Man pages for LDATS
Latent Dirichlet Allocation Coupled with Time Series Analyses

AICcCalculate AICc
autocorr_plotProduce the autocorrelation panel for the TS diagnostic plot...
check_changepointsCheck that a set of change point locations is proper
check_controlCheck that a control list is proper
check_document_covariate_tableCheck that the document covariate table is proper
check_document_term_tableCheck that document term table is proper
check_formulaCheck that a formula is proper
check_formulasCheck that formulas vector is proper and append the response...
check_LDA_modelsCheck that LDA model input is proper
check_nchangepointsCheck that nchangepoints vector is proper
check_seedsCheck that nseeds value or seeds vector is proper
check_timenameCheck that the time vector is proper
check_topicsCheck that topics vector is proper
check_weightsCheck that weights vector is proper
count_tripsCount trips of the ptMCMC particles
diagnose_ptMCMCCalculate ptMCMC summary diagnostics
document_weightsCalculate document weights for a corpus
ecdf_plotProduce the posterior distribution ECDF panel for the TS...
est_changepointsUse ptMCMC to estimate the distribution of change point...
est_regressorsEstimate the distribution of regressors, unconditional on the...
expand_TSExpand the TS models across the factorial combination of LDA...
iftrueReplace if TRUE
jornadaJornada rodent data
LDA_msgCreate the model-running-message for an LDA
LDA_setRun a set of Latent Dirichlet Allocation models
LDA_set_controlCreate control list for set of LDA models
LDATSPackage to conduct two-stage analyses combining Latent...
LDA_TSRun a full set of Latent Dirichlet Allocations and Time...
LDA_TS_controlCreate the controls list for the LDATS model
logLik.LDA_VEMCalculate the log likelihood of a VEM LDA model fit
logLik.multinom_TS_fitLog likelihood of a multinomial TS model
logLik.TS_fitDetermine the log likelihood of a Time Series model
logsumexpCalculate the log-sum-exponential (LSE) of a vector
memoise_funLogical control on whether or not to memoise
messageqOptionally generate a message based on a logical input
mirror_vcovCreate a properly symmetric variance covariance matrix
modalvalueDetermine the mode of a distribution
multinom_TSFit a multinomial change point Time Series model
multinom_TS_chunkFit a multinomial Time Series model chunk
normalizeNormalize a vector
package_chunk_fitsPackage the output of the chunk-level multinomial models into...
package_LDA_setPackage the output from LDA_set
package_LDA_TSPackage the output of LDA_TS
package_TSSummarize the Time Series model
package_TS_on_LDAPackage the output of TS_on_LDA
plot.LDA_setPlot a set of LDATS LDA models
plot.LDA_TSPlot the key results from a full LDATS analysis
plot.LDA_VEMPlot the results of an LDATS LDA model
plot.TS_fitPlot an LDATS TS model
posterior_plotProduce the posterior distribution histogram panel for the TS...
prep_chunksPrepare the time chunk table for a multinomial change point...
prep_cptsInitialize and update the change point matrix used in the...
prep_idsInitialize and update the chain ids throughout the ptMCMC...
prep_LDA_controlSet the control inputs to include the seed
prep_pbarInitialize and tick through the progress bar
prep_proposal_distPre-calculate the change point proposal distribution for the...
prep_ptMCMC_inputsPrepare the inputs for the ptMCMC algorithm estimation of...
prep_savesPrepare and update the data structures to save the ptMCMC...
prep_temp_sequencePrepare the ptMCMC temperature sequence
prep_TS_dataPrepare the model-specific data to be used in the TS analysis...
print.LDA_TSPrint the selected LDA and TS models of LDA_TS object
print_model_run_messagePrint the message to the console about which combination of...
print.TS_fitPrint a Time Series model fit
print.TS_on_LDAPrint a set of Time Series models fit to LDAs
proposed_step_modsFit the chunk-level models to a time series, given a set of...
rho_linesAdd change point location lines to the time series plot
rodentsPortal rodent data
select_LDASelect the best LDA model(s) for use in time series
select_TSSelect the best Time Series model
set_gamma_colorsPrepare the colors to be used in the gamma time series
set_LDA_plot_colorsPrepare the colors to be used in the LDA plots
set_LDA_TS_plot_colsCreate the list of colors for the LDATS summary plot
set_rho_hist_colorsPrepare the colors to be used in the change point histogram
set_TS_summary_plot_colsCreate the list of colors for the TS summary plot
sim_LDA_dataSimulate LDA data from an LDA structure given parameters
sim_LDA_TS_dataSimulate LDA_TS data from LDA and TS model structures and...
sim_TS_dataSimulate TS data from a TS model structure given parameters
softmaxCalculate the softmax of a vector or matrix of values
step_chainsConduct a within-chain step of the ptMCMC algorithm
summarize_etasSummarize the regressor (eta) distributions
summarize_rhosSummarize the rho distributions
swap_chainsConduct a set of among-chain swaps for the ptMCMC algorithm
trace_plotProduce the trace plot panel for the TS diagnostic plot of a...
TSConduct a single multinomial Bayesian Time Series analysis
TS_controlCreate the controls list for the Time Series model
TS_diagnostics_plotPlot the diagnostics of the parameters fit in a TS model
TS_on_LDAConduct a set of Time Series analyses on a set of LDA models
TS_summary_plotCreate the summary plot for a TS fit to an LDA model
verify_changepoint_locationsVerify the change points of a multinomial time series model
LDATS documentation built on Sept. 19, 2023, 5:08 p.m.