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shipunov (version 1.3)

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 (2019) . Most useful functions are probably Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering; Recode...() which multiple recode in a fast, flexible and simple way; Misclass() which outputs confusion matrix even if classes are not concerted; Overlap() which calculates overlaps of convex hulls from any projection; and Pleiad() which is fast and flexible correlogram. In fact, there are much more useful functions, please see documentation.

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Version

Install

install.packages('shipunov')

Monthly Downloads

337

Version

1.3

License

GPL (>= 2)

Maintainer

Alexey Shipunov

Last Published

September 18th, 2019

Functions in shipunov (1.3)

Boxplots

Grouped boxplots
Classproj

Class projection
Cosine.dist

Cosine distance
Cor.vec

Calculates correlation and converts results into the named long vector
Class.sample

Samples along the class labels
Coml

Compare checklists
Ex.col

Examples of colors
Ex.font

Examples of fonts
Cor

Correlation matrix with p-values
Files

Textual file system browser
CVs

Coefficients of variation
Coeff.det

Average coefficients of determination for each variable
Co.test

Correlation test between cophenetic and original distances
DNN

Distance matrix based kNN classification
Dotchart

Improved dotcharts
Gower.dist

Gower distance
Fill

Fill data values downstream, like in spreadsheets
Ex.margins

Example of plot margins
Bclabels

Plot bootstrap values
Dev

Which object is predicted with less accuracy?
Ex.lty

Examples of line types
Ploth

Changes the appearance of cluster dendrogram
MRH

Matrix Representation of Hierarchical Clustering
Gradd

Classification grid
Mag

Interpreter for effect sizes
Points

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

Histogram with overlaid curve
Ell

Plot ellipse
Topm

Stacks correlation matrix
Gap.code

Gap coding
MrBayes

Calls MrBayes
Ls

Ls
Saynodynamite

Say ``no'' to dynamite plots!
Hulls

Groups' hulls
Normality

Check normality
MDSv

MDS: explained variance (surrogate)
Ex.pch

Point examples
Ex.plots

Examples of plot types
Infill

Rarefaction curves
Squares

Polygons' squares
dolbli

dolbli
Updist

Educated distances for semi-supervised clustering
Gridmoon

Draw with 'R'
Overlap

Polygons' overlap
Miney

Miney game
%-%

Minus names
Hcl2mat

Clustering to matrix
Peaks

Find local maxima
Gen.cl.data

Generates datasets for clustering
K

Coefficient of divergence
Pleiad

Correlation circles (correlation pleiads)
Phyllotaxis

Plant phyllotaxis
Jclust

Simple bootstrap and jackknife clustering
plantago

plantago
Misclass

Misclassification (confusion) table
Rostova.tbl

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

Chaetocnema flea beetles
Missing.map

Textual plot of missing data
Root1

Roots phylogenetic trees even if outgroup is not monophyletic
classifs

Classification lists
salix_leaves

salix_leaves
drosera

drosera
Recode

Basic multiple recoding
atmospheres

atmospheres
Table2df

Convert table to data frame saving structure
Str

'str()' enchanced for data frames
Read.tri.nts

Read 'NTSYSpc' files
Xpager

Separate terminal pager for Linux
pairwise.Rro.test

Robust rank order test post hoc derivative
pairwise.Table2.test

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

Adds confidence bands to the simple linear model plots
Cdate

System date, time plus easy save history
Ellipses

Groups' confidence ellipses
Plot.phylocl

Plot phylogenetic tree with clades collapsed
Hclust.match

Counts matches between two hierarchical clusterings
Hcoords

Plot bootstrap values on 'hclust' plot
Ex.boxplot

Boxplot explanation
PlotBest.dist

Plots dotchart with best base distance method
R

Imitation (!) of the modern 'R' logo
Is.tax.inform.char

Taxonomic informativeness
plot.nnet

Plots 'nnet' object
Rro.test

Robust rank order test
Read.fasta

Read 'FASTA' files
S.value

S-value
Write.fasta

Write 'FASTA' files
pairwise.Eff

Pairwise table of effects with magnitudes
moldino

moldino
VTcoeffs

Effect sizes of association between categorical variables
Life

Game of Life
Linechart

Dotchart-like plot sfor every scaled variable grouped by factor
PlotBest.hclust

Plots dotchart with best clustering method
Rpart2newick

Converts 'rpart' object into Newick tree
PlotBest.mdist

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

Rresults shell script
Toclip

Insert content to Linux X11 clipboard
Tobin

Binarize (make dummy variables)
eq

eq
haltica

Haltica flea beetles
hwc

hwc
keys

Diagnostic keys
Bclust

Bootstrapped hclust
BootKNN

Bootstrap with kNN
Adj.Rand

Adjusted Rand index
BestOverlap

Calculates the best overlap
Biokey

Convert diagnostic keys and classification lists
Aggregate1

Aggregates by one vector and uses it for row names
Alldups

Finds all duplicates
BootRF

Bootstrap with 'randomForest()'
BootA

Bootstrap clustering