Tags: furrer-lab/abn
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export abn output to other format(s) (#227) * updated packages and lock file * import jsonlite package * minimal skeletton of export function * helper for object preparation to test export function * minimal non-functional tests for export function. * new method for class `abnDag` that converts the adjacency matrix to a data frame. * refactored for being ready for other export formats. * export to json * prepared skeleton for export of abnFit objects from "method='bayes'". * export abnFit objects from `method = "mle"` and no grouping (without mixed-effect, hence only fixed-effects). * updated and extended tests for current export function. * improved test coverage * create test abnFit object with grouping * setup preliminary failing test for export of abnFit w/ grouping * fixed object name of grouping variable for correct dispatch. * now starting with mle w/ grouping: basic skeletton * changed JSON object name from "group_var" to snake case "groupVar" * add to JSON graph object the names of nodes/variables that the random-effect acts on (`grouped.vars`) * extract node specfic parameters when mle with grouping * validate input of fitAbn under mle w/ grouping for node specific parameters. * test node specific parameter extraction for fitAbn under mle with grouping. * add workaround to set R environment for debugging r-containers issues * add debugging steps for r-containers issues in CRAN checks workflow * remove unnecessary installation and session info commands from R script in CRAN checks workflow * add step to print library paths in CRAN checks workflow * enhance debugging output in CRAN checks workflow * add R Home information to debugging output in CRAN checks workflow * Revert "add workaround to set R environment for debugging r-containers issues" This reverts commit 5bc4ebf. * updated doc of export_abnFit * changed `export_to_json` to new structure and simplified. * updated test for `export_abnFit()` with new structure * added optional scenario_id and label * updated `export_abnFit_mle` to new structure. * updated `export_abnFit_mle_nodes` to new format. * updated `extract_parameters_by_distribution` to new format. * first implementation of `export_abnFit_mle_grouped_nodes` * updated `export_abnFit_mle_graph` to new structure * prepared code skeleton for exporting abnFit with `method = "bayes"`. * replaced `extract_parameters_mixed_effects` with `extract_parameters_mixed_effects` to adhere to new structure. * minor bug fix in extracting the dag as a matrix from the abnFit object. * Fixed bug since childs are in rows and parents in columns. * update tests for optional top-level scenario_id and label * removed deprecated test of graph metadata since it's not applicable anymore * check JSON for correct variable structure. * updated test to check the parameter array * updated tests to check the arc structure correctly. * test grouped mle model exports parameters correctly. * test link function mapping. * suppress warnings related to non-convergence in poisson CPP * fixed error in roxygen2 writing the function documentations. Doesn't like "|" in a function name. * generated function documentation for updated export functions. * updated INLA version in renv.lock file * enhanced function documentation with explicit JSON Schema description.
202 skipping re building of vignette outputs due to unavailable depen… …dencies on nosuggests flavours (#205) * evaluate chuncks conditional on availability of vignette dependencies. Addressing #202 * conditionally running the benchmarks only if the microbenchmark package is available. Addressing #202. * Automated Vignette Compilation * removed Suggests from VignetteDepends --------- Co-authored-by: GitHub Vignette Bot <vignettebot@github.com>
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