Code

Optimization develop roxugen#411

Code

Merged

klevdiamanti merged 84 commits intooptimization_developOlink-Proteomics/OlinkRPackage:optimization_developfrom optimization_develop_roxugenOlink-Proteomics/OlinkRPackage:optimization_develop_roxugenCopy head branch name to clipboardJul 18, 2024

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Commits

Commits on May 31, 2024

• Merge pull request #380 from Olink-Proteomics/optimization_develop

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Commits on Jun 11, 2024

• adding check_olinkid

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• Document

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Commits on Jul 3, 2024

• adding duplicate_sampleID and all_na_assays

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• Document

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Commits on Jul 10, 2024

• check_npx function added and internal functions moved to same script

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• Document

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Commits on Jul 17, 2024

• Add title on check_npx function

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• Update check_npx description

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• Update description of input variables in check_npx

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• Reshape example from check_npx

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• Update names of variables returned by check_npx

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• Reshape check_npx function

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• Modify check_npx_col_names title.

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• Update description of check_npx_col_names

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• Update return of check_npx_col_names function

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• Change description of df input variable to check_npx based on check_npx_col_names

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• Add details about preferred_names to details of check_npx

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• Upgrade to RoxygenNote 7.3.2

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• Update examples of check_npx_col_names

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• Bring examples from check_npx_col_names to check_npx

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• Check if preferred_names is NULL in check_npx

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• check_npx_col_names add "wrap = FALSE" in cli::cli_abort

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• No need to check preferred_names in check_npx

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• Reshape check_npx_update_col_names

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• check_npx_col_names and check_npx: switch from NPX_2 to PCNormalizedNPX to make it match the example below.

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• Update descriptions

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• Allow R code snippets on RoxygenNote

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• Update documentation for check_npx-related functions

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• Update documentation for check_npx_olinkid

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• Reshape check_npx_olinkid

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• "wrap = FALSE" instead of "wrap = NULL"

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• Fix some linting issues and update documentation for check_npx_all_na_assays

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• Add some sections in functions check_npx_olinkid

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• Update documentation for check_npx_duplicate_sample_ids and check_npx_all_na_assays

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• Export check_npx

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• Undo "Roxygen: list(markdown = TRUE)"

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• Intrpduce "Roxygen: list(markdown = TRUE)"

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• Update check_is_boolean functions

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• Minor update check_is_boolean

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• Define default for error in check_is_boolean

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• Update documentation for check_is_character

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• Update check_columns

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• Update check_df

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• Update check_file_exists

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• Update check_file

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• Update check_is_integer

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• Minor documentation update

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• Update check_library_installed

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• Update check_list

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• Rename check_library_installed

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• Update check_is_numeric

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• Update data

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• Update utils

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• Update read_npx

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• Update read_npx_delim

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• Update read_npx_excel

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• Bugfix read_npx_delim

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• Update read_npx_format

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• Minor updates read_npx

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• Replace "call = NULL" with "call = rlang::caller_env()" in cli::cli_abort

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• Update read_npx_legacy

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• Update read_npx_format for bugs

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• Document

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Commits on Jul 18, 2024

• Update read_npx_parquet

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• Update read_npx_utils

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• Update read_npx_wide

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• Minor update read_npx_wide

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• Upodate read_npx_zip

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• Update check_npx_colnames

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• Minor updates in documentation of all check_npx functions.

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• Update check_npx error/warning messages

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• Add duckdb and dbplyr as suggested packages

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• Minor documentation update.

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• Reshape tests and add one more for arrow input in all-NA assays

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• Update read_npx documentation

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• Merge branch 'optimization_develop_roxugen' into opt_dev_checknpx_internal_funcs

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• Document

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• Merge pull request #412 from Olink-Proteomics/opt_dev_checknpx_internal_funcs

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• One skip_if_not_installed per package

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• Move dbplyr and duckdb to Imported packages

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• Move readxl to Suggested packages

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• Fix NOTE from devtools::check for dbplyr and duckdb

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