.Rbuildignore
.gitignore
.readthedocs.yaml
DESCRIPTION
NAMESPACE
NEWS.md
R/1_spear.R
R/2_helpers.R
R/3_SPEARobject.R
R/RcppExports.R
R/data.R
README.md
SPEAR_github.Rproj
data/su_covid19_multiomics.rda
docs/Makefile
docs/SPEAR.md
docs/_build/doctrees/SPEAR.doctree
docs/_build/doctrees/environment.pickle
docs/_build/doctrees/functions/SPEAR.help.doctree
docs/_build/doctrees/functions/add.data.doctree
docs/_build/doctrees/functions/assess.doctree
docs/_build/doctrees/functions/check.fit.doctree
docs/_build/doctrees/functions/check.fold.ids.doctree
docs/_build/doctrees/functions/color.text.doctree
docs/_build/doctrees/functions/create.params.doctree
docs/_build/doctrees/functions/cv.evaluate.doctree
docs/_build/doctrees/functions/estimate_num_factors.doctree
docs/_build/doctrees/functions/generate.fold.ids.doctree
docs/_build/doctrees/functions/get.contributions.doctree
docs/_build/doctrees/functions/get.correlation.matrix.doctree
docs/_build/doctrees/functions/get.cv.loss.doctree
docs/_build/doctrees/functions/get.data.doctree
docs/_build/doctrees/functions/get.factor.scores.doctree
docs/_build/doctrees/functions/get.factor.scores.manual.doctree
docs/_build/doctrees/functions/get.features.doctree
docs/_build/doctrees/functions/get.misclassification.doctree
docs/_build/doctrees/functions/get.predictions.doctree
docs/_build/doctrees/functions/get.weights.doctree
docs/_build/doctrees/functions/get.widx.from.method.doctree
docs/_build/doctrees/functions/impute.z.doctree
docs/_build/doctrees/functions/load.SPEARobject.doctree
docs/_build/doctrees/functions/make.SPEARobject.doctree
docs/_build/doctrees/functions/one_hot_encode.doctree
docs/_build/doctrees/functions/plot.circos.doctree
docs/_build/doctrees/functions/plot.class.probabilities.doctree
docs/_build/doctrees/functions/plot.coef.prob.doctree
docs/_build/doctrees/functions/plot.coefficients.doctree
docs/_build/doctrees/functions/plot.contributions.doctree
docs/_build/doctrees/functions/plot.cv.loss.doctree
docs/_build/doctrees/functions/plot.embedding.doctree
docs/_build/doctrees/functions/plot.factor.correlations.doctree
docs/_build/doctrees/functions/plot.factor.scores.doctree
docs/_build/doctrees/functions/plot.feature.expression.doctree
docs/_build/doctrees/functions/plot.features.doctree
docs/_build/doctrees/functions/plot.network.doctree
docs/_build/doctrees/functions/plot.predictions.doctree
docs/_build/doctrees/functions/plot.probabilities.doctree
docs/_build/doctrees/functions/preparation.doctree
docs/_build/doctrees/functions/print.out.doctree
docs/_build/doctrees/functions/run.cv.spear.doctree
docs/_build/doctrees/functions/run.spear.doctree
docs/_build/doctrees/functions/save.model.doctree
docs/_build/doctrees/functions/set.color.scheme.doctree
docs/_build/doctrees/functions/set.response.doctree
docs/_build/doctrees/functions/set.weights.doctree
docs/_build/doctrees/functions/simulate_data.doctree
docs/_build/doctrees/functions/spear.doctree
docs/_build/doctrees/functions/update.dimnames.doctree
docs/_build/doctrees/functions/update_model.doctree
docs/_build/doctrees/index.doctree
docs/_build/doctrees/vignettes/01_SPEAR_Quick_Walkthrough.doctree
docs/_build/doctrees/vignettes/02_Preparing_Data_for_SPEAR.doctree
docs/_build/doctrees/vignettes/03_Making_a_SPEARobject.doctree
docs/_build/doctrees/vignettes/04_Running_SPEAR.doctree
docs/_build/doctrees/vignettes/05_SPEAR_plots.doctree
docs/_build/doctrees/vignettes/06_SPEARgaussian.doctree
docs/_build/doctrees/vignettes/07_SPEARordinal.doctree
docs/_build/doctrees/vignettes/SPEAR.doctree
docs/_build/html/.buildinfo
docs/_build/html/SPEAR.html
docs/_build/html/_sources/SPEAR.md.txt
docs/_build/html/_sources/functions/SPEAR.help.md.txt
docs/_build/html/_sources/functions/add.data.md.txt
docs/_build/html/_sources/functions/assess.md.txt
