Man pages for kimberlyroche/ROL
What the package does (short line)
| agglomerate_data | Agglomerate ABRP 16S data to desired taxonomic level |
| assign_concise_taxonomy | Get concise taxonomic labels for microbes |
| build_design_matrix | Build the design matrix |
| build_design_matrix_predict | Build the design matrix for prediction by interpolating... |
| calc_autocorrelation | Calculate lagged autocorrelation |
| calc_microbe_universality_score | Calculate a score (0.0 to 1.0) for the "universality" of... |
| calc_posterior_distance_row | Calculate Riemannian distances between one sample and all... |
| calc_posterior_distances | Calculate distances between all posterior samples of either... |
| calc_se_decay | Define bandwidth of squared exponential kernel |
| calculate_emd | Calculate Earth Mover's Distance between two 2D summaries |
| calc_universality_score | Calculate a score (0.0 to 1.0) for the "universality" of... |
| check_output_dir | Create output directory/ies that may not already exist |
| convert_series_clr | CLR-convert a set of species abundance series, calculate... |
| embed_posteriors | Embeds posterior samples using MDS and a pre-calculated... |
| filter_data | Filter out low abundance taxa |
| filter_taxa_2D_summary | Given a count table, label taxa with at least 0.1... |
| fit_DLM | Fit a dynamic linear model to a single host series using... |
| fit_GP | Fit a Gaussian process to a single host series using basset |
| fix_MAP_dims | Trivially expands the dimensions of the posterior estimates... |
| fold_error | Utility function to calculate fold change (as error) |
| formalize_parameters | Generate empirical estimates for variance components to use... |
| generate_env_link | Generate matrix that encodes per-species response to... |
| generate_highcontrast_palette | Generate a random high-contrast palette (for bar plotting) |
| generate_innate_params | Generate baseline abundances and cooperative/competitive... |
| generate_series | Use a generalized stochastic Lotka-Volterra model to... |
| get_all_vs_one_correlations | Get correlations between one microbe and all others at... |
| get_deepest_assignment | Get highest taxonomic level to which a microbe is resolved... |
| get_fitted_model_list | Pulls a list of fitted basset models from the designated... |
| get_Gamma | Define a kernel (function) over samples |
| get_other_labels | Get other annotations (e.g. sample number) for hosts in data... |
| get_pairwise_correlations | Get all pairwise (MAP) correlations between microbes at... |
| get_pairwise_proportionalities | Get all pairwise (MAP) proportionalities between microbes at... |
| get_Rdist_pair | Calculate pairwise distances (slowly) by calling... |
| get_taxonomy | Get taxonomy, reordered to reflect altered ALR reference |
| get_universal_interactions | Identify and plot "universal" interactions at the designated... |
| get_Xi | Set up a basic ALR prior |
| load_ABRP_2D_summary | Parse correlation matrix for Amboseli data |
| load_Caporaso_2D_summary | Load data from Caporaso et al. (2011) |
| load_data | Load ABRP 16S data and filter out low abundance taxa |
| load_David_2D_summary | Load data from David et al. (2014) |
| load_DethlefsenRelman_2D_summary | Load data from Dethlefsen & Relman (2011) |
| load_DIABIMMUNE_2D_summary | Load data from DIABIMMUNE study |
| load_full_posteriors | Load full posterior estimates of microbial covariances from... |
| load_Grossart_2D_summary | Load data from Grossart German lakes study |
| load_Johnson_2D_summary | Load data from Johnson et al. (2019) |
| load_MAP_estimates | Load MAP estimates of microbial covariances from fitted... |
| load_McMahon_deep_2D_summary | Load hypolimnion (deep water) data from McMahon Wisconsin, US... |
| load_McMahon_shallow_2D_summary | Load epilimnion (shallow water) data from McMahon Wisconsin,... |
| load_outcomes | Loads fitness annotations associated with hosts from file |
| log_rmse | Utility function to calculate RMSE |
| n_pairwise_combos | Utility function to calculate the number of unique... |
| PER | Periodic kernel |
| perform_cv | Perform k-fold cross-validation for a given host and kernel... |
| plot_axes | Plot a pair of principal coordinates |
| plot_bars | Plot relative abundances as stacked bars |
| plot_bounded_autocorrelation | Renders autocorrelation plot with uncertainty estimates |
| plot_gLV_bars | Plot a random 50-day segment from a gLV simulation |
| plot_gLV_heatmap | Plot a gLV simulation as a heatmap |
| plot_gLV_hockeystick | Plot a gLV simulation as a 2D summary (hockeystick) |
| plot_gLV_lines | Plot a gLV simulation as lines |
| plot_interaction_heatmap | Plot heatmap over all pairwise (MAP) correlations between... |
| plot_MAP_covariance | Plot MAP covariance matrix for designated host |
| plot_mean_autocorrelation | Renders autocorrelation plot (without uncertainty estimates) |
| plot_ordination | Plot first several principle coordinates of ordination |
| plot_posterior_predictive | Plot posterior predictive intervals of Eta (denoised ALR... |
| plot_timecourse | Render bar plots for an individual host's series |
| rcppeigen_hello_world | Set of functions in example RcppEigen package |
| read_file | Load file with existence check |
| Riemann_dist_pair | Calculate distances between positive-definite covariance... |
| Riemann_dist_samples | Calculate distances between a matrix of positive-definite... |
| Riemann_dist_sets | Calculate distances between all pairs of samples from two... |
| ROL_package | ROL: Code base for Rules of Life microbial dynamics analysis |
| ROL-package | What the package does (short line) |
| summarize_all_pairs_2D | Summarizes a matrix of correlations (rows are hosts, columns... |
| summarize_pairs_2D | Helper function for hockeystick plot that calculates a 2D... |
