Package: lakhesis 0.0.2

lakhesis: Consensus Seriation for Binary Data

Determining consensus seriations for binary incidence matrices, using a two-step process of Procrustes-fit correspondence analysis for heuristic selection of partial seriations and iterative regression to establish a single consensus. Contains the Lakhesis Calculator, a graphical platform for identifying seriated sequences. Collins-Elliott (2024) <https://volweb.utk.edu/~scolli46/sceLakhesis.pdf>.

Authors:Stephen A. Collins-Elliott [aut, cre]

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lakhesis.pdf |lakhesis.html✨
lakhesis/json (API)

# Install 'lakhesis' in R:

install.packages('lakhesis', repos = c('https://scollinselliott.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/scollinselliott/lakhesis/issues

Datasets:

qfStrands - Quattro Fontanili - Strands
quattrofontanili - Quattro Fontanili

On CRAN:

archaeology binary-data correspondence-analysis ecology seriation

5.18 score 5 stars 2 scripts 476 downloads 15 exports 66 dependencies

Last updated 4 months agofrom:11ff093ae8. Checks:1 OK, 8 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 19 2025
R-4.5-win	WARNING	Mar 19 2025
R-4.5-mac	WARNING	Mar 19 2025
R-4.5-linux	WARNING	Mar 19 2025
R-4.4-win	WARNING	Mar 19 2025
R-4.4-mac	WARNING	Mar 19 2025
R-4.4-linux	WARNING	Mar 19 2025
R-4.3-win	WARNING	Mar 19 2025
R-4.3-mac	WARNING	Mar 19 2025

Exports:ca_procrustes ca_procrustes_ser conc_col conc_kappa element_eval im_long im_merge im_read_csv im_ref lakhesize LC spearman_sq strand_add strand_extract strand_suppress

Dependencies:base64enc bit bit64 bslib ca cachem cli clipr colorspace commonmark cpp11 crayon digest fansi farver fastmap fontawesome fs ggplot2 glue gtable hms htmltools httpuv isoband jquerylib jsonlite labeling later lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme pillar pkgconfig prettyunits progress promises R6 rappdirs rbibutils RColorBrewer Rcpp Rdpack readr rlang sass scales shiny shinydashboard sourcetools tibble tidyselect tzdb utf8 vctrs viridisLite vroom withr xtable

A Guide to Lakhesis

Rendered fromguide-to-lakhesis.Rmdusingknitr::rmarkdownon Mar 19 2025.

Last update: 2024-06-25
Started: 2024-06-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Kendall-Doran Concentration	conc_col
Kappa Concentration	conc_kappa
Evaluating Element Fit	element_eval element_eval.incidence_matrix element_eval.matrix
Convert Incidence Matrix to Pairs (Long Format)	im_long im_long.incidence_matrix im_long.matrix
Merge Two Incidence Matrices	im_merge im_merge.incidence_matrix im_merge.matrix
Read csv File to Incidence Matrix	im_read_csv plot.incidence_matrix
Create Reference Matrix	im_ref im_ref.matrix
Lakhesize	lakhesize lakhesize.default lakhesize.strands plot.lakhesis
Lakhesis Calculator	LC
Correspondence Analysis with Procrustes Fitting	ca_procrustes ca_procrustes.incidence_matrix ca_procrustes.matrix plot.procrustean
Seriate Using Reference Curve for Procrustes-Fit CA Scores	ca_procrustes_ser ca_procrustes_ser.incidence_matrix ca_procrustes_ser.matrix plot.strand
Quattro Fontanili - Strands	qfStrands
Quattro Fontanili	quattrofontanili
Spearman Correlation Squared	spearman_sq
Add Strand to List of Strands	strand_add strand_add.strand
Strand Extract	strand_extract strand_extract.strands
Suppress Element from Strands	strand_suppress strand_suppress.default strand_suppress.strands