Files in AlmaasLab/micInt
Find microbial interactions
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
NAMESPACE
R/OTU_stats.R
R/ccrepe.R
R/ccrepe.utilities.R
R/ccrepeSampleTestFunction.R
R/ccrepe_analysis.R
R/cross_validate.R
R/data.R
R/data_refinement.R
R/integralSystem.R
R/nc.score.R
R/nc.score.utilities.R
R/outputargs.R
R/package.R
R/phyloseq_subset.R
R/plot_trajectory.R
R/ridge_fit.R
R/significance_pipeline.R
R/sim_measure_class.R
R/similarity_measures.R
R/solve_system.R
R/time_series_class.R
README.md
data/seawater.RData
debug.R
dependence_script.R
inst/CITATION
inst/citation.bib
man/OTU_stats.Rd
man/OTU_time_series-class.Rd
man/as.edgelist.interaction_table.Rd
man/autoplot.cvLV.Rd
man/autoplot.interaction_table.Rd
man/ccrepe-package.Rd
man/ccrepe.Rd
man/ccrepeSampleTestFunction.Rd
man/ccrepe_analysis.Rd
man/collapse_taxonomy.Rd
man/countInteractions.Rd
man/create_interaction_table.Rd
man/create_prefix.Rd
man/cv.LV.Rd
man/edgelist.Rd
man/integralSystem.Rd
man/mean_scale.Rd
man/micInt-package.Rd
man/nc.score.Rd
man/noisify.Rd
man/output_ccrepe_data.Rd
man/plot_trajectory.Rd
man/predict.LV.Rd
man/ratio_shared_interactions.Rd
man/refine_data.Rd
man/ridge_fit.Rd
man/runAnalysis.Rd
man/scale_by_column.Rd
man/seawater.Rd
man/sim.measure-class.Rd
man/sim.measure.attributes-class.Rd
man/similarity_measures.Rd
man/stack_equations.Rd
man/subdivide_by_environment.Rd
man/summary.interaction_table.Rd
man/write.interaction_table.Rd
micInt.Rproj
scetch.R
tests/create_reference.R
tests/nc_score_input_test.txt
tests/p.values.results.txt
tests/p.values.results_absolute.txt
tests/q.values.results.txt
tests/q.values.results_absolute.txt
tests/sim.score.results.txt
tests/sim.score.results_absolute.txt
tests/testthat.R
tests/testthat/test_LV.R
tests/testthat/test_ReBoot.R
tests/testthat/test_ccrepe.R
tests/testthat/test_nc_score.R
tests/testthat/test_utils.R
tests/testthat/toy_phyloseq.rds
tests/z.stat.results.txt
tests/z.stat.results_absolute.txt
vignettes/ccrepe-concordance.tex
vignettes/ccrepe.Rnw
vignettes/ccrepe.bib
