsFactors = FALSE within each function excplicity. Value returns to TRUE when complete This solves the memory issue assocaited with articulation and association.

v1.2.2 - Dec 10, 2017

OsteoSort:

A statistical osteological sorting R package for commingled human remains using metric, 2D, and 3D data.

Changes for OsteoSort version 1.2.2:

Modules:

Updated 2D to include fragmentary shape registration and pair-matching.

Added match.3d() function (currently broken) for 3D pair-matching.

Minor changes:

Momocs dependency removed: replaced EFA from Momocs with modified version for 2D and 3D EFA.

Pracma dependency removed: replaced distmat from pracma with modified version.

Shapes dependency removed: removed Procrustes distance function call as an option from 2D settings.

Moved code for matching matrices names and alpha color for plots into two internal functions.

Moderate changes:

Renamed segmented_hausdorff_dist() function to hausdorff_dist().

Renamed match.2d.invariant() function to match.2d().

Re-wrote the base code for match.2d() to be more efficient with looping for distance calculations.

Re-wrote the base code for write.TPS to use lists with unequal landmarks and 3D matrices with equal landmarks.

Re-wrote all file output into output_options() including TPS, excel, and plots.

Added pca_align() function to return rotated PCA scores for alignment prior to 3D analysis

Re-wrote the backend for Hausdorff with RcppParallel to use parallel processing for large point clouds. max_directional_hausdorff_rcpp(), mean_directional_hausdorff_rcpp(), dilated_directional_hausdorff_rcpp()

Added new functions, fragment_margins(), remove_fragment_margins(), and minimum_euclidean_deistances_ind() , which are ussed to identifyssss the indices of fragment margins along a orderly 2D outline and remove any non-overlapping landmark from the calculation of Hausdorff distances.

The regression model used for antemortem stature association has been switched to calculate the point estimate of the measurement rather than vice versa.

Added statistical option to change from 1 to 2 tail t-tests.

Switched terminology from cores to threads for functions.

Bug fixes:

v1.2.1 - Oct 28, 2017

OsteoSort:

A statistical osteological sorting R package for commingled human remains using metric, 2D, and 3D data.

Changes for OsteoSort version 1.2.1:

Modules:

Added a new module to test the strength of evidence for an antemortem stature to postmortem measurement

Minor changes:

Added ability to switch output metric between inches, millimeters, and centimeters for the statsort function.

Adjusted resolution of graphs to 400x400.

Re-ran roxygenize for man pages.

Adjusted reference to previous code by Julien Claude (Morphometrics with R 2008).

Bug fixes:

Fixed Trotter data in outlier analysis for the over correction by 10 mm

Standard error was estimated slightly wrong for the t-statistic in regression association. This has been fixed.

v1.1.1 - Aug 8, 2017

Minor update for bug fix with measurement names.