LC {lakhesis}

Lakhesis Calculator

Description

Launch Lakhesis Calculator, a graphical interface to explore binary matrices via correspondence analysis, select potentially well-seriated sequences, and perform consensus seriation. Interface is made with ggplot2, shiny, shinydashboard, and bslib (Wickham 2016; Chang et al. 2024; Chang and Borges Ribeiro 2021; Sievert et al. 2024).

Usage

LC()

Details

Input is done in the calculator, via a "long" format a two-column .csv file giving pairs of row and column incidences. See im.csv.read for details. Conversion of a pre-existing incidence matrix to long format can be performed with im.long.

Results can be downloaded from the calculator as an .rds file containing a list of the following:

• results The consensus seriation, PCA, and coefficients of agreement and concentration (lakhesize).

• strands The strands selected by the investigator.

• im.seriated The incidence matrix of the consensus seriation.

Value

Opens the Lakhesis Calculator.

References

Chang W, Borges Ribeiro B (2021). shinydashboard: Create Dashboards with 'Shiny'. https://CRAN.R-project.org/package=shinydashboard.

Chang W, Cheng J, Allaire JJ, Sievert C, Schloerke B, Xie Y, Allen J, McPherson J, Dipert A, Borges B (2024). shiny: Web Application Framework for R. R package version 1.8.1.9001; https://github.com/rstudio/shiny, https://shiny.posit.co.

Sievert C, Cheng J, Aden-Buie G (2024). bslib: Custom ‘Bootstrap’ ‘Sass’ Themes for ‘shiny’ and ‘rmarkdown’. R package version 0.7.0, https://github.com/rstudio/bslib, https://rstudio.github.io/bslib/.

Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer, New York.