docs/_build/html/_sources/functions/check.fit.md.txt
docs/_build/html/_sources/functions/check.fold.ids.md.txt
docs/_build/html/_sources/functions/color.text.md.txt
docs/_build/html/_sources/functions/create.params.md.txt
docs/_build/html/_sources/functions/cv.evaluate.md.txt
docs/_build/html/_sources/functions/estimate_num_factors.md.txt
docs/_build/html/_sources/functions/generate.fold.ids.md.txt
docs/_build/html/_sources/functions/get.contributions.md.txt
docs/_build/html/_sources/functions/get.correlation.matrix.md.txt
docs/_build/html/_sources/functions/get.cv.loss.md.txt
docs/_build/html/_sources/functions/get.data.md.txt
docs/_build/html/_sources/functions/get.factor.scores.manual.md.txt
docs/_build/html/_sources/functions/get.factor.scores.md.txt
docs/_build/html/_sources/functions/get.features.md.txt
docs/_build/html/_sources/functions/get.misclassification.md.txt
docs/_build/html/_sources/functions/get.predictions.md.txt
docs/_build/html/_sources/functions/get.weights.md.txt
docs/_build/html/_sources/functions/get.widx.from.method.md.txt
docs/_build/html/_sources/functions/impute.z.md.txt
docs/_build/html/_sources/functions/load.SPEARobject.md.txt
docs/_build/html/_sources/functions/make.SPEARobject.md.txt
docs/_build/html/_sources/functions/one_hot_encode.md.txt
docs/_build/html/_sources/functions/plot.circos.md.txt
docs/_build/html/_sources/functions/plot.class.probabilities.md.txt
docs/_build/html/_sources/functions/plot.coef.prob.md.txt
docs/_build/html/_sources/functions/plot.coefficients.md.txt
docs/_build/html/_sources/functions/plot.contributions.md.txt
docs/_build/html/_sources/functions/plot.cv.loss.md.txt
docs/_build/html/_sources/functions/plot.embedding.md.txt
docs/_build/html/_sources/functions/plot.factor.correlations.md.txt
docs/_build/html/_sources/functions/plot.factor.scores.md.txt
docs/_build/html/_sources/functions/plot.feature.expression.md.txt
docs/_build/html/_sources/functions/plot.features.md.txt
docs/_build/html/_sources/functions/plot.network.md.txt
docs/_build/html/_sources/functions/plot.predictions.md.txt
docs/_build/html/_sources/functions/plot.probabilities.md.txt
docs/_build/html/_sources/functions/preparation.md.txt
docs/_build/html/_sources/functions/print.out.md.txt
docs/_build/html/_sources/functions/run.cv.spear.md.txt
docs/_build/html/_sources/functions/run.spear.md.txt
docs/_build/html/_sources/functions/save.model.md.txt
docs/_build/html/_sources/functions/set.color.scheme.md.txt
docs/_build/html/_sources/functions/set.response.md.txt
docs/_build/html/_sources/functions/set.weights.md.txt
docs/_build/html/_sources/functions/simulate_data.md.txt
docs/_build/html/_sources/functions/spear.md.txt
docs/_build/html/_sources/functions/update.dimnames.md.txt
docs/_build/html/_sources/functions/update_model.md.txt
docs/_build/html/_sources/index.rst.txt
docs/_build/html/_sources/vignettes/01_SPEAR_Quick_Walkthrough.md.txt
docs/_build/html/_sources/vignettes/02_Preparing_Data_for_SPEAR.md.txt
docs/_build/html/_sources/vignettes/03_Making_a_SPEARobject.md.txt
docs/_build/html/_sources/vignettes/04_Running_SPEAR.md.txt
docs/_build/html/_sources/vignettes/05_SPEAR_plots.md.txt
docs/_build/html/_sources/vignettes/06_SPEARgaussian.md.txt
docs/_build/html/_sources/vignettes/07_SPEARordinal.md.txt
docs/_build/html/_sources/vignettes/SPEAR.md.txt
docs/_build/html/_static/_sphinx_javascript_frameworks_compat.js
docs/_build/html/_static/basic.css
docs/_build/html/_static/css/badge_only.css
docs/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff
docs/_build/html/_static/css/fonts/Roboto-Slab-Bold.woff2
docs/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff
docs/_build/html/_static/css/fonts/Roboto-Slab-Regular.woff2
docs/_build/html/_static/css/fonts/fontawesome-webfont.eot
