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LDATS-v0.2.7.zip

weecology-LDATS-9c09c0f
- .DS_Store 6.1 kB
- .Rbuildignore 200 Bytes
- .gitignore 75 Bytes
- .travis.yml 586 Bytes
- .zenodo.json 1.4 kB
- CODE_OF_CONDUCT.md 3.2 kB
- CONTRIBUTING.md 4.4 kB
- DESCRIPTION 2.2 kB
- LDATS_model.pdf 660.4 kB
- LICENSE 38 Bytes
- LICENSE.md 1.1 kB
- NAMESPACE 3.6 kB
- NEWS.md 10.7 kB
- R
  - LDA.R 12.0 kB
  - LDATS.R 2.5 kB
  - LDA_TS.R 17.2 kB
  - LDA_TS_plots.R 6.8 kB
  - LDA_plots.R 8.8 kB
  - TS.R 42.0 kB
  - TS_on_LDA.R 27.5 kB
  - TS_plots.R 24.8 kB
  - data.R 2.9 kB
  - multinom_TS.R 16.3 kB
  - ptMCMC.R 37.9 kB
  - simulate.R 8.5 kB
  - utilities.R 9.9 kB
- README.md 6.2 kB
- _pkgdown.yml 4.1 kB
- cran-comments.md 880 Bytes
- data
  - jornada.RData 1.0 kB
  - rodents.RData 8.3 kB
- doc
  - LDATS_codebase.R 453 Bytes
  - LDATS_codebase.Rmd 3.9 kB
  - LDATS_codebase.html 13.2 kB
  - paper-comparison.R 24.1 kB
  - paper-comparison.Rmd 33.9 kB
  - paper-comparison.html 232.9 kB
  - rodents-example.R 4.2 kB
  - rodents-example.Rmd 8.4 kB
  - rodents-example.html 105.0 kB
- inst
  - WORDLIST 735 Bytes
- man
  - AICc.Rd 513 Bytes
  - LDATS.Rd 1.8 kB
  - LDA_TS.Rd 6.5 kB
  - LDA_TS_control.Rd 3.3 kB
  - LDA_msg.Rd 679 Bytes
  - LDA_set.Rd 2.8 kB
  - LDA_set_control.Rd 1.1 kB
  - TS.Rd 7.8 kB
  - TS_control.Rd 2.7 kB
  - TS_diagnostics_plot.Rd 1.6 kB
  - TS_on_LDA.Rd 4.6 kB
  - TS_summary_plot.Rd 2.9 kB
  - autocorr_plot.Rd 626 Bytes
  - check_LDA_models.Rd 914 Bytes
  - check_changepoints.Rd 581 Bytes
  - check_control.Rd 538 Bytes
  - check_document_covariate_table.Rd 1.1 kB
  - check_document_term_table.Rd 797 Bytes
  - check_formula.Rd 1.4 kB
  - check_formulas.Rd 1.1 kB
  - check_nchangepoints.Rd 597 Bytes
  - check_seeds.Rd 645 Bytes
  - check_timename.Rd 905 Bytes
  - check_topics.Rd 563 Bytes
  - check_weights.Rd 732 Bytes
  - count_trips.Rd 1.8 kB
  - diagnose_ptMCMC.Rd 2.8 kB
  - document_weights.Rd 825 Bytes
  - ecdf_plot.Rd 812 Bytes
  - est_changepoints.Rd 3.4 kB
  - est_regressors.Rd 4.8 kB
  - expand_TS.Rd 2.2 kB
  - iftrue.Rd 468 Bytes
  - jornada.Rd 1.2 kB
  - logLik.LDA_VEM.Rd 1.7 kB
  - logLik.TS_fit.Rd 1.1 kB
  - logLik.multinom_TS_fit.Rd 1.3 kB
  - logsumexp.Rd 435 Bytes
  - memoise_fun.Rd 646 Bytes
  - messageq.Rd 667 Bytes
  - mirror_vcov.Rd 979 Bytes
  - modalvalue.Rd 506 Bytes
  - multinom_TS.Rd 4.1 kB
  - multinom_TS_chunk.Rd 2.7 kB
  - normalize.Rd 363 Bytes
  - package_LDA_TS.Rd 1.8 kB
  - package_LDA_set.Rd 1.4 kB
  - package_TS.Rd 5.5 kB
  - package_TS_on_LDA.Rd 1.8 kB
  - package_chunk_fits.Rd 1.8 kB
  - plot.LDA_TS.Rd 2.3 kB
  - plot.LDA_VEM.Rd 2.8 kB
