Learn R Programming

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

shipunov (version 1.7)

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 does multiple recoding 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; Biarrows() which converts any scatterplot into biplot, and Pleiad() which is fast and flexible correlogram. There are much more useful functions, please see documentation.

Copy Link

Version

Install

install.packages('shipunov')

Monthly Downloads

286

Version

1.7

License

GPL (>= 2)

Maintainer

Alexey Shipunov

Last Published

March 18th, 2020

Functions in shipunov (1.7)

Bclabels

Plot bootstrap values
Biokey

Convert diagnostic keys and classification lists
Adj.Rand

Adjusted Rand index
Aggregate1

Aggregates by one vector and uses it for row names
BootA

Bootstrap clustering
Bclust

Bootstrapped hclust
BootRF

Bootstrap with 'randomForest()'
Alldups

Finds all duplicates
Cdate

System date, time plus easy save history
BootKNN

Bootstrap with kNN
BestOverlap

Calculates the best overlap
Biarrows

Adds correlation arrows to the scatterplot
Classproj

Class projection
Coml

Compare checklists
CVs

Coefficients of variation
Cor

Correlation matrix with p-values
Boxplots

Grouped boxplots
Class.sample

Samples along the class labels
Cladd

Adds confidence bands to the simple linear model plots
Coeff.det

Average coefficients of determination for each variable
Ellipses

Groups' confidence ellipses
Dotcharts

Improved dotcharts
Ex.col

Examples of colors
Ex.font

Examples of fonts
DNN

Distance matrix based kNN classification
Gower.dist

Gower distance
Cor.vec

Calculates correlation and converts results into the named long vector
Ex.pch

Point examples
Ditto

Removes duplicated data values downstream
Ex.boxplot

Boxplot explanation
Gradd

Classification grid and decision boundaries
Ex.plots

Examples of plot types
Files

Textual file system browser
Fill

Fill data values downstream, like in spreadsheets
MRH

Matrix Representation of Hierarchical Clustering
Hcoords

Plot bootstrap values on 'hclust' plot
Ex.lty

Examples of line types
MDSv

MDS: dimension importance ("explained variance" surrogate)
Cosine.dist

Cosine distance
Hclust.match

Counts matches between two hierarchical clusterings
Ell

Plot ellipse
Ex.margins

Example of plot margins
Infill

Rarefaction curves
Ploth

Changes the appearance of cluster dendrogram
Points

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

Polygons' squares
Read.fasta

Read 'FASTA' files
%-%

Minus names
Misclass

Misclassification (confusion) table
Read.tri.nts

Read 'NTSYSpc' files
Gridmoon

Draw with 'R'
Jclust

Simple bootstrap and jackknife clustering
Life

Game of Life
Missing.map

Textual plot of missing data
K

Coefficient of divergence
Pleiad

Correlation circles (correlation pleiads)
Str

'str()' enchanced for data frames
eq

eq
drosera

drosera
Gen.cl.data

Generates datasets for clustering
Plot.phylocl

Plot phylogenetic tree with clades collapsed
Phyllotaxis

Plant phyllotaxis
Gap.code

Gap coding
Pull

Select rows from data frame
Hcl2mat

Clustering to matrix
S.value

S-value
moldino

moldino
Write.fasta

Write 'FASTA' files
Miney

Miney game
Mag

Interpreter for effect sizes
Saynodynamite

Say ``no'' to dynamite plots!
Xpager

Separate terminal pager for Linux
Normality

Check normality
MrBayes

Calls MrBayes
pairwise.Table2.test

Pairwise Chi-squared or Fisher test for 2-dimensional tables
R.logo

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

Diagnostic keys
Histr

Histogram with overlaid curve
Recode

Basic multiple recoding
PlotBest.dist

Plots dotchart with best base distance method
Overlap

Polygons' overlap
Hulls

Groups' hulls
Rresults

Rresults shell script
plantago

plantago
Ls

Ls
PlotBest.hclust

Plots dotchart with best clustering method
classifs

Classification lists
Linechart

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

Plots dotchart with best distance method, use multiple non-base distances
Rro.test

Robust rank order test
Root1

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

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

Insert content to Linux X11 clipboard
Topm

Stacks correlation matrix
Table2df

Convert table to data frame saving structure
VTcoeffs

Effect sizes of association between categorical variables
dolbli

dolbli
Rpart2newick

Converts 'rpart' object into Newick tree
atmospheres

atmospheres
salix_leaves

salix_leaves
Tobin

Binarize (make dummy variables)
Updist

Educated distances for semi-supervised clustering
haltica

Haltica flea beetles
hwc

hwc
pairwise.Eff

Pairwise table of effects with magnitudes
pairwise.Rro.test

Robust rank order test post hoc derivative
chaetocnema

Chaetocnema flea beetles