Simple M/M/s queuing model: R DES RAP v0.5.0

This update adds new performance measures and tests, improves the GitHub actions, implements some fixes and documentation improvements, among other changes.

New features

• Add choice of operating system when manually trigger R-CMD-check GitHub action.
• Add check in model validation for non-null file path when log_to_file = TRUE.
• Calculate test coverage.
• Environment - add covr and queueing and DT and switched to "all" snapshot type.
• Add seed_offset and ran sensitivity analysis on seed in choosing_replications.Rmd.
• Add test comparing against analytical queueing theory model from queueing package.
• Add mean time in system to performance measures.
• Add CODE_OF_CONDUCT.md.

Bug fixes

• Skip parallel processing test on Mac GitHub action.
• Fix deviation calculation so it doesn't get stuck for NA/0.
• Corrected choice of warm-up to run model for longer.
• Fixed/expanded back tests.

Other changes

• Replaced rap_template_r_des with rdesrap_mms.
• Changed all magrittr's %>% to be base R's >| (as per tidyverse style guide).
• Improved README.md and CONTRIBUTING.md.
• Simplify package loading.
• Reorganised tests.
• Update parameters to match python version of model.
• Adjusted analysis.Rmd bin widths to be more consistent with python version of analysis.
• Other minor corrections and amendments (e.g., linting, docstrings, tests).

R DES RAP Template 0.4.0

Major changes include: addition of two new metrics (queue length and patients in service); input modelling; and synthetic data. Also, enabled solutions below the defined initial replications for the replications algorithm.

New features

• Add synthetic data and explanation in README.
• Add input_modelling.Rmd.
• Add unit tests for find_position().
• Add mock paper with figures mentioned in .Rmd/README.
• Add CITATION.
• Add printing of parameters when running model.
• Add two new metrics: queue length and patients in service.

Bug fixes

• Add find_position() which allows us to find a solution below the initial replications set when using ReplicationsAlgorithm.

Other changes

• Changed desired precision when choosing replications to 0.1.
• Made README simpler/clearer, so it focuses on describing the repository, rather than on being a template.
• Add fitdistrplus, lubridate and plotly, and updated some packages.
• Set renv snapshot type to implicit (was previously all).
• In choosing_cores.Rmd, set devtools::install(upgrade = "never") (else would try to update packages).
• GitHub action runs tests on latest mac, windows and ubuntu (but not on development or old ubuntu anymore).

R DES RAP Template 0.3.0

Major changes include addition of functions/classes for choosing the warm-up length and number of replications. Other changes include tests, possibility to override seeds in runner, a bug fix for the mean wait time and serve length, code refactoring, and others.

New features

• Add file explaining how set_attributes() changes results (using_set_attributes.Rmd).
• Add functions for choosing warm-up length (choose_warmup) and an example file (choosing_warmup.Rmd).
• Add some extra checks in functional tests using the unseen metrics.
• Add classes/functions for automated choice of the number of replications (choose_replications.R) and an example file explaining these (choosing_replications.Rmd), along with tests for these (test-backtest-replications.R, test-functionaltest-replications.R, test-unittest-replications.R).
• Add options in runner() to override future.seed and use the run numbers as seeds (allowing consistency with model()) (and add test using it).
• Add unit test for parallel processing.

Bug fixes

• Corrected calculation of mean wait and serve length (previously dropped all arrivals NA for end_time - now bases on wait_time, and so includes people who are midway through appointment at end of simulation).

Other changes

• Split calculations from get_run_results() into seperate functions for simplicity, and to make them reusable for other purposes.
• Simplified calculation of utilisation (same output, simpler code).
• Add example of calculating overall results table to analysis.Rmd.
• Add "how does model work" and "acknowledgements" sections to README.

R DES RAP Template 0.2.0

Warm-up period, "unseen" metrics and tests. Note that the alteration to record service duration altered the order of random number generation, so results now differ from before.

New features

• Add warm-up period (filter_warmup()).
• Add measurement of when service starts and its duration during the model run (set_attribute("nurse_serve_start", ... and set_attribute("nurse_serve_length", ...).
• Add count and wait time for unseen patients in the run results.
• Add tests for warm-up, unseen metrics, and logs.
• Add arrivals and resources to base case back test.

Bug fixes

• Include all patients in the run results arrivals count (and not only those who completed the service).
• Include patients partway through service in the mean_waiting_time and mean_service_time (and not only those who completed the service).
• Use devtools::install() in choosing_cores.Rmd (required to get updated package for parallel processing).

Other changes

• Simplify scenario back test.
• Add DOI and Zenodo citation to README.

R DES RAP Template 0.1.0

🌱 First release of the R DES template.