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shipunov (version 1.13)

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

1.13

License

GPL (>= 2)

Maintainer

Alexey Shipunov

Last Published

January 4th, 2021

Functions in shipunov (1.13)

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