_pkgdown.yml

url: https://weecology.github.io/ldats
development:
  mode: auto
navbar:
  title: "LDATS"
  structure:
    left: [home, articles, reference, news]
    right: [twitter, github] 
  components: 
    articles:
      text: "Vignettes"
      menu: 
        - text: "Rodents example"
          href: articles/rodents-example.html
        - text: "Comparison to Christensen et al."
          href: articles/paper-comparison.html
        - text: "LDATS codebase"
          href: articles/LDATS_codebase.html
    reference: 
      text: "Functions"
      href: reference/index.html
    news: 
      text: "News"
      href: news/index.html
    twitter:
      icon: fa-twitter
      href: https://twitter.com/weecology
    github:
      icon: fa-github
      href: https://github.com/weecology
      
reference:
  - title: "Joint LDA and Time Series"
    desc: "Functions for top-level LDATS modeling"
    contents:
      - LDA_TS
      - package_LDA_TS
      - print.LDA_TS
      - plot.LDA_TS
      - set_LDA_TS_plot_cols
  - title: "Latent Dirichlet Allocation"
    desc: "Functions to extend exisiting LDA functionality"
    contents:
      - LDA_set
      - package_LDA_set
      - logLik.LDA_VEM
      - select_LDA
      - LDA_msg
      - plot.LDA_set
      - plot.LDA_VEM
      - set_LDA_plot_colors
  - title: "Time Series"
    desc: "Functions to execute and evaluate the overall TS model with changepoints and regression components"
    contents:
      - TS
      - package_TS
      - logLik.TS_fit
      - print.TS_fit
      - plot.TS_fit
      - TS_diagnostics_plot
      - trace_plot
      - ecdf_plot
      - posterior_plot
      - autocorr_plot
      - set_TS_summary_plot_cols
      - TS_summary_plot
      - pred_gamma_TS_plot
      - rho_lines
      - rho_hist
      - set_rho_hist_colors
      - set_gamma_colors
      - summarize_etas
      - summarize_rhos
      - est_regressors
      - est_changepoints
      - prep_pbar
  - title: "Multinomial Time Series modeling"
    desc: "Functions to fit the multinomial time series models making up an overall TS model"
    contents:
      - multinom_TS
      - logLik.multinom_TS_fit
      - multinom_TS_chunk
      - prep_chunks
      - package_chunk_fits
      - verify_changepoint_locations
  - title: "Parallel tempering Markov Chain Monte Carlo"
    desc: "Functions to execute ptMCMC optimization"
    contents:
      - prep_ptMCMC_inputs
      - prep_ids
      - prep_proposal_dist
      - prep_saves
      - prep_cpts
      - prep_temp_sequence
      - diagnose_ptMCMC
      - count_trips
      - swap_chains
      - step_chains
      - proposed_step_mods
  - title: "Time Series on LDA output"
    desc: "Functions to facilitate connection running multiple TS models on LDA output"
    contents:
      - TS_on_LDA
      - package_TS_on_LDA
      - print.TS_on_LDA
      - expand_TS
      - prep_TS_data
      - select_TS
      - print_model_run_message
  - title: "Simulation"
    desc: "Functions for simulating input data"
    contents:
      - sim_LDA_data
      - sim_TS_data
      - sim_LDA_TS_data
  - title: "Control options"
    desc: "Functions to set function options defined through control lists"
    contents:
      - LDA_TS_control
      - LDA_set_control
      - TS_control
      - prep_LDA_control
  - title: "Input checking"
    desc: "Functions to tidy code by condensing input object verification"
    contents:
      - check_changepoints
      - check_control
      - check_document_covariate_table
      - check_document_term_table
      - check_formula
      - check_formulas
      - check_LDA_models
      - check_nchangepoints
      - check_seeds
      - check_timename
      - check_topics
      - check_weights
  - title: "Utilities"
    desc: "A variety of helpful little functions"
    contents:
      - AICc
      - document_weights
      - iftrue
      - logsumexp
      - modalvalue
      - memoise_fun
      - messageq
      - mirror_vcov
      - normalize
      - softmax
  - title: "Data and Package"
    desc: "Datasets provided and the package"
    contents:
      - jornada
      - rodents
      - LDATS