Man pages for shipunov
Miscellaneous Functions from Alexey Shipunov

Adj.RandAdjusted Rand index
Aggregate1Aggregates by one vector and uses it for row names
AlldupsFinds all duplicates
atmospheresatmospheres
BclabelsPlot bootstrap values
BclustBootstrapped hclust
BestOverlapCalculates the best overlap
BiarrowsAdds correlation arrows to the scatterplot
BiokeyConvert diagnostic keys and classification lists
BootABootstrap clustering
BootKNNBootstrap with kNN
BootRFBootstrap with 'randomForest()'
BoxplotsGrouped boxplots
CdateSystem date, time plus easy save history
chaetocnemaChaetocnema flea beetles
CladdAdds confidence bands to the simple linear model plots
classifsClassification lists
ClassprojClass projection
Class.sampleSamples along the class labels
ClustergramClustergram: visualize the cluster structure
Coeff.detAverage coefficients of determination for each variable
ComlCompare checklists
CorCorrelation matrix with p-values
Cor.vecCalculates correlation and converts results into the named...
CVsCoefficients of variation
DittoRemoves duplicated data values downstream
DNNDistance matrix based kNN classification
dolblidolbli
DotchartsImproved dotcharts
droseradrosera
EllPlot ellipse
EllipsesConfidence ellipses
eqeq
Ex.boxplotBoxplot explanation
Ex.colExamples of colors
Ex.fontExamples of fonts
Ex.ltyExamples of line types
Ex.marginsExample of plot margins
Ex.pchPoint examples
Ex.plotsExamples of plot types
FenceColorize tips of 'hclust' plot
FilesTextual file system browser
FillFill data values downstream, like in spreadsheets
Gap.codeGap coding
Gen.cl.dataGenerates datasets for clustering
GiniCompute the simple Gini coefficient
Gower.distGower distance
GraddClassification grid and decision boundaries
GridmoonDraw with 'R'
halticaHaltica flea beetles
Hcl2matClustering to matrix
Hclust.matchCounts matches between two hierarchical clusterings
HcoordsCalculates coordinates of nodes from 'hclust' plot
HistrHistogram with overlaid curve
hrahnAngiosperm families: morphological characters
HullsConvex hulls for multiple groups
hwchwc
InfillRarefaction curves
JclustSimple bootstrap and jackknife clustering
KCoefficient of divergence
keysDiagnostic keys
LifeGame of Life
LinechartDotchart-like plot sfor every scaled variable grouped by...
LsLs
MagInterpreter for effect sizes
MDSvMDS: dimension importance ("explained variance" surrogate)
MineyMiney game
Minus.namesMinus names
MisclassMisclassification (confusion) table
Missing.mapTextual plot of missing data
moldinomoldino
MrBayesCalls MrBayes
MRHMatrix Representation of Hierarchical Clustering
NC.distNormalized Compression Distance
NormalityCheck normality
OverlapCalculates overlap between polygons
pairwise.EffPairwise table of effects with magnitudes
pairwise.Rro.testRobust rank order test post hoc derivative
pairwise.Table2.testPairwise Chi-squared or Fisher test for 2-dimensional tables
PhyllotaxisPlant phyllotaxis
PinhullPoint in hull
plantagoplantago
PleiadCorrelation circles (correlation pleiads)
PlotBest.distDotchart which reflects the "best" base distance method
PlotBest.hclustPlots dotchart with best clustering method
PlotBest.mdistDotchart which reflects the "best" of non-base distances
PlothChanges the appearance of cluster dendrogram
Plot.phyloclPlot phylogenetic tree with clades collapsed
PointsNumber of cases in each location reflected in the point size
PolyareaArea of the polygon
PolycenterCenter of the polygon
PullSelect rows from data frame
Read.fastaRead 'FASTA' files
Read.tri.ntsRead 'NTSYSpc' files
RecodeBasic multiple recoding
R.logoImitation (!) of the modern 'R' logo
Root1Roots phylogenetic trees even if outgroup is not monophyletic
Rostova.tblCalculates multiple correlation matrices (via 'factor1') and...
Rpart2newickConverts 'rpart' object into Newick tree
RresultsRresults shell script
Rro.testRobust rank order test
salixsalix_leaves
SaynodynamiteSay "no" to dynamite plots!
SM.distSimple Match distance
SquaresAreas of polygons
Str'str()' enchanced for data frames
S.valueS-value
Table2dfConvert table to data frame saving structure
TcoordsCalculates coordinates of tips from 'hclust' plot
TctextEasy way to add text labels to 'hclust' plot
TobinBinarize (make dummy variables)
ToclipInsert content to Linux X11 clipboard
TopmStacks correlation matrix
TtcolsText-to-columns
UpdistEducated distances for semi-supervised clustering
VicinitiesArrange observations by the distance from center
VTcoeffsEffect sizes of association between categorical variables
Write.fastaWrite 'FASTA' files
XpagerSeparate terminal pager for Linux
shipunov documentation built on Feb. 16, 2023, 9:05 p.m.