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shipunov (version 1.5)

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

1.5

License

GPL (>= 2)

Maintainer

Alexey Shipunov

Last Published

February 21st, 2020

Functions in shipunov (1.5)

Rostova.tbl

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

System date, time plus easy save history
Coml

Compare checklists
BootA

Bootstrap clustering
Alldups

Finds all duplicates
Cladd

Adds confidence bands to the simple linear model plots
Gap.code

Gap coding
Ex.col

Examples of colors
Biokey

Convert diagnostic keys and classification lists
BootRF

Bootstrap with 'randomForest()'
Cor.vec

Calculates correlation and converts results into the named long vector
Bclabels

Plot bootstrap values
Ex.font

Examples of fonts
S.value

S-value
%-%

Minus names
Histr

Histogram with overlaid curve
Ex.plots

Examples of plot types
Hcoords

Plot bootstrap values on 'hclust' plot
Ex.pch

Point examples
Recode

Basic multiple recoding
Cosine.dist

Cosine distance
Infill

Rarefaction curves
Gen.cl.data

Generates datasets for clustering
CVs

Coefficients of variation
Class.sample

Samples along the class labels
Fill

Fill data values downstream, like in spreadsheets
Boxplots

Grouped boxplots
Ellipses

Groups' confidence ellipses
Ex.margins

Example of plot margins
Is.tax.inform.char

Taxonomic informativeness
Cor

Correlation matrix with p-values
DNN

Distance matrix based kNN classification
Points

Number of cases in each location reflected in the point size
Ex.boxplot

Boxplot explanation
Hclust.match

Counts matches between two hierarchical clusterings
Ex.lty

Examples of line types
Hulls

Groups' hulls
atmospheres

atmospheres
MrBayes

Calls MrBayes
MRH

Matrix Representation of Hierarchical Clustering
Str

'str()' enchanced for data frames
Squares

Polygons' squares
Ploth

Changes the appearance of cluster dendrogram
Life

Game of Life
Classproj

Class projection
Linechart

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

Plots dotchart with best clustering method
Root1

Roots phylogenetic trees even if outgroup is not monophyletic
Pull

Select rows from data frame
Mag

Interpreter for effect sizes
drosera

drosera
Gower.dist

Gower distance
Ditto

Removes duplicated data values downstream
Ell

Plot ellipse
haltica

Haltica flea beetles
PlotBest.mdist

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

Insert content to Linux X11 clipboard
Jclust

Simple bootstrap and jackknife clustering
Overlap

Polygons' overlap
Dotcharts

Improved dotcharts
Gradd

Classification grid
Files

Textual file system browser
Updist

Educated distances for semi-supervised clustering
Missing.map

Textual plot of missing data
pairwise.Eff

Pairwise table of effects with magnitudes
R.logo

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

Stacks correlation matrix
Misclass

Misclassification (confusion) table
eq

eq
Peaks

Find local maxima
keys

Diagnostic keys
Ls

Ls
pairwise.Table2.test

Pairwise Chi-squared or Fisher test for 2-dimensional tables
Hcl2mat

Clustering to matrix
Gridmoon

Draw with 'R'
Miney

Miney game
hwc

hwc
K

Coefficient of divergence
MDSv

MDS: explained variance (surrogate)
Table2df

Convert table to data frame saving structure
dolbli

dolbli
Read.fasta

Read 'FASTA' files
VTcoeffs

Effect sizes of association between categorical variables
Normality

Check normality
pairwise.Rro.test

Robust rank order test post hoc derivative
Phyllotaxis

Plant phyllotaxis
Rresults

Rresults shell script
classifs

Classification lists
Tobin

Binarize (make dummy variables)
Pleiad

Correlation circles (correlation pleiads)
Plot.phylocl

Plot phylogenetic tree with clades collapsed
moldino

moldino
PlotBest.dist

Plots dotchart with best base distance method
Rpart2newick

Converts 'rpart' object into Newick tree
Saynodynamite

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

Write 'FASTA' files
plantago

plantago
Read.tri.nts

Read 'NTSYSpc' files
Xpager

Separate terminal pager for Linux
Rro.test

Robust rank order test
salix_leaves

salix_leaves
chaetocnema

Chaetocnema flea beetles
Bclust

Bootstrapped hclust
Coeff.det

Average coefficients of determination for each variable
BestOverlap

Calculates the best overlap
Co.test

Correlation test between cophenetic and original distances
BootKNN

Bootstrap with kNN
Aggregate1

Aggregates by one vector and uses it for row names
Adj.Rand

Adjusted Rand index