Learn R Programming

⚠️There's a newer version (1.17.1) of this package.Take me there.

shipunov (version 1.4)

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.

Copy Link

Version

Install

install.packages('shipunov')

Monthly Downloads

337

Version

1.4

License

GPL (>= 2)

Maintainer

Alexey Shipunov

Last Published

December 6th, 2019

Functions in shipunov (1.4)

Bclabels

Plot bootstrap values
Alldups

Finds all duplicates
Co.test

Correlation test between cophenetic and original distances
BootKNN

Bootstrap with kNN
Coeff.det

Average coefficients of determination for each variable
BestOverlap

Calculates the best overlap
Classproj

Class projection
Bclust

Bootstrapped hclust
Class.sample

Samples along the class labels
Ditto

Removes duplicated data values downstream
Gradd

Classification grid
Ex.lty

Examples of line types
Ex.font

Examples of fonts
Dotchart

Improved dotcharts
Aggregate1

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

Adjusted Rand index
Cor.vec

Calculates correlation and converts results into the named long vector
Cdate

System date, time plus easy save history
Cladd

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

Gap coding
Dev

Which object is predicted with less accuracy?
Fill

Fill data values downstream, like in spreadsheets
DNN

Distance matrix based kNN classification
Is.tax.inform.char

Taxonomic informativeness
Jclust

Simple bootstrap and jackknife clustering
Biokey

Convert diagnostic keys and classification lists
Gridmoon

Draw with 'R'
MDSv

MDS: explained variance (surrogate)
MRH

Matrix Representation of Hierarchical Clustering
Misclass

Misclassification (confusion) table
%-%

Minus names
BootA

Bootstrap clustering
BootRF

Bootstrap with 'randomForest()'
Boxplots

Grouped boxplots
Cosine.dist

Cosine distance
Ex.plots

Examples of plot types
Coml

Compare checklists
Missing.map

Textual plot of missing data
Files

Textual file system browser
PlotBest.hclust

Plots dotchart with best clustering method
PlotBest.dist

Plots dotchart with best base distance method
CVs

Coefficients of variation
Rostova.tbl

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

Calls MrBayes
Rows

Select rows from data frame
Read.tri.nts

Read 'NTSYSpc' files
Rro.test

Robust rank order test
Read.fasta

Read 'FASTA' files
S.value

S-value
Cor

Correlation matrix with p-values
Ex.boxplot

Boxplot explanation
Hcoords

Plot bootstrap values on 'hclust' plot
Ex.col

Examples of colors
K

Coefficient of divergence
Histr

Histogram with overlaid curve
Saynodynamite

Say ``no'' to dynamite plots!
chaetocnema

Chaetocnema flea beetles
classifs

Classification lists
Squares

Polygons' squares
pairwise.Table2.test

Pairwise Chi-squared or Fisher test for 2-dimensional tables
pairwise.Rro.test

Robust rank order test post hoc derivative
Xpager

Separate terminal pager for Linux
atmospheres

atmospheres
hwc

hwc
Gower.dist

Gower distance
Gen.cl.data

Generates datasets for clustering
Pleiad

Correlation circles (correlation pleiads)
Life

Game of Life
Ell

Plot ellipse
keys

Diagnostic keys
Ls

Ls
Phyllotaxis

Plant phyllotaxis
Hclust.match

Counts matches between two hierarchical clusterings
R.logo

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

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

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

Find local maxima
Hcl2mat

Clustering to matrix
Ellipses

Groups' confidence ellipses
Plot.phylocl

Plot phylogenetic tree with clades collapsed
PlotBest.mdist

Plots dotchart with best distance method, use multiple non-base distances
Ex.pch

Point examples
Miney

Miney game
Infill

Rarefaction curves
Hulls

Groups' hulls
Ex.margins

Example of plot margins
Overlap

Polygons' overlap
Mag

Interpreter for effect sizes
Normality

Check normality
Recode

Basic multiple recoding
Ploth

Changes the appearance of cluster dendrogram
Toclip

Insert content to Linux X11 clipboard
Tobin

Binarize (make dummy variables)
Rpart2newick

Converts 'rpart' object into Newick tree
Write.fasta

Write 'FASTA' files
haltica

Haltica flea beetles
eq

eq
VTcoeffs

Effect sizes of association between categorical variables
Rresults

Rresults shell script
plantago

plantago
drosera

drosera
dolbli

dolbli
plot.nnet

Plots 'nnet' object
salix_leaves

salix_leaves
Topm

Stacks correlation matrix
Table2df

Convert table to data frame saving structure
Root1

Roots phylogenetic trees even if outgroup is not monophyletic
Updist

Educated distances for semi-supervised clustering
Str

'str()' enchanced for data frames
moldino

moldino
pairwise.Eff

Pairwise table of effects with magnitudes