# shipunov v1.13

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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 (2020) <http://ashipunov.info/shipunov/software/r/r-en.htm>.
Most useful functions:
Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering;
Recode() which does multiple recoding in a fast, simple and flexible way;
Misclass() which outputs confusion matrix even if classes are not concerted;
Overlap() which measures group separation on any projection;
Biarrows() which converts any scatterplot into biplot;
and Pleiad() which is fast and flexible correlogram.

## Functions in shipunov

Name | Description | |

Biarrows | Adds correlation arrows to the scatterplot | |

Alldups | Finds all duplicates | |

BootKNN | Bootstrap with kNN | |

BootA | Bootstrap clustering | |

Bclust | Bootstrapped hclust | |

Adj.Rand | Adjusted Rand index | |

BestOverlap | Calculates the best overlap | |

Biokey | Convert diagnostic keys and classification lists | |

Bclabels | Plot bootstrap values | |

Coml | Compare checklists | |

Aggregate1 | Aggregates by one vector and uses it for row names | |

Cor.vec | Calculates correlation and converts results into the named long vector | |

Dotcharts | Improved dotcharts | |

BootRF | Bootstrap with 'randomForest()' | |

Ditto | Removes duplicated data values downstream | |

Cdate | System date, time plus easy save history | |

CVs | Coefficients of variation | |

DNN | Distance matrix based kNN classification | |

Ell | Plot ellipse | |

Ex.margins | Example of plot margins | |

Boxplots | Grouped boxplots | |

Classproj | Class projection | |

Gen.cl.data | Generates datasets for clustering | |

Gap.code | Gap coding | |

Ellipses | Confidence ellipses | |

Histr | Histogram with overlaid curve | |

Cor | Correlation matrix with p-values | |

Hclust.match | Counts matches between two hierarchical clusterings | |

Cladd | Adds confidence bands to the simple linear model plots | |

Class.sample | Samples along the class labels | |

Ex.pch | Point examples | |

Ex.font | Examples of fonts | |

Fill | Fill data values downstream, like in spreadsheets | |

Files | Textual file system browser | |

Hcl2mat | Clustering to matrix | |

Gridmoon | Draw with 'R' | |

%-% | Minus names | |

Ex.lty | Examples of line types | |

Gower.dist | Gower distance | |

Missing.map | Textual plot of missing data | |

K | Coefficient of divergence | |

Life | Game of Life | |

MrBayes | Calls MrBayes | |

Coeff.det | Average coefficients of determination for each variable | |

Gradd | Classification grid and decision boundaries | |

Misclass | Misclassification (confusion) table | |

Hcoords | Calculates coordinates of nodes from 'hclust' plot | |

Ploth | Changes the appearance of cluster dendrogram | |

Tcoords | Calculates coordinates of tips from 'hclust' plot | |

Pull | Select rows from data frame | |

Jclust | Simple bootstrap and jackknife clustering | |

PlotBest.mdist | Dotchart which reflects the "best" of non-base distances | |

Polycenter | Center of the polygon | |

Table2df | Convert table to data frame saving structure | |

Infill | Rarefaction curves | |

Hulls | Convex hulls for multiple groups | |

PlotBest.dist | Dotchart which reflects the "best" base distance method | |

Ex.plots | Examples of plot types | |

Ex.col | Examples of colors | |

Ex.boxplot | Boxplot explanation | |

Linechart | Dotchart-like plot sfor every scaled variable grouped by factor | |

Mag | Interpreter for effect sizes | |

Miney | Miney game | |

Xpager | Separate terminal pager for Linux | |

Read.tri.nts | Read 'NTSYSpc' files | |

atmospheres | atmospheres | |

Recode | Basic multiple recoding | |

Pleiad | Correlation circles (correlation pleiads) | |

Str | 'str()' enchanced for data frames | |

Tctext | Easy way to add text labels to 'hclust' plot | |

hrahn | Angiosperm families: morphological characters | |

Squares | Areas of polygons | |

PlotBest.hclust | Plots dotchart with best clustering method | |

Ls | Ls | |

Tobin | Binarize (make dummy variables) | |

Vicinities | Arrange observations by the distance from center | |

Phyllotaxis | Plant phyllotaxis | |

Write.fasta | Write 'FASTA' files | |

Pinhull | Point in hull | |

keys | Diagnostic keys | |

Root1 | Roots phylogenetic trees even if outgroup is not monophyletic | |

Rostova.tbl | Calculates multiple correlation matrices (via 'factor1') and stacks them together | |

Plot.phylocl | Plot phylogenetic tree with clades collapsed | |

Fence | Colorize tips of 'hclust' plot | |

MDSv | MDS: dimension importance ("explained variance" surrogate) | |

Rpart2newick | Converts 'rpart' object into Newick tree | |

R.logo | Imitation (!) of the modern 'R' logo | |

Read.fasta | Read 'FASTA' files | |

hwc | hwc | |

Rresults | Rresults shell script | |

Updist | Educated distances for semi-supervised clustering | |

SM.dist | Simple Match distance | |

Saynodynamite | Say ``no'' to dynamite plots! | |

MRH | Matrix Representation of Hierarchical Clustering | |

Normality | Check normality | |

VTcoeffs | Effect sizes of association between categorical variables | |

Points | Number of cases in each location reflected in the point size | |

Overlap | Calculates overlap between polygons | |

moldino | moldino | |

Polyarea | Area of the polygon | |

eq | eq | |

chaetocnema | Chaetocnema flea beetles | |

salix_leaves | salix_leaves | |

Rro.test | Robust rank order test | |

pairwise.Rro.test | Robust rank order test post hoc derivative | |

pairwise.Eff | Pairwise table of effects with magnitudes | |

haltica | Haltica flea beetles | |

classifs | Classification lists | |

S.value | S-value | |

Toclip | Insert content to Linux X11 clipboard | |

Topm | Stacks correlation matrix | |

drosera | drosera | |

dolbli | dolbli | |

pairwise.Table2.test | Pairwise Chi-squared or Fisher test for 2-dimensional tables | |

plantago | plantago | |

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## Last month downloads

## Details

Type | Package |

Date | 2020-12-20 |

License | GPL (>= 2) |

LazyLoad | yes |

LazyData | yes |

NeedsCompilation | no |

Packaged | 2020-12-20 05:07:44 UTC; alexey |

Repository | CRAN |

Date/Publication | 2021-01-04 12:00:05 UTC |

suggests | apcluster , ape , class , cluster , dbscan , e1071 , effsize , grid , ips , kernlab , MASS , mclust , meanShiftR , nnet , phangorn , randomForest , rpart , smirnov , StatMatch , tapkee , tree , vegan |

imports | PBSmapping |

Contributors | Emmanuel Paradis, R team, Paul Murrell, Sebastian Gibb, Alexey Shipunov, Roger Koenker, Roland Rau, Marcello D'Orazio, Weiliang Qiu, Stephen Turner, Eugeny Altshuler, Marcus Beck |

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