  - plot.LDA_set.Rd 662 Bytes
  - plot.TS_fit.Rd 2.6 kB
  - posterior_plot.Rd 796 Bytes
  - prep_LDA_control.Rd 809 Bytes
  - prep_TS_data.Rd 2.2 kB
  - prep_chunks.Rd 1.7 kB
  - prep_cpts.Rd 4.3 kB
  - prep_ids.Rd 2.1 kB
  - prep_pbar.Rd 1.4 kB
  - prep_proposal_dist.Rd 1.9 kB
  - prep_ptMCMC_inputs.Rd 3.4 kB
  - prep_saves.Rd 3.0 kB
  - prep_temp_sequence.Rd 1.0 kB
  - print.LDA_TS.Rd 832 Bytes
  - print.TS_fit.Rd 972 Bytes
  - print.TS_on_LDA.Rd 1.1 kB
  - print_model_run_message.Rd 1.8 kB
  - proposed_step_mods.Rd 1.9 kB
  - rho_lines.Rd 965 Bytes
  - rodents.Rd 1.8 kB
  - select_LDA.Rd 1.2 kB
  - select_TS.Rd 1.6 kB
  - set_LDA_TS_plot_cols.Rd 3.3 kB
  - set_LDA_plot_colors.Rd 1.5 kB
  - set_TS_summary_plot_cols.Rd 2.7 kB
  - set_gamma_colors.Rd 1.5 kB
  - set_rho_hist_colors.Rd 1.8 kB
  - sim_LDA_TS_data.Rd 2.3 kB
  - sim_LDA_data.Rd 1.8 kB
  - sim_TS_data.Rd 1.7 kB
  - softmax.Rd 508 Bytes
  - step_chains.Rd 4.3 kB
  - summarize_etas.Rd 1.3 kB
  - summarize_rhos.Rd 1.4 kB
  - swap_chains.Rd 3.3 kB
  - trace_plot.Rd 727 Bytes
  - verify_changepoint_locations.Rd 1.4 kB
- tests
  - figs
    - check-lda-plot-functions
      - base-lda-plot-bottom-panel.svg 17.9 kB
      - base-lda-plot-top-panel.svg 17.5 kB
      - base-lda-plot.svg 35.3 kB
      - base-lda-set-selected-plot.svg 57.8 kB
      - lda-plot-with-time-x.svg 35.3 kB
    - check-lda-ts-plot-functions
      - base-lda-ts-non-interactive-plot.svg 147.3 kB
    - check-ts-plot-functions
      - base-ts-autocorr-plot.svg 8.5 kB
      - base-ts-diagnostic-plot.svg 33.3 kB
      - base-ts-ecdf-plot.svg 8.3 kB
      - base-ts-eta-diagnostic-plot.svg 34.6 kB
      - base-ts-gamma-plot.svg 17.8 kB
      - base-ts-plot.svg 113.1 kB
      - base-ts-posterior-plot.svg 6.4 kB
      - base-ts-rho-diagnostic-plot.svg 28.5 kB
      - base-ts-rho-plot.svg 95.1 kB
      - base-ts-summary-plot.svg 113.1 kB
      - base-ts-trace-plot.svg 5.9 kB
      - rho-line-plot.svg 6.1 kB
    - deps.txt 67 Bytes
  - testthat
    - test-01-data.R 444 Bytes
    - test-02-lda.R 2.3 kB
    - test-03-lda_plot.R 2.2 kB
    - test-04-LDA_TS.R 2.5 kB
    - test-05-LDA_TS_plots.R 1.3 kB
    - test-06-multinom_TS.R 3.6 kB
    - test-07-ptMCMC.R 9.2 kB
    - test-08-simulate.R 3.7 kB
    - test-09-TS.R 8.6 kB
    - test-10-TS_on_LDA.R 9.3 kB
    - test-11-TS_plots.R 6.1 kB
    - test-12-utilities.R 5.0 kB
  - testthat.R 261 Bytes
- vignettes
  - .DS_Store 6.1 kB
  - LDATS_codebase.Rmd 3.9 kB
  - paper-comparison.Rmd 33.9 kB
  - rodents-example-files
    - changepoint_models.Rds 459.1 kB
    - lda_model_set.Rds 797.4 kB
    - lda_ts_results.Rds 1.4 MB
  - rodents-example.Rmd 8.4 kB