Update `<epiparameter>` constructor function and internal refactor#381

Merged

joshwlambert merged 50 commits intomainfrom constructor_sig

Sep 30, 2024

+1,212-936

Commits on Sep 23, 2024

renamed create_prob_dist to create_prob_distribution
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rename create_prob_dist R and test file to create_prob_distribution
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return character from create_prob_distribution if parameters not given
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rename create_prob_distribution args to prob_distribution and prob_distribution_params
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clean prob_distribution in create_prob_distribution to prevent string matching issues
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rename is_epiparameter_params args prob_distribution and prob_distribution_params
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rename .clean_params args to prob_distribution and prob_distribution_params and update usage
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add parameter standardisation to create_prob_distribution
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update create_prob_distribution test error messages
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rename .calc_dist_params args to prob_distribution and prob_distribution_params
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remove prob_distribution_params argument from .calc_dist_params and call convert_summary_stats_to_params internally
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remove truncation argument from new_epiparameter
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remove discretise argument from new_epiparameter
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remove copying mean from summary_stats to prob_dist_params in new_epiparameter
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remove .clean_string call in new_epiparameter as its now called in create_prob_distribution
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remove stopifnot that checks uncertainty and parameters match as this can be done in epiparameter() before calling new_epiparameter
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replace prob_dist and prob_dist_params arguments in new_epiparameter with prob_distribution
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simplified new_epiparameter with prob_distribution from create_prob_distribution
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remove prob_distribution_params arg from epiparameter() and use create_prob_distribution as default for prob_distribution arg
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replace assert_character with stopifnot to check for char or distribution object in epiparameter()
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move uncertainty checking after new_epiparameter call in epiparameter() and make checks stricter
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remove prob_dist_params and rename prob_distribution argument from new_epiparameter call in epiparameter()
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update assert_epiparameter and test_epiparameter to use prob_distribution instead of prob_dist
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move prob_distribution and prob_distribution_params args documentation to create_prob_distribution
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inherit arg documentation from create_prob_distribution in is_epiparameter_params
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remove discretise argument from epiparameter()
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remove truncation argument from epiparameter()
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move auto_calc_params to last named argument in epiparameter() and new_epiparameter()
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add documentation for prob_distribution arg in epiparameter()
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Commits on Sep 25, 2024