Man pages for kimberlyroche/rulesoflife
| build_between_within_distributions | Sample to construct between- and within-host distributions of... |
| calc_consensus_sign | Calculate a consensus CLR correlation sign for a given... |
| calc_se_decay | Define bandwidth of squared exponential kernel |
| calc_universality_score | Calculate a score (0.0 to 1.0) for the "universality" of... |
| calc_universality_score_taxon | Calculate a score (0.0 to 1.0) for the "universality" of... |
| check_dir | Create output directory/ies that may not already exist |
| convert_alr_Sigma_clr | Convert an ALR covariance matrix to a CLR correlation matrix |
| convert_series_clr | CLR-convert a set of species abundance series, calculate... |
| downsample_counts | Simulate count data from the generative model, downsampling... |
| filter_data | This function loads the raw ABRP data (as a phyloseq object)... |
| filter_joint_zeros | Return a vector indicating whether the frequency of 0-0... |
| fit_GP | Fit MLN Gaussian process model to a given host's series using... |
| generate_env_link | Generate matrix that encodes per-species response to... |
| generate_highcontrast_palette | Generate a random high-contrast palette (for bar plotting) |
| generate_highcontrast_palette2 | Generate a color palette suitable for stacked bar plots given... |
| generate_innate_params | Generate baseline abundances and cooperative/competitive... |
| generate_palette | Generate a color palette suitable for stacked bar plots given... |
| generate_scrambled_data | Permute the data within samples, maintaining relative... |
| generate_series | Use a generalized stochastic Lotka-Volterra model to... |
| get_Gamma | Define a kernel (function) over samples |
| get_host_social_groups | Assign host social group as social group in which a given... |
| get_mean_clr_abundance | Get the mean CLR abundance for all taxa |
| get_paired_trajectories | Pull a collection date-aligned trajectories for a pair of... |
| get_predictions_host_list | Pulling a collection date-aligned trajectories for a pair of... |
| get_reference_hosts | Find host with largest numbers of samples in each social... |
| get_tax_label | Return a human-readable taxon label |
| get_trajectory_df | Pull collection date-aligned trajectories from a given host's... |
| get_Xi | Set up a basic ALR prior |
| hello | Hello, World! |
| load_data | This function wrangles the filtered ABRP data and metadata |
| load_fit | Pull a fitted model object from the specified directory |
| load_predictions | Pull a prediction object from the specified directory |
| load_scrambled_data | Load scrambled data |
| order_rug_col_phylogenetic | Reorder columns of the "rug" based on phylogenetic distance |
| order_rug_cols_mean_abundance | Reorder columns of the "rug" from taxa with the least to most... |
| order_rug_row_baseline | Reorder rows of the "rug" based on Aitchison distance between... |
| order_rug_row_diversity | Reorder rows of the "rug" based on average taxonomic average... |
| order_rug_row_group | Reorder rows of the "rug" based on primary social group |
| order_rug_row_pedigree | Reorder rows of the "rug" based on known pedigree |
| percent_to_k | Converts a percent to a relative count |
| plot_aligned_trajectories | Render date-aligned trajectories for a pair of taxa and a... |
| plot_clr_vs_diet | Render line plot of a given CLR taxon against diet PC1 for a... |
| plot_correlation_histogram | Renders the host x pairwise associations as a histogram |
| plot_downsampling | Boxplot data simulated from downsample_counts() |
| plot_enrichment | Plot relative representation of ASV pairs (using family... |
| plot_enrichment_old | Plot relative representation of ASV pairs (using family... |
| 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_lines | Plot a gLV simulation as lines |
| plot_kernel_or_cov_matrix | Renders a kernel or covariance matrix as a square heatmap. |
| plot_rug | Renders the "rug" (host x pairwise association matrix) as a... |
| plot_trajectories_top_pairs | Render date-aligned trajectories for the most universal... |
| plot_trajectory | Visualize inferred logratio trajectories (CLR by default) |
| predict_GP_mean | Predict mean trajectories (Lambda) for all CLR taxa in a... |
| predict_trajectory | Draw predictions from a fido::basset model in the CLR... |
| prune_data | Description TBD |
| pull_series | Pull the predicted host x taxon series from a data.frame of... |
| pull_Sigmas | Gather all host ASV-ASV (MAP) correlation matrices into a 3D... |
| render_universal_pairs | Utility function to plot aligned series for the pair of taxa... |
| rug_phylogenetic_distances | Calculate phylogenetic distances on pairs of taxa |
| sequence_distance | Compute sequence distances across ASVs |
| simulate_series | Simulate series for one host |
| summarize_Sigmas | Summarize the pairwise correlations (optionally via... |
