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shipunov (version 1.2)

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

84

Version

1.2

License

GPL (>= 2)

Maintainer

Alexey Shipunov

Last Published

June 12th, 2019

Functions in shipunov (1.2)

Cdate

System date, time plus easy save history
Ex.lty

Examples of line types
Jclust

Simple bootstrap and jackknife clustering
CVs

Coefficients of variation
Ex.font

Examples of fonts
Ex.plots

Examples of plot types
Files

Textual file system browser
Is.tax.inform.char

Taxonomic informativeness
Mag

Interpreter for effect sizes
Boxplots

Grouped boxplots
Ell

Plot ellipse
Ellipses

Groups' confidence ellipses
Phyllotaxis

Plant phyllotaxis
Read.tri.nts

Read 'NTSYSpc' files
Toclip

Insert content to Linux X11 clipboard
Pleiad

Correlation circles (correlation pleiads)
Miney

Miney game
Topm

Stacks correlation matrix
Recode

Basic multiple recoding (similar to 'SQL' left join)
Plot.phylocl

Plot phylogenetic tree with clades collapsed
Co.test

Correlation test between cophenetic and original distances
PlotBest.dist

Plots dotchart with best base distance method
Updist

Educated distances for semi-supervised clustering
Root1

Roots phylogenetic trees even if outgroup is not monophyletic
Rostova.tbl

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

Correlation matrix with p-values
Dev

Which object is predicted with less accuracy?
Coml

Compare checklists
Bclabels

Plot bootstrap values
Class.sample

Samples along the class labels
Coeff.det

Average coefficients of determination for each variable
moldino

moldino
VTcoeffs

Effect sizes of association between categorical variables
pairwise.Table2.test

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

Diagnostic keys
Dotchart

Improved dotcharts
K

Coefficient of divergence
Ex.pch

Point examples
plantago

plantago
Ex.margins

Example of plot margins
classifs

Classification lists
Cladd

Adds confidence bands to the simple linear model plots
Cor.vec

Calculates correlation and converts results into the named long vector
DNN

Distance matrix based kNN classification
MrBayes

Calls MrBayes
Gradd

Classification grid
Normality

Check normality
Hcl2mat

Clustering to matrix
Hclust.match

Counts matches between two hierarchical clusterings
Classproj

Class projection
Gridmoon

Draw with 'R'
Ex.boxplot

Boxplot explanation
Overlap

Polygons' overlap
Life

Game of Life
dolbli

dolbli
MDSv

MDS: explained variance (surrogate)
MRH

Matrix Representation of Hierarchical Clustering
Ploth

Changes the appearance of cluster dendrogram
Points

Number of cases in each location reflected in the point size
Gap.code

Gap coding
Fill

Fill data values downstream, like in spreadsheets
Ex.col

Examples of colors
Rresults

Rresults shell script
Infill

Rarefaction curves
Hulls

Groups' hulls
Gen.cl.data

Generates datasets for clustering
Gower.dist

Gower distance
Misclass

Misclassification (confusion) table
Peaks

Find local maxima
S.value

S-value
Hcoords

Plot bootstrap values
Histr

Histogram with overlaid curve
Saynodynamite

Say ``no'' to dynamite plots!
Write.fasta

Write 'FASTA' files
Rro.test

Robust rank order test
Missing.map

Textual plot of missing data
chaetocnema

Chaetocnema flea beetles
atmospheres

atmospheres
Str

'str()' enchanced for data frames
Squares

Polygons' squares
PlotBest.hclust

Plots dotchart with best clustering method
Linechart

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

Ls
PlotBest.mdist

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

Separate terminal pager for Linux
Tobin

Binarize (make dummy variables)
Table2df

Convert table to data frame saving structure
hwc

hwc
haltica

Haltica flea beetles
salix_leaves

salix_leaves
plot.nnet

Plots 'nnet' object
R

Imitation (!) of the modern 'R' logo
Read.fasta

Read 'FASTA' files
drosera

drosera
eq

eq
pairwise.Rro.test

Robust rank order test post hoc derivative
pairwise.Eff

Pairwise table of effects with magnitudes
Alldups

Finds all duplicates
BootRF

Bootstrap with 'randomForest()'
BootKNN

Bootstrap with kNN
Biokey

Convert diagnostic keys and classification lists
Aggregate1

Aggregates by one vector and uses it for row names
Bclust

Bootstrapped hclust
BootA

Bootstrap clustering
Adj.Rand

Adjusted Rand index
BestOverlap

Calculates the best overlap