LDATS Codebase"
In 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: