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shipunov (version 1.12)

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

286

Version

1.12

License

GPL (>= 2)

Maintainer

Alexey Shipunov

Last Published

October 19th, 2020

Functions in shipunov (1.12)

Alldups

Finds all duplicates
Bclust

Bootstrapped hclust
BootA

Bootstrap clustering
BestOverlap

Calculates the best overlap
Aggregate1

Aggregates by one vector and uses it for row names
BootKNN

Bootstrap with kNN
Adj.Rand

Adjusted Rand index
Bclabels

Plot bootstrap values
Biarrows

Adds correlation arrows to the scatterplot
Biokey

Convert diagnostic keys and classification lists
CVs

Coefficients of variation
Class.sample

Samples along the class labels
Cladd

Adds confidence bands to the simple linear model plots
Cdate

System date, time plus easy save history
Cor

Correlation matrix with p-values
Ell

Plot ellipse
Ellipses

Confidence ellipses
Coml

Compare checklists
Ex.lty

Examples of line types
Ex.font

Examples of fonts
Gap.code

Gap coding
Gen.cl.data

Generates datasets for clustering
Boxplots

Grouped boxplots
Classproj

Class projection
Files

Textual file system browser
Coeff.det

Average coefficients of determination for each variable
BootRF

Bootstrap with 'randomForest()'
Cor.vec

Calculates correlation and converts results into the named long vector
Fill

Fill data values downstream, like in spreadsheets
Dotcharts

Improved dotcharts
Ex.margins

Example of plot margins
Ditto

Removes duplicated data values downstream
Linechart

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

Game of Life
Ls

Ls
K

Coefficient of divergence
Pleiad

Correlation circles (correlation pleiads)
Gradd

Classification grid and decision boundaries
DNN

Distance matrix based kNN classification
Gower.dist

Gower distance
Ex.boxplot

Boxplot explanation
Plot.phylocl

Plot phylogenetic tree with clades collapsed
Ex.pch

Point examples
Hcl2mat

Clustering to matrix
Gridmoon

Draw with 'R'
Hclust.match

Counts matches between two hierarchical clusterings
Ex.col

Examples of colors
Ex.plots

Examples of plot types
Infill

Rarefaction curves
Fence

Colorize tips of 'hclust' plot
MDSv

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

Matrix Representation of Hierarchical Clustering
Recode

Basic multiple recoding
Read.tri.nts

Read 'NTSYSpc' files
Hcoords

Calculates coordinates of nodes from 'hclust' plot
Missing.map

Textual plot of missing data
MrBayes

Calls MrBayes
PlotBest.mdist

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

Changes the appearance of cluster dendrogram
Root1

Roots phylogenetic trees even if outgroup is not monophyletic
Histr

Histogram with overlaid curve
Pinhull

Point in hull
Phyllotaxis

Plant phyllotaxis
eq

eq
Toclip

Insert content to Linux X11 clipboard
Hulls

Convex hulls for multiple groups
Topm

Stacks correlation matrix
Rro.test

Robust rank order test
Rostova.tbl

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

Haltica flea beetles
Polyarea

Area of the polygon
Points

Number of cases in each location reflected in the point size
SM.dist

Simple Match distance
Tctext

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

Binarize (make dummy variables)
Rpart2newick

Converts 'rpart' object into Newick tree
salix_leaves

salix_leaves
Rresults

Rresults shell script
classifs

Classification lists
chaetocnema

Chaetocnema flea beetles
Misclass

Misclassification (confusion) table
%-%

Minus names
PlotBest.dist

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

Plots dotchart with best clustering method
Polycenter

Center of the polygon
Tcoords

Calculates coordinates of tips from 'hclust' plot
Table2df

Convert table to data frame saving structure
S.value

S-value
Pull

Select rows from data frame
Vicinities

Arrange observations by the distance from center
Jclust

Simple bootstrap and jackknife clustering
Xpager

Separate terminal pager for Linux
Mag

Interpreter for effect sizes
Miney

Miney game
Saynodynamite

Say ``no'' to dynamite plots!
keys

Diagnostic keys
Overlap

Calculates overlap between polygons
Normality

Check normality
R.logo

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

dolbli
Write.fasta

Write 'FASTA' files
hwc

hwc
atmospheres

atmospheres
hrahn

Angiosperm families: morphological characters
drosera

drosera
pairwise.Eff

Pairwise table of effects with magnitudes
Updist

Educated distances for semi-supervised clustering
Squares

Areas of polygons
VTcoeffs

Effect sizes of association between categorical variables
Read.fasta

Read 'FASTA' files
Str

'str()' enchanced for data frames
moldino

moldino
pairwise.Rro.test

Robust rank order test post hoc derivative
plantago

plantago
pairwise.Table2.test

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