Allow selecting subset of variables when using as_cmdstan_fit()
#1121
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Still need to add tests |
| if (!is.null(variables)) { | ||
| csv_contents$metadata$variables <- posterior::variables(csv_contents$post_warmup_draws) | ||
| } |
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Overriding the metadata$variables is necessary to avoid errors when subsequently calling methods like draws.
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Doing csv_contents$metadata$variables <- variables doesn't work because variables can contain names of non-scalar parameters and we need the names of the individual elements (e.g. variables = "beta" but we need metadata$variables = c("beta[1]", "beta[2]"), etc.).
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Ideally we would also override metadata$stan_variables and metadata$stan_variable_sizes, but those are bit trickier to get right and I don't think the methods that use those are even available after creating an object just from CSV files (e.g. methods like unconstrain_draws() and others that require calling init_model_methods won't be available if we can't recompile).
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #1121 +/- ##
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+ Coverage 87.17% 87.35% +0.17%
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Lines 5973 6002 +29
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| metadata$variables <- union(metadata$sampler_diagnostics, metadata$variables) | ||
| if (!user_variables_subset) { | ||
| # because for pathfinder variables and diagnostics are read in together, | ||
| # if user hasn't selected a custom subset of variables we need to include | ||
| # all diagnostics | ||
| variables <- union(metadata$sampler_diagnostics, variables) | ||
| } |
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Pathfinder is a special case because diagnostics and variables are read in together (mcmc reads them in separately). So some special handling was needed to subset properly for pathfinder.
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Summary
Adds
variablesargument toas_cmdstan_fit()to allow creating objects from a subset of variables in the CSV files.Copyright and Licensing
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