Man pages for weecology/LDATS
Detect Community-Types from Data and Identify Break Points

aic_modelAIC model selection for LDA using VEM method
aic_model_gibbsAIC model selection for LDA using Gibbs sampler method
annual_histHistogram showing percentage of MCMC samples that contained a...
batch_LDARun a batch of LDA models in parallel
calculate_LDA_distanceCalculates multiple LDA models using different seeds
changepoint_modelModel to locate given number of change points in an LDA model...
chpoint_histogramPlot histogram of changepoint locations - WIP
community_compositionMake table of species composition of topics
count_tripsNumber of times the particle went from hottest chain to the...
cp_hists_fileSave out a multi-panel histogram of the change points for a...
cp_modelsRun a suite of changepoint models for the same data set
create_rodent_tableCreate rodent species table
create_sim_data_2topiccreate simulated data for demonstrating LDA analysis 2 topics
create_sim_data_2topic_nonuniformvariation: create simulated data for demonstrating LDA...
create_sim_data_3topiccreate simulated data for demonstrating LDA analysis 3 topics
downsampleDownsample a time series
find_changepoint_locationFind changepoint locations
fit_chunk_non_memoizedFit a model to dates in (start,end] and return the log...
fit_sectionFit a model to dates in (start,end] and return data frame for...
get_ll_non_memoizedGet the log-likelihood associated with a set of breakpoints
get_ll_non_memoized_plotadapted get_ll_non_memoized for plotting purposes
HellingerCompute hellinger distance
LDA_analysis_gibbsRun through whole pipeline of LDA analysis, Gibbs method -...
LDA_analysis_VEMRun through whole pipeline of LDA analysis, VEM method
min_HFind the configuration with the minimum Hellinger distance...
ntopic_hist_fileSave out a histogram of the topics for a dataset
plot_community_compositionPlot species composition of topics
plot_community_composition_ggggplot version of plot_community_composition
plot_component_communitiesPlot component communities
plot_component_communities_gibbsPlot component communities
plot_component_communities_gibbs_crediblePlot component communities including credible intervals -...
plot_component_communities_smoothPlot component communities - smoothed
plot_gammaPlot gamma
plot_sectionsplot all the fit sections
repeat_VEMrepeat VEM a bunch of times with different seeds and...
weecology/LDATS documentation built on Jan. 22, 2018, 2:27 a.m.