Man pages for AlmaasLab/micInt
Find microbial interactions
| as.edgelist.interaction_table | Creates an 'igraph' object from 'interaction_table' |
| autoplot.cvLV | Create cross-validation colorplot |
| autoplot.interaction_table | autoplot.interaction_table |
| ccrepe | Calculates compositionality-corrected p-values and q-values... |
| ccrepe_analysis | Conduct ccrepe analysis |
| ccrepe-package | A package for analysis of sparse compositional data. Allows... |
| ccrepeSampleTestFunction | ccrepeSampleTestFunction - Simple example of a test measurent... |
| collapse_taxonomy | Collapse taxonomy into single strings |
| countInteractions | countInteractions |
| create_interaction_table | Create table of significant interactions |
| create_prefix | create_prefix |
| cv.LV | Cross-validate fit for Lotka-Volterra coefficients |
| edgelist | Convert an object to a list of edges |
| integralSystem | Make Lotka-Volterra coefficient system |
| mean_scale | mean_scale |
| micInt-package | micInt: Find microbial interactions |
| nc.score | nc.score |
| noisify | Noisify |
| OTU_stats | OTU statistics |
| OTU_time_series-class | Time series class for OTU tables |
| output_ccrepe_data | output_ccrepe_data |
| plot_trajectory | Plot trajectory for time series |
| predict.LV | Predict trajectory of a Lotka-Volterra system from estimated... |
| ratio_shared_interactions | ratio_shared_interactions |
| refine_data | Refine raw OTU table |
| ridge_fit | Solve OTU equation systems by ridge regularization |
| runAnalysis | Run an integrated co-occurence analysis for a microbial... |
| scale_by_column | Scale a phyloseq object |
| seawater | An example dataset |
| similarity_measures | Get premade similarity measure objects |
| sim.measure.attributes-class | Attributes of similarity measures |
| sim.measure-class | Similarity measure |
| stack_equations | Stack equations from different time series |
| subdivide_by_environment | Nest phyloseq objects according to sample variables |
| summary.interaction_table | Create summary of 'interaction_table' |
| write.interaction_table | write.interaction_table |
