In weecology/LDATS: Latent Dirichlet Allocation Coupled with Time Series Analyses

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(LDATS)
vers <- packageVersion("LDATS")
today <- Sys.Date()

Overview

This vignette outlines the code base for the LDATS package. It was constructed using LDATS version r vers on r today.

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()

weecology/LDATS documentation built on March 28, 2020, 11:20 a.m.