Package: DiscreteGapStatistic 0.1.0

DiscreteGapStatistic: An Extension of the Gap Statistic for Ordinal/Categorical Data

The gap statistic approach is extended to estimate the number of clusters for categorical response format data. This approach and accompanying software is designed to be used with the output of any clustering algorithm and with distances specifically designed for categorical (i.e. multiple choice) or ordinal survey response data.

Authors:Jeffrey Miecznikowski [aut], Eduardo Cortes [aut, cre]

# Install 'DiscreteGapStatistic' in R:

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

Bug tracker:https://github.com/ecortesgomez/discretegapstatistic/issues

Datasets:

concussion - Concussion Data
mass - Mass data

On CRAN:

3.93 score 3 scripts 17 exports 97 dependencies

Last updated 7 days agofrom:d69841d533. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 26 2024
R-4.5-win	OK	Oct 26 2024
R-4.5-linux	OK	Oct 26 2024
R-4.4-win	OK	Oct 26 2024
R-4.4-mac	OK	Oct 26 2024
R-4.3-win	OK	Oct 26 2024
R-4.3-mac	OK	Oct 26 2024

Exports:BhattacharyyaDist ChisqDist clusGapDiscr cramersVmod CramerV dissbhattacharyya disschisquare disscramerv disshamming disshellinger distanceHeat distancematrix findK HellingerDist likert.heat.plot2 ResHeatmap SimData

Dependencies:backports base64enc BiocGenerics bslib cachem checkmate circlize cli clue cluster codetools colorspace combinat ComplexHeatmap cpp11 crayon cultevo data.table digest doParallel dplyr evaluate fansi farver fastmap fontawesome foreach foreign Formula fs generics GetoptLong ggplot2 GlobalOptions glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets IRanges isoband iterators jquerylib jsonlite knitr labeling lattice lifecycle magrittr MASS Matrix matrixStats memoise mgcv mime munsell nlme nnet pheatmap pillar pkgconfig plyr png Polychrome pspearman purrr R6 rappdirs RColorBrewer Rcpp reshape2 rjson rlang rmarkdown rpart rstudioapi S4Vectors sass scales scatterplot3d shape stringi stringr tibble tidyr tidyselect tinytex utf8 vctrs viridis viridisLite withr xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Bhattacharyya distance core function	BhattacharyyaDist
Chi-square distance core function	ChisqDist
Discrete application of clusGap Based on the implementation of the function found in the `cluster` R package	clusGapDiscr
Concussion Data	concussion
Cramer's V modified pairwise vector function based on the function found in lsr package This is simple wrapper of the usual chisq.test fun This is actually an adjusted version of the pi = sqrt(Chisq2/N) guaranteeing that values are within 0 (no association) and 1 (association)	cramersVmod
Cramer's V core function	CramerV
Bhattacharyya's wrapper Function	dissbhattacharyya
Chi-square distance wrapper function	disschisquare
Cramer's V distance wrapper function	disscramerv
Hamming distance wrapper function Function based on cultevo's package implementation	disshamming
Hellinger's distance wrapper Function	disshellinger
sample-to-sample heatmap clustering samples according to a given categorical distance Exploratory tool that helps to visualize/cluster blocks of observations across columns ordered according to given categorical distance. The final output is a clustered distance matrix. This plot is aimed to guide the `DiscreteClusGap` user to give an idea which type of categorical distance would accommodate better to the inputted data. `sample2sampleHeat` is based on the `pheatmap` function from the `pheatmap` R package. Thus, any parameter found in pheatmap can be specified to `sample2sampleHeat`.	distanceHeat
Function invoking discrete distance functions	distancematrix
Criteria to determine number of clusters k	findK
Hellinger distance core function	HellingerDist
Summary Heatmap for categorical/Likert data Heatmap representation summarizing categorical/likert data. Modified version of `likert.heat.plot` from `likert` package. Does not allow different categorical ranges across questions. The function outputs a ggplot object where additional layers can be added for customization purposes. The output plot preserves the question order given by columns of `x`.	likert.heat.plot2
mass data	mass
Heatmap assuming a given a distance function and a known number of clusters. Function to display a categorical data matrix given a user defined number of clusters `nCl`, a categorical distance `distName` and a predefined clustering method `FUNcluster`. The output displays a heatmap separating and color-labelling resulting clusters vertically in the rows and allowing unsupervised clustering on questions in the columns. Each cell is colored according to the categorical values provided or found in the data. The clustergram is based on the `pheatmap` function from the pheatmap R package. Thus, any parameter found in pheatmap can be specified to `clusGapDiscrHeat`. This function can be used to examine number of clusters before running `clusGapDiscrHeat` but also after number of clusters is determined.	ResHeatmap
Simulate Data	SimData