Package: shipunov 1.17.1

shipunov: Miscellaneous Functions from Alexey Shipunov

A collection of functions for data manipulation, plotting and statistical computing, to use separately or with the book "Visual Statistics. Use R!": Shipunov (2020) <http://ashipunov.info/shipunov/software/r/r-en.htm>. Dr Alexey Shipunov died in December 2022. Most useful functions: Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering; Recode() which does multiple recoding in a fast, simple and flexible way; Misclass() which outputs confusion matrix even if classes are not concerted; Overlap() which measures group separation on any projection; Biarrows() which converts any scatterplot into biplot; and Pleiad() which is fast and flexible correlogram.

Authors:Alexey Shipunov [aut, cre], Paul Murrell [ctb], Marcello D'Orazio [ctb], Stephen Turner [ctb], Eugeny Altshuler [ctb], Roland Rau [ctb], Marcus W Beck [ctb], Sebastian Gibb [ctb], Weiliang Qiu [ctb], Emmanuel Paradis [ctb], Roger Koenker [ctb], R Core Team [ctb]

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shipunov.pdf |shipunov.html✨
shipunov/json (API)
NEWS

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

Peer review:

Datasets:

On CRAN:

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

132 exports 0.36 score 1 dependencies 1 mentions 8 scripts 445 downloads

Last updated 2 years agofrom:8cd6acac88. Checks:ERROR: 1 NOTE: 4 OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesFAILAug 25 2024
R-4.5-winNOTEAug 25 2024
R-4.5-linuxNOTEAug 25 2024
R-4.4-winNOTEAug 25 2024
R-4.4-macNOTEAug 25 2024
R-4.3-winOKAug 25 2024
R-4.3-macOKAug 25 2024

Exports:%-%Adj.RandAggregate1AlldupsBclabelsBclustBestOverlapBiarrowsBiokeyBootABootKNNBootRFBoxplotsCdateCladdClass.sampleClassprojClustergramCoeff.detComlCorCor.vecCor2CtimeCVsDittoDnnDNNDotchartDotchart1Dotchart3EllEllipsesEx.boxplotEx.colEx.colsEx.fontEx.fontsEx.linesEx.ltyEx.marginsEx.pchEx.plotsEx.pointsEx.typesFenceFibonacciFilesFillGap.codeGen.cl.dataGiniGower.distGraddGridmoonHcl2matHclust.matchHcoordsHistrHullsInfillJclustKLifeLinechartLsMagMDSvMineyMisclassMissing.mapMrBayesMRHNC.distNormalityNumranksOverlappairwise.Effpairwise.Rro.testpairwise.Table2.testPhyllotaxisPinhullPleiadplot.Bclustplot.Infillplot.JclustPlot.phyloclPlotBest.distPlotBest.hclustPlotBest.mdistPlothPointsPolyareaPolycenterPPointsprint.Jclustprint.KPullR.logoRead.fastaRead.tri.ntsRecodeRecode4Recode4RRecodeRRoot1Rostova.tblRpart2newickRresultsRro.testS.valueSave.historySaynodynamiteSM.distSquaresStrsummary.Comlsummary.Infillsummary.Ksummary.OverlapTable2dfTcoordsTctextTobinToclipTopmTtcolsUpdistVicinitiesVTcoeffsWrite.fastaXpager

