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shipunov (version 1.17.1)

Miscellaneous Functions from Alexey Shipunov

Description

A collection of functions for data manipulation, plotting and statistical computing, to use separately or with the book "Visual Statistics. Use R!": Shipunov (2020) . 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.

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Version

Install

install.packages('shipunov')

Monthly Downloads

420

Version

1.17.1

License

GPL (>= 2)

Maintainer

Last Published

February 5th, 2023

Functions in shipunov (1.17.1)

Finds all duplicates

Samples along the class labels

Bootstrap clustering

Bootstrap with kNN

Distance matrix based kNN classification

Plot bootstrap values

Adjusted Rand index

Adds confidence bands to the simple linear model plots

Removes duplicated data values downstream

Aggregates by one vector and uses it for row names

Improved dotcharts

Coefficients of variation

Average coefficients of determination for each variable

Fill data values downstream, like in spreadsheets

Convert diagnostic keys and classification lists

Calculates coordinates of nodes from 'hclust' plot

Counts matches between two hierarchical clusterings

Compare checklists

Bootstrapped hclust

Adds correlation arrows to the scatterplot

Class projection

Clustergram: visualize the cluster structure

Examples of colors

Examples of fonts

Textual file system browser

Colorize tips of 'hclust' plot

Calculates the best overlap

System date, time plus easy save history

Bootstrap with 'randomForest()'

Normalized Compression Distance

Check normality

Rarefaction curves

Clustering to matrix

Examples of plot types

Correlation matrix with p-values

Grouped boxplots

Dotchart-like plot sfor every scaled variable grouped by factor

PlotBest.hclust

Plots dotchart with best clustering method

Dotchart which reflects the "best" of non-base distances

Misclassification (confusion) table

Calculates overlap between polygons

Simple bootstrap and jackknife clustering

Plot phylogenetic tree with clades collapsed

Dotchart which reflects the "best" base distance method

Confidence ellipses

MDS: dimension importance ("explained variance" surrogate)

Matrix Representation of Hierarchical Clustering

Simple Match distance

Plant phyllotaxis

Boxplot explanation

Generates datasets for clustering

Area of the polygon

Center of the polygon

Converts 'rpart' object into Newick tree

Compute the simple Gini coefficient

Calculates multiple correlation matrices (via 'factor1') and stacks them together

Histogram with overlaid curve

Changes the appearance of cluster dendrogram

Coefficient of divergence

Convex hulls for multiple groups

Number of cases in each location reflected in the point size

Say ``no'' to dynamite plots!

Areas of polygons

Stacks correlation matrix

Text-to-columns

Basic multiple recoding

Read 'FASTA' files

Read 'NTSYSpc' files

'str()' enchanced for data frames

Insert content to Linux X11 clipboard

Arrange observations by the distance from center

Convert table to data frame saving structure

Robust rank order test

Rresults shell script

Correlation circles (correlation pleiads)

Separate terminal pager for Linux

Binarize (make dummy variables)

Chaetocnema flea beetles

Write 'FASTA' files

Roots phylogenetic trees even if outgroup is not monophyletic

pairwise.Rro.test

Robust rank order test post hoc derivative

Pairwise table of effects with magnitudes

Educated distances for semi-supervised clustering

Angiosperm families: morphological characters

Examples of line types

Classification grid and decision boundaries

Example of plot margins

Interpreter for effect sizes

Calculates correlation and converts results into the named long vector

pairwise.Table2.test

Pairwise Chi-squared or Fisher test for 2-dimensional tables

Effect sizes of association between categorical variables

Classification lists

Diagnostic keys

Select rows from data frame

Imitation (!) of the modern 'R' logo

Textual plot of missing data

Easy way to add text labels to 'hclust' plot

Calculates coordinates of tips from 'hclust' plot

Haltica flea beetles