LDATS Codebase

Overview

This vignette outlines the code base for the LDATS package. It was constructed using LDATS version 0.3.0 on 2023-09-18.

Installation

To obtain the most recent version of LDATS, install the most recent version from GitHub:

install.packages("devtools")
devtools::install_github("weecology/LDATS")

Analytical Pipeline

The full LDATS analysis can be executed using the LDA_TS function, which is the top-level of the coding pipeline’s hierarchy of functions:

• LDA_TS()
  • check_LDA_TS_inputs()
    • check_timename()
    • check_formulas()
    • check_nchangepoints()
    • check_weights()
    • check_control()
    • check_document_term_table()
    • check_document_covariate_table()
      
    • check_topics()
    • check_seeds()
  • LDA_set()
    • check_LDA_TS_inputs()
      • check_control()
      • check_document_term_table()
      • check_topics()
      • check_seeds()
    • loop over models
      • prep_LDA_control()
      • LDA()
  • select_LDA()
    • applies the measurer and selector functions supplied via LDA_controls_list()
  • TS_on_LDA()
    • check_LDA_TS_inputs()
      • check_LDA_models()
      • check_formulas()
      • check_nchangepoints()
      • check_timename()
      • check_control()
      • check_weights()
      • check_document_covariate_table()
        
    • expand_TS()
    • loop over models
      • prep_TS_data()
      • TS()
        • check_TS_inputs()
          • check_formulas()
          • check_nchangepoints()
          • check_control()
          • check_weights()
        • est_changepoints()
          • prep_saves()
          • prep_ptMCMC_inputs()
          • prep_cpts()
            • loop over chains
              • multinom_TS()
          • prep_ids()
          • prep_pbar()
          • loop over iterations
            • update_pbar()
            • step_chains()
              • propose_step()
                • proposed_step_mods()
                  • loop over chains
                    • multinom_TS()
              • eval_step()
              • take_step()
            • swap_chains()
              • loop over chain neighbors
            • update_saves()
            • update_cpts()
            • update_ids()
        • est_regressors()
          • loop over unique realizations of change point locations
            • multinom_TS()
            • loop over chunks
              • mirror_vcov()
              • rmvnorm()
        • summarize_TS()
          • diagnose_ptMCMC()
            • count_trips()
          • summarize_rhos()
          • measure_rho_vcov()
          • summarize_etas()
          • measure_eta_vcov()
    • select_TS()
      • applies the measurer and selector functions supplied via TS_controls_list()
    • package_LDA_TS()

Each component model’s function (LDA_set() and TS()) can be run independently, as well.

Controls Lists

To minimize the length of argument lists and facilitate simple default usage throughout the pipeline, we implement an options/controls list approach, where each of the main functions (LDA_TS, LDA_set, and TS) and its subfunctions have a control argument that takes a list to replace the defaults returned by its _control function:

• LDA_TS_control()
• LDA_set_control()
• TS_control()