Patching CRAN issues with vignette building

• Dependencies are being managed different now
• For the paper comparison vignette, all of the code is pre-run and saved in the LDATS-replications repository
• Allows removal of otherwise unused packages from this package's dependency list

Patching a bug in tests for r-devel

• straingsAsFactors update
• only involved patching one test

General editing of simulation functions

• Don't need to make a sparse matrix to pass in now
• Tweaking the simulation functions to simplify X

Patching a bug in sim_TS

• Using only as.matrix() fails if there is only 1 year in a segment and there are multiple covariates. In that case, as.matrix(X[in1, ]) returns a matrix of n_covariates rows x 1 column, instead of a matrix of 1 row and n_covariates columns. This edit should fix that by forcing it into a matrix of the correct number of rows.

Edits for resubmission to CRAN

• Added space between braces for auto-linking in the description text.

Edits for resubmission to CRAN

• Output given by print/cat has been replaced with message messages.
• Added examples in documentation (and replacement of \duntrun{} with \donttest{})
• Editing of description file for specs
• Reduction of test runtimes

Changed functions

• messageq replaces qprint

Edits for submission to CRAN

• Including appropriate files in the Rbuildignore

Minor patching of vignette code

• Handling the downloads so they work robustly locally

Vignette update

• Incorporates Hao's feedback and edits on the paper comparison vignette
• Updates the vignette to work with the contemporary version of the package
• Allowed removal of the large model cache files

Zenodo json

• Inclusion of the json file for the Zenodo page

Tidying of the model doc

• The .pdf describing the model (the manuscript work in progress) is now at the top level and named "LDATS_model.pdf", to allow the full model description to remain stable while the ms development happens elsewhere.

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 #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 #130)

Fixed and updated example code to improve user experience

• Reduced the complexity of the example in the README (addresses #115)
• Added control input in the plot call in the example in the README (addresses #116)
• Reduced the number of seeds in the rodent vignette example (addresses #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 #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 #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 #122) and navbar formatting.