Learn R Programming

multiDimBio (version 1.2.5)

Multivariate Analysis and Visualization for Biological Data

Description

Code to support a systems biology research program from inception through publication. The methods focus on dimension reduction approaches to detect patterns in complex, multivariate experimental data and places an emphasis on informative visualizations. The goal for this project is to create a package that will evolve over time, thereby remaining relevant and reflective of current methods and techniques. As a result, we encourage suggested additions to the package, both methodological and graphical.

Copy Link

Version

Install

install.packages('multiDimBio')

Monthly Downloads

209

Version

1.2.5

License

GPL (>= 3.0)

Maintainer

Samuel V Scarpino

Last Published

May 13th, 2025

Functions in multiDimBio (1.2.5)

boxWhisker

A function to create a box and whisker plot by group ID
Power

A function to estimate the error rate for FSelect and PermuteLDA.
Scores

Principle component scores based on the data in Nuclei
PPCA

A function to perform a probabilistic principle component analysis
completeData

Function to impute missing data.
binomPower

Power analysis for estimating the heritability of a binomial trait
ldaPlot

A function to visualize the results of a discriminant analysis
multiDimBio-package

Multivariate Analysis and Visualization for Biological Data
PercentMax

A function to scale data to the percent of the maximum observed
partialF

A function to compute partial F statistics
ZTrans

A function to convert data into a z-score
makeCompMat

A function to create a pairwise comparison matrix
plotBinomPower

A function to plot the results of a binomPower run
simPower

An internal function of binomPower, which actually calculates the p value
Loadings

A function to visualize trait loadings onto discriminant function and principle component axes
MeanCent

A function to scale data to mean 0
LandscapePlot

A function to visualize the Functional Landscape of measured traits
Nuclei

Brain activity in 14 brain regions for 71 individuals
FSelect

A Function to perform step-wise discriminant analysis using F statistics
CondB

Stress condition for animals contained in the data set Nuclei
IntPlot

A function to visualize the results of a MANOVA
CondA

Treatment condition for animals contained in the data set Nuclei
Groups

The group ID for animals contained in the data set Nuclei
Dyad

Housing dyad for animals contained in the data set Nuclei
getP

An internal function for getting empirical p values
h2Estimate

Estimates the heritability of a binomial trait
PermuteLDA

A function to determine whether two groups are in statistically different locations in multivariate space See Collyer and Adams 2007