Code

Add input validation#476

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sbfnk merged 59 commits intomainepiforecasts/EpiNow2:mainfrom input-valepiforecasts/EpiNow2:input-valCopy head branch name to clipboardNov 14, 2023

+457-116

Commits

Commits on Nov 10, 2023

• Add function to check validity of reports input

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• Adopt reports checking function

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• Import checkmate

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• Linting: remove whitespace

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• Remove explicit namespacing

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• Import checkmate functions

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• Revise function description

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• Make _opts functions return their own class

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• Import functions for use

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• Add input checking to the estimation functions

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• Return an object of class secondary_opts

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• Allow for NULL inputs

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• Change burn_in check from integer to numeric

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• Update returned objects

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• Allow NULL args

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• Make lower bound of horizon 0

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• Don't import assert_integer

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• Pass delays to delay_opts

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• Don't return a class

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• Catch the dot-dot-dot and modify iter if present

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• Convert argument to stan_opts objects

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• Revise wording of return type

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• Remove import of assert_integer

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• Linting: Remove trailing whitespace

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• Linting: trim white space

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• Add tests for check_reports_valid function

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• Automatic readme update

  

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• Check inputs of simulate_infection()

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• Check inputs of epinow function

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• Check that target_date is a string, not a date

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• Check that target_folder is specified as a directory

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• Import functions for assertions

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• Check that estimates input contains a "fit" element

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• Various checks on "R" input

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• Fix docs of check_reports_valid

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• Fix docs of check_reports_valid

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• Fix docs of check_reports_valid

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• Fix docs of check_reports_valid

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• Error if column names are outside of allowed set

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• Remove boolean argument in favour of enumerated options

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• Generate fixed doc

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• Update docs to mention returned class

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• Replace binary argument with enumerated argument

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• Don't allow null values

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• Revert to have a minimal set of allowed columns

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• Improve documentation

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• Allow model argument to be null.

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• Improve typesetting

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• Styling

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• Fix a wrong function link in docs

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• Remove awkward line breaks

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• Use rlang arg_match() to prevent partial match

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• Add news item

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Commits on Nov 13, 2023

• Pass arguments to stan_opts as list in tests

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• Linting: Use == to match length-1 scalars, not %in%

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• Linting: Switch logic of ifelse statement

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• Linting: contruct paths with file.path() instead of paste0.

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Commits on Nov 14, 2023

• Linting: Fix indentation

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• Fix wrong return value

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