LDATS 0.2.0

[juniperlsimonis]

API updates

• At the LDA_TS function level, the separate inputs for data tables (document_term_table and document_covariate_table) have been merged into a single input data, which can be just the document_term_table or a list including the document_term_table and optionally also a document_covariate_table. If covariates aren't provided, the function now constructs a covariate table assuming equi-spaced observations. If using a list, the function assumes that one and only one element of the list will have a name containing the letters "term", and at most one element containing the letters "covariate" (regular expressions are used for matching). addresses Data API design questions #119
• timename has been moved from within the TS_controls_list to a main argument in all associated functions.
• The control lists have been made easier to interact with. Primarily, the arguments that previously required LDA_controls_list, TS_controls_list, or LDA_TS_controls_list inputs now take general list inputs (so LDA_TS does not need to have a nested set of control functions). Each control list is passed through a function (LDA_set_control, TS_control, or LDA_TS_control) to set any non-input values to their defaults. This also allows the removal of those controls list class definitions. (addresses set up the controls lists to just be lists #130)

Fixed and updated example code to improve user experience

• Reduced the complexity of the example in the README (addresses Shorten run time and reduce memory of initial example #115)
• Added control input in the plot call in the example in the README (addresses plot not working with simplified example #116)
• Reduced the number of seeds in the rodent vignette example (addresses Reduce number of seeds in vignette #117)

Updated calculation of the number of observations in LDA

• The number of observations for a VEM-fit LDA is now calculated as the number of entries in the document-term matrix (following Hoffman et al. and Buntine, see ?logLik.LDA_VEM for references.
• Associated, we now include an AICc function that is general and works in this specific case as defined (addresses add AICc functionality back in #129)

Fixed bug in plotting across multiple outputs

• A few plotting functions use devAskNewPage to help flip through multiple outputs, but were only resetting it with devAskNewPage(FALSE) at the end of a clean execution. The code has been updated with on.exit(devAskNewPage(FALSE)), which accounts for failed executions. (addresses Plotting full model set first triggers plotting selected model to prompt for next plot #118)

Renamed functions

• summarize_TS has been renamed package_TS to align with the other package_ functions that package model output.

Simulate functions

• Basic simulation functionality has been added for help with generating data sets to analyze. (addresses issue 114)
• sim_LDA_data simulates an LDA model's document-term-matrix
• sim_TS_data simulates an TS model's document-topic distribution matrix
• sim_LDA_TS_data simulates an LDA_TS model's document-term-matrix
• softmax and logsumexp are added as utility functions

Improved pkgdown site

• Function organization (addresses organize functions in pkgdown ref? #122) and navbar formatting.

[juniperlsimonis]

@Renata I tagged you as a reviewer as I'd like to make sure the update to the API works smoothly for your integration with MATSS and to make sure that I've covered all the updates that need to happen with the vignettes. I'm not completely done with this PR yet, but take a look and let me know what you think.

[codecov-io]

Codecov Report

Merging #131 into master will increase coverage by 0.38%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #131      +/-   ##
==========================================
+ Coverage   97.18%   97.56%   +0.38%     
==========================================
  Files          10       11       +1     
  Lines        1030     1191     +161     
==========================================
+ Hits         1001     1162     +161     
  Misses         29       29

Impacted Files	Coverage Δ
R/simulate.R	100% <100%> (ø)
R/LDA_TS.R	100% <100%> (ø)	⬆️
R/utilities.R	100% <100%> (ø)	⬆️
R/multinom_TS.R	100% <100%> (ø)	⬆️
R/LDA_TS_plots.R	94.44% <100%> (ø)	⬆️
R/TS_plots.R	88.17% <100%> (+0.12%)	⬆️
R/TS_on_LDA.R	99.35% <100%> (+0.04%)	⬆️
R/TS.R	98.68% <100%> (+0.1%)	⬆️
R/LDA_plots.R	98.86% <100%> (ø)	⬆️
R/ptMCMC.R	99.46% <100%> (+0.03%)	⬆️
... and 2 more

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[juniperlsimonis]

@diazrenata i've got all of the updates for v0.2.0 that i wanted to get to in here, so please take a look when you can and let me know what you think/if i need to change anything.
the changes to the api will break pipelines based v0.1.0, so i want to make sure you're squared away before we merge in