docs/_build/html/_static/css/fonts/fontawesome-webfont.svg
docs/_build/html/_static/css/fonts/fontawesome-webfont.ttf
docs/_build/html/_static/css/fonts/fontawesome-webfont.woff
docs/_build/html/_static/css/fonts/fontawesome-webfont.woff2
docs/_build/html/_static/css/fonts/lato-bold-italic.woff
docs/_build/html/_static/css/fonts/lato-bold-italic.woff2
docs/_build/html/_static/css/fonts/lato-bold.woff
docs/_build/html/_static/css/fonts/lato-bold.woff2
docs/_build/html/_static/css/fonts/lato-normal-italic.woff
docs/_build/html/_static/css/fonts/lato-normal-italic.woff2
docs/_build/html/_static/css/fonts/lato-normal.woff
docs/_build/html/_static/css/fonts/lato-normal.woff2
docs/_build/html/_static/css/theme.css
docs/_build/html/_static/doctools.js
docs/_build/html/_static/documentation_options.js
docs/_build/html/_static/file.png
docs/_build/html/_static/jquery-3.6.0.js
docs/_build/html/_static/jquery.js
docs/_build/html/_static/js/badge_only.js
docs/_build/html/_static/js/html5shiv-printshiv.min.js
docs/_build/html/_static/js/html5shiv.min.js
docs/_build/html/_static/js/theme.js
docs/_build/html/_static/language_data.js
docs/_build/html/_static/minus.png
docs/_build/html/_static/plus.png
docs/_build/html/_static/pygments.css
docs/_build/html/_static/searchtools.js
docs/_build/html/_static/sphinx_highlight.js
docs/_build/html/_static/underscore-1.13.1.js
docs/_build/html/_static/underscore.js
docs/_build/html/functions/SPEAR.help.html
docs/_build/html/functions/add.data.html
docs/_build/html/functions/assess.html
docs/_build/html/functions/check.fit.html
docs/_build/html/functions/check.fold.ids.html
docs/_build/html/functions/color.text.html
docs/_build/html/functions/create.params.html
docs/_build/html/functions/cv.evaluate.html
docs/_build/html/functions/estimate_num_factors.html
docs/_build/html/functions/generate.fold.ids.html
docs/_build/html/functions/get.contributions.html
docs/_build/html/functions/get.correlation.matrix.html
docs/_build/html/functions/get.cv.loss.html
docs/_build/html/functions/get.data.html
docs/_build/html/functions/get.factor.scores.html
docs/_build/html/functions/get.factor.scores.manual.html
docs/_build/html/functions/get.features.html
docs/_build/html/functions/get.misclassification.html
docs/_build/html/functions/get.predictions.html
docs/_build/html/functions/get.weights.html
docs/_build/html/functions/get.widx.from.method.html
docs/_build/html/functions/impute.z.html
docs/_build/html/functions/load.SPEARobject.html
docs/_build/html/functions/make.SPEARobject.html
docs/_build/html/functions/one_hot_encode.html
docs/_build/html/functions/plot.circos.html
docs/_build/html/functions/plot.class.probabilities.html
docs/_build/html/functions/plot.coef.prob.html
docs/_build/html/functions/plot.coefficients.html
docs/_build/html/functions/plot.contributions.html
docs/_build/html/functions/plot.cv.loss.html
docs/_build/html/functions/plot.embedding.html
docs/_build/html/functions/plot.factor.correlations.html
docs/_build/html/functions/plot.factor.scores.html
docs/_build/html/functions/plot.feature.expression.html
docs/_build/html/functions/plot.features.html
docs/_build/html/functions/plot.network.html
docs/_build/html/functions/plot.predictions.html
docs/_build/html/functions/plot.probabilities.html
docs/_build/html/functions/preparation.html
docs/_build/html/functions/print.out.html
docs/_build/html/functions/run.cv.spear.html
docs/_build/html/functions/run.spear.html
docs/_build/html/functions/save.model.html
docs/_build/html/functions/set.color.scheme.html
docs/_build/html/functions/set.response.html
docs/_build/html/functions/set.weights.html
docs/_build/html/functions/simulate_data.html
docs/_build/html/functions/spear.html
docs/_build/html/functions/update.dimnames.html
docs/_build/html/functions/update_model.html
docs/_build/html/genindex.html
docs/_build/html/index.html
docs/_build/html/objects.inv
docs/_build/html/search.html
docs/_build/html/searchindex.js
docs/_build/html/vignettes/01_SPEAR_Quick_Walkthrough.html
docs/_build/html/vignettes/02_Preparing_Data_for_SPEAR.html
docs/_build/html/vignettes/03_Making_a_SPEARobject.html
docs/_build/html/vignettes/04_Running_SPEAR.html
docs/_build/html/vignettes/05_SPEAR_plots.html
docs/_build/html/vignettes/06_SPEARgaussian.html
docs/_build/html/vignettes/07_SPEARordinal.html
docs/_build/html/vignettes/SPEAR.html
docs/conf.py
docs/functions/SPEAR.help.md
docs/functions/add.data.md
docs/functions/assess.md
docs/functions/check.fit.md
docs/functions/check.fold.ids.md
docs/functions/color.text.md
docs/functions/create.params.md
docs/functions/cv.evaluate.md
docs/functions/estimate_num_factors.md
docs/functions/generate.fold.ids.md
docs/functions/get.contributions.md
docs/functions/get.correlation.matrix.md
docs/functions/get.cv.loss.md
docs/functions/get.data.md
docs/functions/get.factor.scores.manual.md
docs/functions/get.factor.scores.md
docs/functions/get.features.md
docs/functions/get.misclassification.md
docs/functions/get.predictions.md
docs/functions/get.weights.md
docs/functions/get.widx.from.method.md
docs/functions/impute.z.md
docs/functions/load.SPEARobject.md
docs/functions/make.SPEARobject.md
docs/functions/one_hot_encode.md
docs/functions/plot.circos.md
docs/functions/plot.class.probabilities.md
docs/functions/plot.coef.prob.md
docs/functions/plot.coefficients.md
docs/functions/plot.contributions.md
docs/functions/plot.cv.loss.md
docs/functions/plot.embedding.md
docs/functions/plot.factor.correlations.md
docs/functions/plot.factor.scores.md
docs/functions/plot.feature.expression.md
docs/functions/plot.features.md
docs/functions/plot.network.md
docs/functions/plot.predictions.md
docs/functions/plot.probabilities.md
docs/functions/preparation.md
docs/functions/print.out.md
docs/functions/run.cv.spear.md
docs/functions/run.spear.md
docs/functions/save.model.md
docs/functions/set.color.scheme.md
docs/functions/set.response.md
docs/functions/set.weights.md
docs/functions/simulate_data.md
docs/functions/spear.md
docs/functions/update.dimnames.md
docs/functions/update_model.md
docs/index.rst
docs/make.bat
docs/requirements.txt
docs/vignettes/01_SPEAR_Quick_Walkthrough.md
docs/vignettes/02_Preparing_Data_for_SPEAR.md
docs/vignettes/03_Making_a_SPEARobject.md
docs/vignettes/04_Running_SPEAR.md
docs/vignettes/05_SPEAR_plots.md
docs/vignettes/06_SPEARgaussian.md
docs/vignettes/07_SPEARordinal.md
docs/vignettes/SPEAR.md
man/add.data.Rd
man/assess.Rd
man/check.fit.Rd
man/check.fold.ids.Rd
man/create.params.Rd
man/cv.evaluate.Rd
man/encode.ordinal.Rd
man/estimate.num.factors.Rd
man/figures/github.png
man/figures/logo.png
man/figures/twitter.png
man/generate.fold.ids.Rd
man/generate.spear.ids.Rd
man/get.Y.Rd
man/get.analyte.scores.Rd
man/get.concatenated.X.Rd
man/get.cv.loss.Rd
man/get.data.Rd
man/get.factor.contributions.Rd
man/get.factor.scores.Rd
man/get.predictions.Rd
man/get.signatures.Rd
man/get.variance.explained.Rd
man/get.widx.from.method.Rd
man/new.spear.Rd
man/one.hot.encode.multinomial.Rd
man/plot.cv.loss.Rd
man/plot.factor.contributions.Rd
man/plot.factor.scores.Rd
man/plot.variance.explained.Rd
man/print.out.Rd
man/remove.data.Rd
man/set.color.scheme.Rd
man/set.response.Rd
man/set.weights.Rd
man/spear.Rd
man/train.spear.Rd
man/update.dimnames.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
src/.Rhistory
src/Makevars.win
src/RcppExports.cpp
src/RcppExports.o
src/SPEAR.so
src/_spear.cpp
src/_spear.o
src/approximations.cpp
src/approximations.h
src/approximations.o
src/subroutines.cpp
src/subroutines.h
src/subroutines.o
vignettes/.gitignore
vignettes/SPEAR_vignette.Rmd