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shipunov (version 1.11)

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

337

Version

1.11

License

GPL (>= 2)

Maintainer

Alexey Shipunov

Last Published

July 23rd, 2020

Functions in shipunov (1.11)

BootKNN

Bootstrap with kNN
CVs

Coefficients of variation
Biarrows

Adds correlation arrows to the scatterplot
Biokey

Convert diagnostic keys and classification lists
Bclust

Bootstrapped hclust
Adj.Rand

Adjusted Rand index
Aggregate1

Aggregates by one vector and uses it for row names
Alldups

Finds all duplicates
BestOverlap

Calculates the best overlap
BootA

Bootstrap clustering
BootRF

Bootstrap with 'randomForest()'
Cor

Correlation matrix with p-values
Hclust.match

Counts matches between two hierarchical clusterings
Ex.margins

Example of plot margins
Ex.lty

Examples of line types
Cdate

System date, time plus easy save history
MRH

Matrix Representation of Hierarchical Clustering
DNN

Distance matrix based kNN classification
Ditto

Removes duplicated data values downstream
Hcl2mat

Clustering to matrix
Ellipses

Confidence ellipses
Coml

Compare checklists
Mag

Interpreter for effect sizes
S.value

S-value
Classproj

Class projection
Boxplots

Grouped boxplots
Coeff.det

Average coefficients of determination for each variable
Dotcharts

Improved dotcharts
Ell

Plot ellipse
Ex.boxplot

Boxplot explanation
Cor.vec

Calculates correlation and converts results into the named long vector
Gen.cl.data

Generates datasets for clustering
Ex.font

Examples of fonts
Ex.col

Examples of colors
Cosine.dist

Cosine distance
SM.dist

Simple Match distance
Hcoords

Calculates coordinates of nodes from 'hclust' plot
Files

Textual file system browser
Gap.code

Gap coding
Fence

Colorize tips of 'hclust' plot
Histr

Histogram with overlaid curve
Fill

Fill data values downstream, like in spreadsheets
Plot.phylocl

Plot phylogenetic tree with clades collapsed
Cladd

Adds confidence bands to the simple linear model plots
PlotBest.dist

Plots dotchart with best base distance method
Vicinities

Arrange observations by the distance from center
Class.sample

Samples along the class labels
Bclabels

Plot bootstrap values
Gower.dist

Gower distance
Jclust

Simple bootstrap and jackknife clustering
Ex.pch

Point examples
K

Coefficient of divergence
Ex.plots

Examples of plot types
Ls

Ls
Gradd

Classification grid and decision boundaries
Pinhull

Point in hull
MDSv

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

Draw with 'R'
%-%

Minus names
Pleiad

Correlation circles (correlation pleiads)
Miney

Miney game
Pull

Select rows from data frame
Ploth

Changes the appearance of cluster dendrogram
Life

Game of Life
Phyllotaxis

Plant phyllotaxis
R.logo

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

Calculates overlap between polygons
Updist

Educated distances for semi-supervised clustering
hwc

hwc
pairwise.Table2.test

Pairwise Chi-squared or Fisher test for 2-dimensional tables
Write.fasta

Write 'FASTA' files
MrBayes

Calls MrBayes
hrahn

Angiosperm families: morphological characters
VTcoeffs

Effect sizes of association between categorical variables
Rostova.tbl

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

Dotchart-like plot sfor every scaled variable grouped by factor
Hulls

Convex hulls for multiple groups
Points

Number of cases in each location reflected in the point size
Read.fasta

Read 'FASTA' files
Infill

Rarefaction curves
Rpart2newick

Converts 'rpart' object into Newick tree
Toclip

Insert content to Linux X11 clipboard
Saynodynamite

Say ``no'' to dynamite plots!
Read.tri.nts

Read 'NTSYSpc' files
Squares

Areas of polygons
Tobin

Binarize (make dummy variables)
Topm

Stacks correlation matrix
Tcoords

Calculates coordinates of tips from 'hclust' plot
keys

Diagnostic keys
dolbli

dolbli
drosera

drosera
Rro.test

Robust rank order test
PlotBest.hclust

Plots dotchart with best clustering method
Xpager

Separate terminal pager for Linux
Root1

Roots phylogenetic trees even if outgroup is not monophyletic
Missing.map

Textual plot of missing data
Recode

Basic multiple recoding
Misclass

Misclassification (confusion) table
Rresults

Rresults shell script
plantago

plantago
PlotBest.mdist

Plots dotchart with best distance method, use multiple non-base distances
Polycenter

Center of the polygon
Polyarea

Area of the polygon
Normality

Check normality
Str

'str()' enchanced for data frames
chaetocnema

Chaetocnema flea beetles
moldino

moldino
atmospheres

atmospheres
pairwise.Eff

Pairwise table of effects with magnitudes
pairwise.Rro.test

Robust rank order test post hoc derivative
classifs

Classification lists
Table2df

Convert table to data frame saving structure
haltica

Haltica flea beetles
eq

eq
salix_leaves

salix_leaves