Package: multiDimBio 1.2.2

multiDimBio: Multivariate Analysis and Visualization for Biological Data

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.

Authors:Samuel V. Scarpino

multiDimBio_1.2.2.tar.gz
multiDimBio_1.2.2.zip(r-4.5)multiDimBio_1.2.2.zip(r-4.4)multiDimBio_1.2.2.zip(r-4.3)
multiDimBio_1.2.2.tgz(r-4.4-any)multiDimBio_1.2.2.tgz(r-4.3-any)
multiDimBio_1.2.2.tar.gz(r-4.5-noble)multiDimBio_1.2.2.tar.gz(r-4.4-noble)
multiDimBio_1.2.2.tgz(r-4.4-emscripten)multiDimBio_1.2.2.tgz(r-4.3-emscripten)
multiDimBio.pdf |multiDimBio.html✨
multiDimBio/json (API)

# Install 'multiDimBio' in R:
install.packages('multiDimBio', repos = c('https://scarpino.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/scarpino/multidimbio/issues

Datasets:
  • CondA - Treatment condition for animals contained in the data set Nuclei
  • CondB - Stress condition for animals contained in the data set Nuclei
  • Dyad - Housing dyad for animals contained in the data set Nuclei
  • Groups - The group ID for animals contained in the data set Nuclei
  • Nuclei - Brain activity in 14 brain regions for 71 individuals
  • Scores - Principle component scores based on the data in Nuclei

On CRAN:

20 exports 0.93 score 39 dependencies 1 mentions 26 scripts 228 downloads

Last updated 4 years agofrom:c5127c719c. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 23 2024
R-4.5-winNOTEAug 23 2024
R-4.5-linuxNOTEAug 23 2024
R-4.4-winNOTEAug 23 2024
R-4.4-macNOTEAug 23 2024
R-4.3-winOKAug 23 2024
R-4.3-macOKAug 23 2024

Exports:binomPowerboxWhiskercompleteDataFSelectgetPh2EstimateIntPlotLandscapePlotldaPlotLoadingsmakeCompMatMeanCentpartialFPercentMaxPermuteLDAplotBinomPowerPowerPPCAsimPowerZTrans

Dependencies:BiobaseBiocGenericsbootclicolorspacefansifarverggplot2gluegridGraphicsgtableisobandlabelinglatticelifecyclelme4magrittrMASSMatrixmgcvminqamisc3dmunsellnlmenloptrpcaMethodspillarpkgconfigR6RColorBrewerRcppRcppEigenrlangscalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Multivariate Analysis and Visualization for Biological DatamultiDimBio-package multiDimBio
Power analysis for estimating the heritability of a binomial traitbinomPower
A function to create a box and whisker plot by group IDboxWhisker
Function to impute missing data.completeData
Treatment condition for animals contained in the data set NucleiCondA
Stress condition for animals contained in the data set NucleiCondB
Housing dyad for animals contained in the data set NucleiDyad
A Function to perform step-wise discriminant analysis using F statisticsFSelect
An internal function for getting empirical p valuesgetP
The group ID for animals contained in the data set NucleiGroups
Estimates the heritability of a binomial traith2Estimate
A function to visualize the results of a MANOVAIntPlot
A function to visualize the Functional Landscape of measured traitsLandscapePlot
A function to visualize the results of a discriminant analysisldaPlot
A function to visualize trait loadings onto discriminant function and principle component axesLoadings
A function to create a pairwise comparison matrixmakeCompMat
A function to scale data to mean 0MeanCent
Brain activity in 14 brain regions for 71 individualsNuclei
A function to compute partial F statisticspartialF
A function to scale data to the percent of the maximum observedPercentMax
A function to determine whether two groups are in statistically different locations in multivariate space See Collyer and Adams 2007PermuteLDA
A function to plot the results of a binomPower runplotBinomPower
A function to estimate the error rate for FSelect and PermuteLDA.Power
A function to perform a probabilistic principle component analysisPPCA
Principle component scores based on the data in NucleiScores
An internal function of binomPower, which actually calculates the p valuesimPower
A function to convert data into a z-scoreZTrans