shipunov v1.13

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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>. 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.

Functions in shipunov

Name Description
Biarrows Adds correlation arrows to the scatterplot
Alldups Finds all duplicates
BootKNN Bootstrap with kNN
BootA Bootstrap clustering
Bclust Bootstrapped hclust
Adj.Rand Adjusted Rand index
BestOverlap Calculates the best overlap
Biokey Convert diagnostic keys and classification lists
Bclabels Plot bootstrap values
Coml Compare checklists
Aggregate1 Aggregates by one vector and uses it for row names
Cor.vec Calculates correlation and converts results into the named long vector
Dotcharts Improved dotcharts
BootRF Bootstrap with 'randomForest()'
Ditto Removes duplicated data values downstream
Cdate System date, time plus easy save history
CVs Coefficients of variation
DNN Distance matrix based kNN classification
Ell Plot ellipse
Ex.margins Example of plot margins
Boxplots Grouped boxplots
Classproj Class projection
Gen.cl.data Generates datasets for clustering
Gap.code Gap coding
Ellipses Confidence ellipses
Histr Histogram with overlaid curve
Cor Correlation matrix with p-values
Hclust.match Counts matches between two hierarchical clusterings
Cladd Adds confidence bands to the simple linear model plots
Class.sample Samples along the class labels
Ex.pch Point examples
Ex.font Examples of fonts
Fill Fill data values downstream, like in spreadsheets
Files Textual file system browser
Hcl2mat Clustering to matrix
Gridmoon Draw with 'R'
%-% Minus names
Ex.lty Examples of line types
Gower.dist Gower distance
Missing.map Textual plot of missing data
K Coefficient of divergence
Life Game of Life
MrBayes Calls MrBayes
Coeff.det Average coefficients of determination for each variable
Gradd Classification grid and decision boundaries
Misclass Misclassification (confusion) table
Hcoords Calculates coordinates of nodes from 'hclust' plot
Ploth Changes the appearance of cluster dendrogram
Tcoords Calculates coordinates of tips from 'hclust' plot
Pull Select rows from data frame
Jclust Simple bootstrap and jackknife clustering
PlotBest.mdist Dotchart which reflects the "best" of non-base distances
Polycenter Center of the polygon
Table2df Convert table to data frame saving structure
Infill Rarefaction curves
Hulls Convex hulls for multiple groups
PlotBest.dist Dotchart which reflects the "best" base distance method
Ex.plots Examples of plot types
Ex.col Examples of colors
Ex.boxplot Boxplot explanation
Linechart Dotchart-like plot sfor every scaled variable grouped by factor
Mag Interpreter for effect sizes
Miney Miney game
Xpager Separate terminal pager for Linux
Read.tri.nts Read 'NTSYSpc' files
atmospheres atmospheres
Recode Basic multiple recoding
Pleiad Correlation circles (correlation pleiads)
Str 'str()' enchanced for data frames
Tctext Easy way to add text labels to 'hclust' plot
hrahn Angiosperm families: morphological characters
Squares Areas of polygons
PlotBest.hclust Plots dotchart with best clustering method
Ls Ls
Tobin Binarize (make dummy variables)
Vicinities Arrange observations by the distance from center
Phyllotaxis Plant phyllotaxis
Write.fasta Write 'FASTA' files
Pinhull Point in hull
keys Diagnostic keys
Root1 Roots phylogenetic trees even if outgroup is not monophyletic
Rostova.tbl Calculates multiple correlation matrices (via 'factor1') and stacks them together
Plot.phylocl Plot phylogenetic tree with clades collapsed
Fence Colorize tips of 'hclust' plot
MDSv MDS: dimension importance ("explained variance" surrogate)
Rpart2newick Converts 'rpart' object into Newick tree
R.logo Imitation (!) of the modern 'R' logo
Read.fasta Read 'FASTA' files
hwc hwc
Rresults Rresults shell script
Updist Educated distances for semi-supervised clustering
SM.dist Simple Match distance
Saynodynamite Say ``no'' to dynamite plots!
MRH Matrix Representation of Hierarchical Clustering
Normality Check normality
VTcoeffs Effect sizes of association between categorical variables
Points Number of cases in each location reflected in the point size
Overlap Calculates overlap between polygons
moldino moldino
Polyarea Area of the polygon
eq eq
chaetocnema Chaetocnema flea beetles
salix_leaves salix_leaves
Rro.test Robust rank order test
pairwise.Rro.test Robust rank order test post hoc derivative
pairwise.Eff Pairwise table of effects with magnitudes
haltica Haltica flea beetles
classifs Classification lists
S.value S-value
Toclip Insert content to Linux X11 clipboard
Topm Stacks correlation matrix
drosera drosera
dolbli dolbli
pairwise.Table2.test Pairwise Chi-squared or Fisher test for 2-dimensional tables
plantago plantago
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Type Package
Date 2020-12-20
License GPL (>= 2)
LazyLoad yes
LazyData yes
NeedsCompilation no
Packaged 2020-12-20 05:07:44 UTC; alexey
Repository CRAN
Date/Publication 2021-01-04 12:00:05 UTC

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