Package: biclustermd 0.2.3

biclustermd: Biclustering with Missing Data

Biclustering is a statistical learning technique that simultaneously partitions and clusters rows and columns of a data matrix. Since the solution space of biclustering is in infeasible to completely search with current computational mechanisms, this package uses a greedy heuristic. The algorithm featured in this package is, to the best our knowledge, the first biclustering algorithm to work on data with missing values. Li, J., Reisner, J., Pham, H., Olafsson, S., and Vardeman, S. (2020) Biclustering with Missing Data. Information Sciences, 510, 304–316.

Authors:John Reisner [cre, aut, cph], Hieu Pham [ctb, cph], Jing Li [ctb, cph]

biclustermd_0.2.3.tar.gz
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biclustermd_0.2.3.tgz(r-4.4-any)biclustermd_0.2.3.tgz(r-4.3-any)
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biclustermd.pdf |biclustermd.html✨
biclustermd/json (API)

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

Bug tracker:https://github.com/jreisner/biclustermd/issues

Datasets:

On CRAN:

4.18 score 3 stars 9 scripts 313 downloads 9 exports 50 dependencies

Last updated 4 years agofrom:975af747fc. Checks:1 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 25 2025
R-4.5-winNOTEJan 25 2025
R-4.5-linuxNOTEJan 25 2025
R-4.4-winNOTEJan 25 2025
R-4.4-macNOTEJan 25 2025
R-4.3-winNOTEJan 25 2025
R-4.3-macNOTEJan 25 2025

Exports:as.Biclustbiclustermdcell_heatmapcell_msecol.namescompare_biclustersmse_heatmaprep_biclustermdtune_biclustermd

Dependencies:additivityTestsapebiclustclassclicodetoolscolorspacecpp11digestdoParalleldplyrfansifarverflexclustforeachgenericsggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmodeltoolsmunsellnlmenycflights13phyclustpillarpkgconfigpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

Biclustering Airport Delay Data

Rendered fromAirports.Rmdusingknitr::rmarkdownon Jan 25 2025.

Last update: 2019-08-13
Started: 2019-07-18

Readme and manuals

Help Manual

Help pageTopics
biclustermd: A package to bicluster data with missing valuesbiclustermd-package
Convert a 'biclustermd' object to a 'Biclust' objectas.Biclust
Make a heatmap of sparse biclustering resultsautoplot.biclustermd
Plot similarity measures between two consecutive biclusterings.autoplot.biclustermd_sim
Plot sums of squared errors (SSEs) consecutive biclustering iterations.autoplot.biclustermd_sse
Bicluster data with non-random missing valuesbiclustermd
Make a binary vector with all values equal to zero except for onebinary_vector_gen
Make a heat map of bicluster cell sizes.cell_heatmap
Make a data frame containing the MSE for each bicluster cellcell_mse
Calculate the sum cluster SSE in each iterationcluster_iteration_sum_sse
Get column names in each column clustercol_cluster_names
A generic to gather column namescol.names
Get data matrix column names and their corresponding column cluster membershipcol.names.biclustermd
Compare two biclusterings or a pair of partition matricescompare_biclusters
Randomly select a column prototype to fill an empty column prototype withfill_empties_P
Randomly select a row prototype to fill an empty row prototype withfill_empties_Q
Format a partition matrixformat_partition
Gather a biclustermd objectgather.biclustermd
Compute the Jaccard similarity coefficient for two clusteringsjaccard_similarity
Make a heatmap of cell MSEsmse_heatmap
Convert a partition matrix to a vectorpart_matrix_to_vector
Generate an intial, random partition matrix with N objects into K subsets/groups.partition_gen
Create a partition matrix with a partition vector ppartition_gen_by_p
Find the index of the first nonzero value in a vectorposition_finder
Print an object of class biclustermdprint.biclustermd
Reorder a bicluster object for making a heat mapreorder_biclust
Repeat a biclustering to achieve a minimum SSE solutionrep_biclustermd
Make a heatmap of sparse biclustering resultsresults_heatmap
Get row names in each row clusterrow_cluster_names
Get data matrix row names and their corresponding row cluster membershiprow.names.biclustermd
Algorithm run time dataruntimes
Synthetic data for examples.synthetic
Bicluster data over a grid of tuning parameterstune_biclustermd