weecology / LDATS

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.