Dependencies:PBSmapping

Readme and manuals

Help Manual

Help pageTopics
Minus names%-%
Adjusted Rand indexAdj.Rand
Aggregates by one vector and uses it for row namesAggregate1
Finds all duplicatesAlldups
atmospheresatmospheres
Plot bootstrap valuesBclabels
Bootstrapped hclustBclust plot.Bclust
Calculates the best overlapBestOverlap
Adds correlation arrows to the scatterplotBiarrows
Convert diagnostic keys and classification listsBiokey Numranks
Bootstrap clusteringBootA
Bootstrap with kNNBootKNN
Bootstrap with 'randomForest()'BootRF
Grouped boxplotsBoxplots
System date, time plus easy save historyCdate Ctime Save.history
Chaetocnema flea beetleschaetocnema
Adds confidence bands to the simple linear model plotsCladd
Samples along the class labelsClass.sample
Classification listsclassifs
Class projectionClassproj
Clustergram: visualize the cluster structureClustergram
Average coefficients of determination for each variableCoeff.det
Compare checklistsComl summary.Coml
Correlation matrix with p-valuesCor Cor2
Calculates correlation and converts results into the named long vectorCor.vec
Coefficients of variationCVs
Removes duplicated data values downstreamDitto
Distance matrix based kNN classificationDNN Dnn
dolblidolbli
Improved dotchartsDotchart Dotchart1 Dotchart3
droseradrosera
Plot ellipseEll
Confidence ellipsesEllipses
eqeq eq_l eq_s
Boxplot explanationEx.boxplot
Examples of colorsEx.col Ex.cols
Examples of fontsEx.font Ex.fonts
Examples of line typesEx.lines Ex.lty
Example of plot marginsEx.margins
Point examplesEx.pch Ex.points
Examples of plot typesEx.plots Ex.types
Colorize tips of 'hclust' plotFence
Textual file system browserFiles
Fill data values downstream, like in spreadsheetsFill
Gap codingGap.code
Generates datasets for clusteringGen.cl.data
Compute the simple Gini coefficientGini
Gower distanceGower.dist
Classification grid and decision boundariesGradd
Draw with 'R'Gridmoon
Haltica flea beetleshaltica
Clustering to matrixHcl2mat
Counts matches between two hierarchical clusteringsHclust.match
Calculates coordinates of nodes from 'hclust' plotHcoords
Histogram with overlaid curveHistr
Angiosperm families: morphological charactershrahn
Convex hulls for multiple groupsHulls
hwchwc hwc2 hwc3
Rarefaction curvesInfill plot.Infill summary.Infill
Simple bootstrap and jackknife clusteringJclust plot.Jclust print.Jclust
Coefficient of divergenceK print.K summary.K
Diagnostic keyskeys
Game of LifeLife
Dotchart-like plot sfor every scaled variable grouped by factorLinechart
LsLs
Interpreter for effect sizesMag
MDS: dimension importance ("explained variance" surrogate)MDSv
Miney gameMiney
Misclassification (confusion) tableMisclass
Textual plot of missing dataMissing.map
moldinomoldino moldino_l
Calls MrBayesMrBayes
Matrix Representation of Hierarchical ClusteringMRH
Normalized Compression DistanceNC.dist
Check normalityNormality
Calculates overlap between polygonsOverlap summary.Overlap
Pairwise table of effects with magnitudespairwise.Eff
Robust rank order test post hoc derivativepairwise.Rro.test
Pairwise Chi-squared or Fisher test for 2-dimensional tablespairwise.Table2.test
Plant phyllotaxisFibonacci Phyllotaxis
Point in hullPinhull
plantagoplantago
Correlation circles (correlation pleiads)Pleiad
Plot phylogenetic tree with clades collapsedPlot.phylocl
Dotchart which reflects the "best" base distance methodPlotBest.dist
Plots dotchart with best clustering methodPlotBest.hclust
Dotchart which reflects the "best" of non-base distancesPlotBest.mdist
Changes the appearance of cluster dendrogramPloth
Number of cases in each location reflected in the point sizePoints PPoints
Area of the polygonPolyarea
Center of the polygonPolycenter
Select rows from data framePull
Imitation (!) of the modern 'R' logoR.logo
Read 'FASTA' filesRead.fasta
Read 'NTSYSpc' filesRead.tri.nts
Basic multiple recodingRecode Recode4 Recode4R RecodeR
Roots phylogenetic trees even if outgroup is not monophyleticRoot1
Calculates multiple correlation matrices (via 'factor1') and stacks them togetherRostova.tbl
Converts 'rpart' object into Newick treeRpart2newick
Rresults shell scriptRresults
Robust rank order testRro.test
S-valueS.value
salix_leavessalix_leaves salix_plants salix_pop
Say ``no'' to dynamite plots!Saynodynamite
Simple Match distanceSM.dist
Areas of polygonsSquares
'str()' enchanced for data framesStr
Convert table to data frame saving structureTable2df
Calculates coordinates of tips from 'hclust' plotTcoords
Easy way to add text labels to 'hclust' plotTctext
Binarize (make dummy variables)Tobin
Insert content to Linux X11 clipboardToclip
Stacks correlation matrixTopm
Text-to-columnsTtcols
Educated distances for semi-supervised clusteringUpdist
Arrange observations by the distance from centerVicinities
Effect sizes of association between categorical variablesVTcoeffs
Write 'FASTA' filesWrite.fasta
Separate terminal pager for LinuxXpager