Files in parafac4microbiome

Parallel Factor Analysis Modelling of Longitudinal Microbiome Data

NEWS.md README.md R/parafac_fun.R R/calculateFMS.R R/multiwayCLR.R R/utils-pipe.R R/calculateSparsity.R R/transformPARAFACloadings.R R/plotModelMetric.R R/data.R R/importTreeSummarizedExperiment.R R/assessModelQuality.R R/parafac_gradient.R R/plotModelStability.R R/calculateVarExp.R R/importMicrobiotaProcess.R R/parafac4microbiome-package.R R/initializePARAFAC.R R/plotModelTCCs.R R/importPhyloseq.R R/parafac.R R/parafac_core_als.R R/reshapeData.R R/multiwayCenter.R R/corcondia.R R/assessModelStability.R R/plotPARAFACmodel.R R/processDataCube.R R/multiwayScale.R R/utils.R inst/doc/PARAFAC_introduction.R inst/doc/Fujita2023_analysis.R inst/doc/Fujita2023_analysis.Rmd inst/doc/Shao2019_analysis.Rmd inst/doc/PARAFAC_introduction.Rmd inst/doc/vanderPloeg2024_analysis.Rmd inst/doc/vanderPloeg2024_analysis.R inst/doc/Shao2019_analysis.R tests/testthat.R tests/testthat/test-parafac_core_als.R tests/testthat/test-plotModelStability.R tests/testthat/test-calculateSparsity.R tests/testthat/test-plotPARAFACmodel.R tests/testthat/test-reshapeData.R tests/testthat/test-multiwayCLR.R tests/testthat/test-utils.R tests/testthat/test-processDataCube.R tests/testthat/test-assessModelStability.R tests/testthat/test-plotModelMetric.R tests/testthat/test-corcondia.R tests/testthat/test-multiwayScale.R tests/testthat/test-importTreeSummarizedExperiment.R tests/testthat/test-importMicrobiotaProcess.R tests/testthat/test-parafac_gradient.R tests/testthat/test-calculateFMS.R tests/testthat/test-transformPARAFACloadings.R tests/testthat/test-importPhyloseq.R tests/testthat/test-parafac_fun.R tests/testthat/test-assessModelQuality.R tests/testthat/test-plotModelTCCs.R tests/testthat/test-initializePARAFAC.R tests/testthat/test-calculateVarExp.R tests/testthat/test-parafac.R tests/testthat/test-multiwayCenter.R vignettes/Fujita2023_analysis.Rmd vignettes/Shao2019_analysis.Rmd vignettes/PARAFAC_introduction.Rmd vignettes/vanderPloeg2024_analysis.Rmd man/assessModelStability.Rd man/calculateSparsity.Rd man/plotModelMetric.Rd man/vanderPloeg2024.Rd man/reshapeData.Rd man/parafac_fun.Rd man/multiwayCLR.Rd man/parafac.Rd man/initializePARAFAC.Rd man/reinflateTensor.Rd man/assessModelQuality.Rd man/multiwayCenter.Rd man/plotModelStability.Rd man/calculateVarExp.Rd man/reinflateFac.Rd man/flipLoadings.Rd man/corcondia.Rd man/plotPARAFACmodel.Rd man/pipe.Rd man/fac_to_vect.Rd man/plotModelTCCs.Rd man/importMicrobiotaProcess.Rd man/parafac_core_als.Rd man/Shao2019.Rd man/processDataCube.Rd man/parafac4microbiome-package.Rd man/multiwayScale.Rd man/parafac_gradient.Rd man/transformPARAFACloadings.Rd man/importPhyloseq.Rd man/calculateFMS.Rd man/calcVarExpPerComponent.Rd man/sortComponents.Rd man/importTreeSummarizedExperiment.Rd man/vect_to_fac.Rd man/Fujita2023.Rd