Package: dispersionIndicators 0.1.5

dispersionIndicators: Indicators for the Analysis of Dispersion of Datasets with Batched and Ordered Samples

Provides methods for analyzing the dispersion of tabular datasets with batched and ordered samples. Based on convex hull or integrated covariance Mahalanobis, several indicators are implemented for inter and intra batch dispersion analysis. It is designed to facilitate robust statistical assessment of data variability, supporting applications in exploratory data analysis and quality control, for such datasets as the one found in metabololomics studies. For more details see Salanon (2024) <doi:10.1016/j.chemolab.2024.105148> and Salanon (2025) <doi:10.1101/2025.08.01.668073>.

Authors:Brice Mulot [aut], Elfried Salanon [ctb], Etienne Jules [aut, cre], INRAE [cph]

dispersionIndicators_0.1.5.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
dispersionIndicators/json (API)
NEWS

# Install 'dispersionIndicators' in R:
install.packages('dispersionIndicators', repos = c('https://etiennejls.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.18 score 144 downloads 7 exports 18 dependencies

Last updated from:155777bf14. Checks:8 OK, 1 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK129
source / vignettesOK167
linux-release-x86_64OK127
macos-release-arm64OK120
macos-oldrel-arm64OK134
windows-develOK82
windows-releaseERROR80
windows-oldrelOK88
wasm-releaseOK102

Exports:calculate_convex_hullcalculate_convex_indicatorscompute_icm_distancesconvex_analysis_of_variablesplot_all_convex_hullsplot_convex_hullsave_icm_distances_csv

Dependencies:clicorpcorcpp11farverggplot2gluegtableisobandlabelinglifecycleR6RColorBrewerrlangS7scalesvctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Calculate Convex Hulls for one variablecalculate_convex_hull
Calculate the intra/inter batch dispersion indicators and their ratio on convex hulls of a single variable.calculate_convex_indicators
Compute ICM (Integrated Covariance Mahalanobis) Distancescompute_icm_distances
Computes Integrated Covariance Mahalanobis (ICM) distances for individuals, in PCA-reduced space, against either global or batch-wise references.compute_individual
Computes Integrated Covariance Mahalanobis (ICM) distances of all individuals in PCA-reduced space, against their batch-wise barycenter reference.compute_individual_batch
Computes Integrated Covariance Mahalanobis (ICM) distances of all individuals in PCA-reduced space, against their global barycenter reference.compute_individual_global
Computes Integrated Covariance Mahalanobis (ICM) distances between batches barycenters in PCA-reduced space, using a reference bacth and either mean or median for center references.compute_inter
Calculate the inter batch dispersion indicator on convex hulls of a single variablecompute_inter_batch_dispersion
Computes Integrated Covariance Mahalanobis (ICM) mean distances within each batch in PCA-reduced space, using median and mean for center references.compute_intra
Calculate the intra batch dispersion indicator on convex hulls of a single variablecompute_intra_batch_dispersion
Calculate the intra/inter batch dispersion ratio indicator on convex hulls of a single variable.compute_ratio
Compute the shoelace core for convex hulls of a single variablecompute_shoelace_core
Analyze a set of variables using convex hulls.convex_analysis_of_variables
Function to check if hull_data_list is a valid list of data frameshull_data_list_check
Plot all convex hulls for each variable in a PDF file.plot_all_convex_hulls
Plot the convex hulls of a single variable.plot_convex_hull
Save ICM Distances to CSV Filessave_icm_distances_csv
Function to check if a single variable data frame is validsingle_variable_df_check