Package: CommKern 1.0.1

CommKern: Network-Based Communities and Kernel Machine Methods

Analysis of network community objects with applications to neuroimaging data. There are two main components to this package. The first is the hierarchical multimodal spinglass (HMS) algorithm, which is a novel community detection algorithm specifically tailored to the unique issues within brain connectivity. The other is a suite of semiparametric kernel machine methods that allow for statistical inference to be performed to test for potential associations between these community structures and an outcome of interest (binary or continuous).

Authors:Alexandria Jensen [aut, cre], Peter DeWitt [ctb], Debashis Ghosh [ths]

CommKern_1.0.1.tar.gz
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CommKern.pdf |CommKern.html✨
CommKern/json (API)
NEWS

# Install 'CommKern' in R:
install.packages('CommKern', repos = c('https://aljensen89.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/aljensen89/commkern/issues

Datasets:
  • SBM_net - Simulated functional and structural connectivity with nested hierarchical community structure
  • simasd_array - Simulated Array
  • simasd_comm_df - Simulated partitions of nodes to communities from HMS algorithm
  • simasd_covars - Simulated demographics dataset modeled of a subset of the preprocessed ABIDE database
  • simasd_hamil_df - Simulated Hamiltonian values from HMS algorithm

On CRAN:

4.11 score 26 scripts 224 downloads 20 exports 35 dependencies

Last updated 2 years agofrom:82f9840ba6. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 10 2024
R-4.5-winNOTENov 10 2024
R-4.5-linuxNOTENov 10 2024
R-4.4-winNOTENov 10 2024
R-4.4-macNOTENov 10 2024
R-4.3-winOKNov 10 2024
R-4.3-macOKNov 10 2024

Exports:adj_RIcommunity_allegiancecommunity_plotconsensus_similarityext_distancegroup_adj_perturbgroup_network_perturbham_distanceheatbath_multimodalhmskernelmatrix_plotmatrix_to_dfNMIpurityscore_cont_nonparamscore_cont_semiparamscore_log_nonparamscore_log_semiparamsubset_matrix_to_df

Dependencies:clicolorspacefansifarverggnewscaleggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr

Analysis of Network Community Structures Using the CommKern Package

Rendered fromCommKern.Rmdusingknitr::rmarkdownon Nov 10 2024.

Last update: 2022-09-21
Started: 2022-08-05

Readme and manuals

Help Manual

Help pageTopics
Adjusted Rand Index (ARI)adj_RI
CommKernCommKern
Community Allegiancecommunity_allegiance
Communities by layer plotcommunity_plot
Compute modularity matrixcompute_modularity_matrix
Compute multimodal modularity matrixcompute_multimodal_mod
Consensus Similarityconsensus_similarity
Count pairscount_pairs
Node degree calculationdegree
Entropyentropy
Extrinsic evaluation distance matrix creationext_distance
Starting temperaturefind_start_temp
Simulated network edge weightsget_weights
Group adjacency matricesgroup_adj_perturb
Simulated group networksgroup_network_perturb
Hamiltonian distance matrix creationham_distance
Multimodal heatbath algorithmheatbath_multimodal
Hierarchical multimodal spinglass algorithmhms
Distance-based kernelkernel
Functional and Structural Matrix Plotmatrix_plot
Convert matrices to dataframe list for networkmatrix_to_df
Normalized mutual information (NMI)NMI
Puritypurity
Simulated functional and structural connectivity with nested hierarchical community structureSBM_net
Nonparametric score function for distance-based kernel and continuous outcome.score_cont_nonparam
Semiparametric score function for distance-based kernel and continuous outcome.score_cont_semiparam
Nonparametric score function for distance-based kernel and binary outcomescore_log_nonparam
Semiparametric score function for distance-based kernelscore_log_semiparam
Simulated Arraysimasd_array
Simulated partitions of nodes to communities from HMS algorithmsimasd_comm_df
Simulated demographics dataset modeled of a subset of the preprocessed ABIDE databasesimasd_covars
Simulated Hamiltonian values from HMS algorithmsimasd_hamil_df
Simulated network data framesimnet_df_perturb
Sort pairssort_pairs
Convert matrices to list of data frames for subnetworkssubset_matrix_to_df
Tracetr
Bounds of grid search functionup_low
Rand z-scorezrand