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 | |
| No Results! | ||
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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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