Closed juniperlsimonis closed 5 years ago
@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.
Merging #131 into master will increase coverage by
0.38%
. The diff coverage is100%
.
@@ Coverage Diff @@
## master #131 +/- ##
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+ Coverage 97.18% 97.56% +0.38%
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Files 10 11 +1
Lines 1030 1191 +161
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+ Hits 1001 1162 +161
Misses 29 29
Impacted Files | Coverage Δ | |
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R/simulate.R | 100% <100%> (ø) |
|
R/LDA_TS.R | 100% <100%> (ø) |
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R/utilities.R | 100% <100%> (ø) |
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R/multinom_TS.R | 100% <100%> (ø) |
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R/LDA_TS_plots.R | 94.44% <100%> (ø) |
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R/TS_plots.R | 88.17% <100%> (+0.12%) |
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R/TS_on_LDA.R | 99.35% <100%> (+0.04%) |
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R/TS.R | 98.68% <100%> (+0.1%) |
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R/LDA_plots.R | 98.86% <100%> (ø) |
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R/ptMCMC.R | 99.46% <100%> (+0.03%) |
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... and 2 more |
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@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
API updates
LDA_TS
function level, the separate inputs for data tables (document_term_table
anddocument_covariate_table
) have been merged into a single inputdata
, which can be just thedocument_term_table
or a list including thedocument_term_table
and optionally also adocument_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 #119timename
has been moved from within theTS_controls_list
to a main argument in all associated functions.LDA_controls_list
,TS_controls_list
, orLDA_TS_controls_list
inputs now take generallist
inputs (soLDA_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
, orLDA_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
control
input in theplot
call in the example in the README (addresses #116)Updated calculation of the number of observations in LDA
?logLik.LDA_VEM
for references.Fixed bug in plotting across multiple outputs
devAskNewPage
to help flip through multiple outputs, but were only resetting it withdevAskNewPage(FALSE)
at the end of a clean execution. The code has been updated withon.exit(devAskNewPage(FALSE))
, which accounts for failed executions. (addresses #118)Renamed functions
summarize_TS
has been renamedpackage_TS
to align with the otherpackage_
functions that package model output.Simulate functions
sim_LDA_data
simulates an LDA model's document-term-matrixsim_TS_data
simulates an TS model's document-topic distribution matrixsim_LDA_TS_data
simulates an LDA_TS model's document-term-matrixsoftmax
andlogsumexp
are added as utility functionsImproved pkgdown site