Files in weecology/LDATS
Latent Dirichlet Allocation Coupled with Time Series Analyses
.DS_Store
.Rbuildignore
.gitignore
.travis.yml
.zenodo.json
CODE_OF_CONDUCT.md
CONTRIBUTING.md
DESCRIPTION
LDATS_model.pdf
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/LDA.R
R/LDATS.R
R/LDA_TS.R
R/LDA_TS_plots.R
R/LDA_plots.R
R/TS.R
R/TS_on_LDA.R
R/TS_plots.R
R/data.R
R/multinom_TS.R
R/ptMCMC.R
R/simulate.R
R/utilities.R
README.md
_pkgdown.yml
cran-comments.md
data/jornada.RData
data/rodents.RData
doc/LDATS_codebase.R
doc/LDATS_codebase.Rmd
doc/LDATS_codebase.html
doc/paper-comparison.R
doc/paper-comparison.Rmd
doc/paper-comparison.html
doc/rodents-example.R
doc/rodents-example.Rmd
doc/rodents-example.html
inst/WORDLIST
man/AICc.Rd
man/LDATS.Rd
man/LDA_TS.Rd
man/LDA_TS_control.Rd
man/LDA_msg.Rd
man/LDA_set.Rd
man/LDA_set_control.Rd
man/TS.Rd
man/TS_control.Rd
man/TS_diagnostics_plot.Rd
man/TS_on_LDA.Rd
man/TS_summary_plot.Rd
man/autocorr_plot.Rd
man/check_LDA_models.Rd
man/check_changepoints.Rd
man/check_control.Rd
man/check_document_covariate_table.Rd
man/check_document_term_table.Rd
man/check_formula.Rd
man/check_formulas.Rd
man/check_nchangepoints.Rd
man/check_seeds.Rd
man/check_timename.Rd
man/check_topics.Rd
man/check_weights.Rd
man/count_trips.Rd
man/diagnose_ptMCMC.Rd
man/document_weights.Rd
man/ecdf_plot.Rd
man/est_changepoints.Rd
man/est_regressors.Rd
man/expand_TS.Rd
man/iftrue.Rd
man/jornada.Rd
man/logLik.LDA_VEM.Rd
man/logLik.TS_fit.Rd
man/logLik.multinom_TS_fit.Rd
man/logsumexp.Rd
man/memoise_fun.Rd
man/messageq.Rd
man/mirror_vcov.Rd
man/modalvalue.Rd
man/multinom_TS.Rd
man/multinom_TS_chunk.Rd
man/normalize.Rd
man/package_LDA_TS.Rd
man/package_LDA_set.Rd
man/package_TS.Rd
man/package_TS_on_LDA.Rd
man/package_chunk_fits.Rd
man/plot.LDA_TS.Rd
man/plot.LDA_VEM.Rd
man/plot.LDA_set.Rd
man/plot.TS_fit.Rd
man/posterior_plot.Rd
man/prep_LDA_control.Rd
man/prep_TS_data.Rd
man/prep_chunks.Rd
man/prep_cpts.Rd
man/prep_ids.Rd
man/prep_pbar.Rd
man/prep_proposal_dist.Rd
man/prep_ptMCMC_inputs.Rd
man/prep_saves.Rd
man/prep_temp_sequence.Rd
man/print.LDA_TS.Rd
man/print.TS_fit.Rd
man/print.TS_on_LDA.Rd
man/print_model_run_message.Rd
man/proposed_step_mods.Rd
man/rho_lines.Rd
man/rodents.Rd
man/select_LDA.Rd
man/select_TS.Rd
man/set_LDA_TS_plot_cols.Rd
man/set_LDA_plot_colors.Rd
man/set_TS_summary_plot_cols.Rd
man/set_gamma_colors.Rd
man/set_rho_hist_colors.Rd
man/sim_LDA_TS_data.Rd
man/sim_LDA_data.Rd
man/sim_TS_data.Rd
man/softmax.Rd
man/step_chains.Rd
man/summarize_etas.Rd
man/summarize_rhos.Rd
man/swap_chains.Rd
man/trace_plot.Rd
man/verify_changepoint_locations.Rd
tests/figs/check-lda-plot-functions/base-lda-plot-bottom-panel.svg
tests/figs/check-lda-plot-functions/base-lda-plot-top-panel.svg
tests/figs/check-lda-plot-functions/base-lda-plot.svg
tests/figs/check-lda-plot-functions/base-lda-set-selected-plot.svg
tests/figs/check-lda-plot-functions/lda-plot-with-time-x.svg
tests/figs/check-lda-ts-plot-functions/base-lda-ts-non-interactive-plot.svg
tests/figs/check-ts-plot-functions/base-ts-autocorr-plot.svg
tests/figs/check-ts-plot-functions/base-ts-diagnostic-plot.svg
tests/figs/check-ts-plot-functions/base-ts-ecdf-plot.svg
tests/figs/check-ts-plot-functions/base-ts-eta-diagnostic-plot.svg
tests/figs/check-ts-plot-functions/base-ts-gamma-plot.svg
tests/figs/check-ts-plot-functions/base-ts-plot.svg
tests/figs/check-ts-plot-functions/base-ts-posterior-plot.svg
tests/figs/check-ts-plot-functions/base-ts-rho-diagnostic-plot.svg
tests/figs/check-ts-plot-functions/base-ts-rho-plot.svg
tests/figs/check-ts-plot-functions/base-ts-summary-plot.svg
tests/figs/check-ts-plot-functions/base-ts-trace-plot.svg
tests/figs/check-ts-plot-functions/rho-line-plot.svg
tests/figs/deps.txt
tests/testthat.R
tests/testthat/test-01-data.R
tests/testthat/test-02-lda.R
tests/testthat/test-03-lda_plot.R
tests/testthat/test-04-LDA_TS.R
tests/testthat/test-05-LDA_TS_plots.R
tests/testthat/test-06-multinom_TS.R
tests/testthat/test-07-ptMCMC.R
tests/testthat/test-08-simulate.R
tests/testthat/test-09-TS.R
tests/testthat/test-10-TS_on_LDA.R
tests/testthat/test-11-TS_plots.R
tests/testthat/test-12-utilities.R
vignettes/.DS_Store
vignettes/LDATS_codebase.Rmd
vignettes/paper-comparison.Rmd
vignettes/rodents-example-files/changepoint_models.Rds
vignettes/rodents-example-files/lda_model_set.Rds
vignettes/rodents-example-files/lda_ts_results.Rds
vignettes/rodents-example.Rmd
