Miscellaneous Functions from Alexey Shipunov

Documentation for package ‘shipunov’ version 1.17.1

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A B C D E F G H I J K L M N O P R S T U V W X misc

-- A --

Adj.Rand	Adjusted Rand index
Aggregate1	Aggregates by one vector and uses it for row names
Alldups	Finds all duplicates
atmospheres	atmospheres

-- B --

Bclabels	Plot bootstrap values
Bclust	Bootstrapped hclust
BestOverlap	Calculates the best overlap
Biarrows	Adds correlation arrows to the scatterplot
Biokey	Convert diagnostic keys and classification lists
BootA	Bootstrap clustering
BootKNN	Bootstrap with kNN
BootRF	Bootstrap with 'randomForest()'
Boxplots	Grouped boxplots

-- C --

Cdate	System date, time plus easy save history
chaetocnema	Chaetocnema flea beetles
Cladd	Adds confidence bands to the simple linear model plots
Class.sample	Samples along the class labels
classifs	Classification lists
Classproj	Class projection
Clustergram	Clustergram: visualize the cluster structure
Coeff.det	Average coefficients of determination for each variable
Coml	Compare checklists
Cor	Correlation matrix with p-values
Cor.vec	Calculates correlation and converts results into the named long vector
Cor2	Correlation matrix with p-values
Ctime	System date, time plus easy save history
CVs	Coefficients of variation

-- D --

Ditto	Removes duplicated data values downstream
DNN	Distance matrix based kNN classification
Dnn	Distance matrix based kNN classification
dolbli	dolbli
Dotchart	Improved dotcharts
Dotchart1	Improved dotcharts
Dotchart3	Improved dotcharts
drosera	drosera

-- E --

Ell	Plot ellipse
Ellipses	Confidence ellipses
eq	eq
eq_l	eq
eq_s	eq
Ex.boxplot	Boxplot explanation
Ex.col	Examples of colors
Ex.cols	Examples of colors
Ex.font	Examples of fonts
Ex.fonts	Examples of fonts
Ex.lines	Examples of line types
Ex.lty	Examples of line types
Ex.margins	Example of plot margins
Ex.pch	Point examples
Ex.plots	Examples of plot types
Ex.points	Point examples
Ex.types	Examples of plot types

-- F --

Fence	Colorize tips of 'hclust' plot
Fibonacci	Plant phyllotaxis
Files	Textual file system browser
Fill	Fill data values downstream, like in spreadsheets

-- G --

Gap.code	Gap coding
Gen.cl.data	Generates datasets for clustering
Gini	Compute the simple Gini coefficient
Gower.dist	Gower distance
Gradd	Classification grid and decision boundaries
Gridmoon	Draw with 'R'

-- H --

haltica	Haltica flea beetles
Hcl2mat	Clustering to matrix
Hclust.match	Counts matches between two hierarchical clusterings
Hcoords	Calculates coordinates of nodes from 'hclust' plot
Histr	Histogram with overlaid curve
hrahn	Angiosperm families: morphological characters
Hulls	Convex hulls for multiple groups
hwc	hwc
hwc2	hwc
hwc3	hwc

-- I --

Infill

Rarefaction curves

-- J --

Jclust

Simple bootstrap and jackknife clustering

-- K --

K	Coefficient of divergence
keys	Diagnostic keys

-- L --

Life	Game of Life
Linechart	Dotchart-like plot sfor every scaled variable grouped by factor
Ls	Ls

-- M --

Mag	Interpreter for effect sizes
MDSv	MDS: dimension importance ("explained variance" surrogate)
Miney	Miney game
Misclass	Misclassification (confusion) table
Missing.map	Textual plot of missing data
moldino	moldino
moldino_l	moldino
MrBayes	Calls MrBayes
MRH	Matrix Representation of Hierarchical Clustering

-- N --

NC.dist	Normalized Compression Distance
Normality	Check normality
Numranks	Convert diagnostic keys and classification lists

-- O --

Overlap

Calculates overlap between polygons

-- P --

pairwise.Eff	Pairwise table of effects with magnitudes
pairwise.Rro.test	Robust rank order test post hoc derivative
pairwise.Table2.test	Pairwise Chi-squared or Fisher test for 2-dimensional tables
Phyllotaxis	Plant phyllotaxis
Pinhull	Point in hull
plantago	plantago
Pleiad	Correlation circles (correlation pleiads)
plot.Bclust	Bootstrapped hclust
plot.Infill	Rarefaction curves
plot.Jclust	Simple bootstrap and jackknife clustering
Plot.phylocl	Plot phylogenetic tree with clades collapsed
PlotBest.dist	Dotchart which reflects the "best" base distance method
PlotBest.hclust	Plots dotchart with best clustering method
PlotBest.mdist	Dotchart which reflects the "best" of non-base distances
Ploth	Changes the appearance of cluster dendrogram
Points	Number of cases in each location reflected in the point size
Polyarea	Area of the polygon
Polycenter	Center of the polygon
PPoints	Number of cases in each location reflected in the point size
print.Jclust	Simple bootstrap and jackknife clustering
print.K	Coefficient of divergence
Pull	Select rows from data frame

-- R --

R.logo	Imitation (!) of the modern 'R' logo
Read.fasta	Read 'FASTA' files
Read.tri.nts	Read 'NTSYSpc' files
Recode	Basic multiple recoding
Recode4	Basic multiple recoding
Recode4R	Basic multiple recoding
RecodeR	Basic multiple recoding
Root1	Roots phylogenetic trees even if outgroup is not monophyletic
Rostova.tbl	Calculates multiple correlation matrices (via 'factor1') and stacks them together
Rpart2newick	Converts 'rpart' object into Newick tree
Rresults	Rresults shell script
Rro.test	Robust rank order test

-- S --

S.value	S-value
salix_leaves	salix_leaves
salix_plants	salix_leaves
salix_pop	salix_leaves
Save.history	System date, time plus easy save history
Saynodynamite	Say "no" to dynamite plots!
SM.dist	Simple Match distance
Squares	Areas of polygons
Str	'str()' enchanced for data frames
summary.Coml	Compare checklists
summary.Infill	Rarefaction curves
summary.K	Coefficient of divergence
summary.Overlap	Calculates overlap between polygons

-- T --

Table2df	Convert table to data frame saving structure
Tcoords	Calculates coordinates of tips from 'hclust' plot
Tctext	Easy way to add text labels to 'hclust' plot
Tobin	Binarize (make dummy variables)
Toclip	Insert content to Linux X11 clipboard
Topm	Stacks correlation matrix
Ttcols	Text-to-columns

-- U --

Updist

Educated distances for semi-supervised clustering

-- V --

Vicinities	Arrange observations by the distance from center
VTcoeffs	Effect sizes of association between categorical variables

-- W --

Write.fasta

Write 'FASTA' files

-- X --

Xpager

Separate terminal pager for Linux

-- misc --

%-%	Minus names