shipunov v1.5

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Miscellaneous Functions from Alexey Shipunov

A collection of functions for data manipulation, plotting and statistical computing, to use separately or with the book "Visual Statistics. Use R!": Shipunov (2019) <http://ashipunov.info/shipunov/software/r/r-en.htm>. 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.

Functions in shipunov

Name Description
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
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Details

Type Package
Date 2020-02-21
License GPL (>= 2)
LazyLoad yes
LazyData yes
NeedsCompilation no
Packaged 2020-02-21 14:22:33 UTC; alexey
Repository CRAN
Date/Publication 2020-02-21 18:00:02 UTC

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