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shipunov (version 1.17)

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) . 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

285

Version

1.17

License

GPL (>= 2)

Maintainer

Alexey Shipunov

Last Published

February 26th, 2022

Functions in shipunov (1.17)

BootA

Bootstrap clustering
Adj.Rand

Adjusted Rand index
Alldups

Finds all duplicates
Biokey

Convert diagnostic keys and classification lists
Bclust

Bootstrapped hclust
Biarrows

Adds correlation arrows to the scatterplot
Aggregate1

Aggregates by one vector and uses it for row names
Bclabels

Plot bootstrap values
BestOverlap

Calculates the best overlap
BootKNN

Bootstrap with kNN
Cladd

Adds confidence bands to the simple linear model plots
Coeff.det

Average coefficients of determination for each variable
Ell

Plot ellipse
Clustergram

Clustergram: visualize the cluster structure
Dotcharts

Improved dotcharts
Classproj

Class projection
Class.sample

Samples along the class labels
Ex.col

Examples of colors
Ex.plots

Examples of plot types
Ex.pch

Point examples
Ex.font

Examples of fonts
CVs

Coefficients of variation
DNN

Distance matrix based kNN classification
Cdate

System date, time plus easy save history
Ditto

Removes duplicated data values downstream
Gen.cl.data

Generates datasets for clustering
Gini

Compute the simple Gini coefficient
Gap.code

Gap coding
Gower.dist

Gower distance
Fill

Fill data values downstream, like in spreadsheets
Gradd

Classification grid and decision boundaries
Infill

Rarefaction curves
Jclust

Simple bootstrap and jackknife clustering
Cor.vec

Calculates correlation and converts results into the named long vector
Mag

Interpreter for effect sizes
Cor

Correlation matrix with p-values
Boxplots

Grouped boxplots
BootRF

Bootstrap with 'randomForest()'
Fence

Colorize tips of 'hclust' plot
Hclust.match

Counts matches between two hierarchical clusterings
Files

Textual file system browser
Ellipses

Confidence ellipses
Ex.boxplot

Boxplot explanation
Hcoords

Calculates coordinates of nodes from 'hclust' plot
Pinhull

Point in hull
R.logo

Imitation (!) of the modern 'R' logo
Miney

Miney game
Pull

Select rows from data frame
Pleiad

Correlation circles (correlation pleiads)
Linechart

Dotchart-like plot sfor every scaled variable grouped by factor
Rro.test

Robust rank order test
Table2df

Convert table to data frame saving structure
Str

'str()' enchanced for data frames
Rresults

Rresults shell script
NC.dist

Normalized Compression Distance
Histr

Histogram with overlaid curve
Life

Game of Life
K

Coefficient of divergence
Ls

Ls
Normality

Check normality
Hulls

Convex hulls for multiple groups
eq

eq
moldino

moldino
atmospheres

atmospheres
SM.dist

Simple Match distance
Polyarea

Area of the polygon
Polycenter

Center of the polygon
S.value

S-value
keys

Diagnostic keys
Overlap

Calculates overlap between polygons
Xpager

Separate terminal pager for Linux
haltica

Haltica flea beetles
Tcoords

Calculates coordinates of tips from 'hclust' plot
MDSv

MDS: dimension importance ("explained variance" surrogate)
Phyllotaxis

Plant phyllotaxis
Ploth

Changes the appearance of cluster dendrogram
Recode

Basic multiple recoding
Points

Number of cases in each location reflected in the point size
Tctext

Easy way to add text labels to 'hclust' plot
Toclip

Insert content to Linux X11 clipboard
Tobin

Binarize (make dummy variables)
Vicinities

Arrange observations by the distance from center
Root1

Roots phylogenetic trees even if outgroup is not monophyletic
Write.fasta

Write 'FASTA' files
chaetocnema

Chaetocnema flea beetles
classifs

Classification lists
MRH

Matrix Representation of Hierarchical Clustering
salix_leaves

salix_leaves
Gridmoon

Draw with 'R'
%-%

Minus names
Ex.margins

Example of plot margins
Ex.lty

Examples of line types
Coml

Compare checklists
Hcl2mat

Clustering to matrix
hrahn

Angiosperm families: morphological characters
hwc

hwc
Missing.map

Textual plot of missing data
Misclass

Misclassification (confusion) table
MrBayes

Calls MrBayes
Read.fasta

Read 'FASTA' files
PlotBest.dist

Dotchart which reflects the "best" base distance method
PlotBest.hclust

Plots dotchart with best clustering method
Read.tri.nts

Read 'NTSYSpc' files
Plot.phylocl

Plot phylogenetic tree with clades collapsed
PlotBest.mdist

Dotchart which reflects the "best" of non-base distances
Rpart2newick

Converts 'rpart' object into Newick tree
Updist

Educated distances for semi-supervised clustering
Rostova.tbl

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

plantago
VTcoeffs

Effect sizes of association between categorical variables
Saynodynamite

Say ``no'' to dynamite plots!
pairwise.Table2.test

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

Areas of polygons
Ttcols

Text-to-columns
pairwise.Eff

Pairwise table of effects with magnitudes
dolbli

dolbli
Topm

Stacks correlation matrix
drosera

drosera
pairwise.Rro.test

Robust rank order test post hoc derivative