Package: ProcMod 1.0.8

ProcMod: Informative Procrustean Matrix Correlation

Estimates corrected Procrustean correlation between matrices for removing overfitting effect. Coissac Eric and Gonindard-Melodelima Christelle (2019) <doi:10.1101/842070>.

Authors:Eric Coissac, Christelle Gonindard-Melodelima

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ProcMod.pdf |ProcMod.html✨
ProcMod/json (API)

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

Peer review:

Datasets:
  • bacteria - DNA metabarcoding Australia South-North Gradient
  • climat - DNA metabarcoding Australia South-North Gradient
  • eukaryotes - DNA metabarcoding Australia South-North Gradient
  • geography - DNA metabarcoding Australia South-North Gradient
  • soil - DNA metabarcoding Australia South-North Gradient

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 158 downloads 15 exports 9 dependencies

Last updated 4 years agofrom:c56c580955. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winOKNov 19 2024
R-4.5-linuxOKNov 19 2024
R-4.4-winOKNov 19 2024
R-4.4-macOKNov 19 2024
R-4.3-winOKNov 19 2024
R-4.3-macOKNov 19 2024

Exports:as_procmod_framebicentercorlscorls_testis_euclidis_procmod_framenmdsorthopcapcoaprocmod_frameprotatesimulate_correlationsimulate_matrixvarls

Dependencies:codetoolsforeachiteratorslatticeMASSMatrixpermuterbibutilsRdpack

Readme and manuals

Help Manual

Help pageTopics
Generate permutation matrix according to a schema..getPermuteMatrix
Internal function coercing the data to a matrix..procmod_coerce_value
Internal function repeating a matrix..rep_matrix
Compute the trace of a square matrix..Trace
Coerce to a ProcMod Frame.as_procmod_frame as_procmod_frame.array as_procmod_frame.list as_procmod_frame.matrix as_procmod_frame.procmod_frame
Converts a 'dist' object to a 'data.frame' object.as.data.frame.dist
Double centering of a matrix.bicenter
Monte-Carlo Test on the sum of the singular values of a procustean rotation.corls_test
Dimensions of a ProcMod Frame.dim.procmod_frame
DNA metabarcoding Australia South-North Gradientbacteria climat eukaryotes geography soil
Test if the distance matrix is euclidean.is_euclid
Check if an object is a ProcMod Frame.is_procmod_frame
The Names of the elements of a Correlation Matrixnames.procmod_corls
The Names of the elements of a Variance / Covariance Matrix.names.procmod_varls
Project a distance matrix in a euclidean space (NMDS).nmds
Project a dataset in a euclidean space.ortho ortho.data.frame ortho.dist ortho.matrix ortho.procmod_frame
Project a set of points in a euclidean space (PCA).pca
Project a distance matrix in a euclidean space (PCOA).pcoa
Print a procrustean Correlation Matrix.print.procmod_corls
Print procrustean Variance / Covariance Matrix.print.procmod_varls
Informative Procrustean Matrix Correlationprocmod
The procmod_frame data structure.procmod_frame
Rotate the 'src' matrix to fit into the space of the 'dest' matrix.protate
Simulate n points of dimension p correlated to a reference matrix.simulate_correlation
Simulate n points of dimension p.simulate_matrix
Subsetting Procmod Framessubset.procmod_frame
Procrustean Correlation, and Variance / Covariance Matrices.corls varls