Detect Community-Types from Data and Identify Break Points

aic_model | AIC model selection for LDA using VEM method |

aic_model_gibbs | AIC model selection for LDA using Gibbs sampler method |

annual_hist | Histogram showing percentage of MCMC samples that contained a... |

batch_LDA | Run a batch of LDA models in parallel |

calculate_LDA_distance | Calculates multiple LDA models using different seeds |

changepoint_model | Model to locate given number of change points in an LDA model... |

chpoint_histogram | Plot histogram of changepoint locations - WIP |

community_composition | Make table of species composition of topics |

count_trips | Number of times the particle went from hottest chain to the... |

cp_hists_file | Save out a multi-panel histogram of the change points for a... |

cp_models | Run a suite of changepoint models for the same data set |

create_rodent_table | Create rodent species table |

create_sim_data_2topic | create simulated data for demonstrating LDA analysis 2 topics |

create_sim_data_2topic_nonuniform | variation: create simulated data for demonstrating LDA... |

create_sim_data_3topic | create simulated data for demonstrating LDA analysis 3 topics |

downsample | Downsample a time series |

find_changepoint_location | Find changepoint locations |

fit_chunk_non_memoized | Fit a model to dates in (start,end] and return the log... |

fit_section | Fit a model to dates in (start,end] and return data frame for... |

get_ll_non_memoized | Get the log-likelihood associated with a set of breakpoints |

get_ll_non_memoized_plot | adapted get_ll_non_memoized for plotting purposes |

Hellinger | Compute hellinger distance |

LDA_analysis_gibbs | Run through whole pipeline of LDA analysis, Gibbs method -... |

LDA_analysis_VEM | Run through whole pipeline of LDA analysis, VEM method |

min_H | Find the configuration with the minimum Hellinger distance... |

ntopic_hist_file | Save out a histogram of the topics for a dataset |

plot_community_composition | Plot species composition of topics |

plot_community_composition_gg | ggplot version of plot_community_composition |

plot_component_communities | Plot component communities |

plot_component_communities_gibbs | Plot component communities |

plot_component_communities_gibbs_credible | Plot component communities including credible intervals -... |

plot_component_communities_smooth | Plot component communities - smoothed |

plot_gamma | Plot gamma |

plot_sections | plot all the fit sections |

repeat_VEM | repeat VEM a bunch of times with different seeds and... |

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