wizaRdry - wizaRdry 0.4.4

fix oracle, hopefully

- R
Published by joshkenney 6 months ago

wizaRdry - wizaRdry 0.4.3

incorporated feedback from UWash and Stanford to address missing data codes in existing data structures and bad floats

- R
Published by joshkenney 6 months ago

wizaRdry - wizaRdry 0.4.2

updated processCaprData to jive with changes to redcap() which rely on updated ndar_subject01 superkey

- R
Published by joshkenney 6 months ago

wizaRdry - wizaRdry 0.4.1

oracle with divya hoping to get working

- R
Published by joshkenney 6 months ago

wizaRdry - wizaRdry 0.4.0

wizaRdry changelog

Version 0.4.0 (Aug 12, 2025)

• Bug Fixes

• Enhancement

- R
Published by joshkenney 7 months ago

wizaRdry - wizaRdry 0.3.3

wizaRdry changelog

Version 0.3.3 (July 10, 2025)

• Bug Fixes
  • Updated ndaRequest.R logic to remove invalid script_name(s) if a match was selected.
  • Fixed an issue where old script_name(s) would still be referenced and try to open a file that wasn't intended.
  • Fixed an issue where users selecting 'n' to "Proceed anyway?" questions wouldn't cause a proper exit in the function logic.
  • Put in some safe guards to avoid invalid responses during readline() prompts (mostly y/n questions).
• Enhancement
  • nda() now has clear messaging to indicate which structure an NDA request is being performed on.
  • Minor spacing updates in nda() prompts to improve readability
  • nda() now tracks failed validations and name changes in script names if data structure name is invalid or is matched to an existing one.

- R
Published by christian-horgan 8 months ago

wizaRdry - wizaRdry 0.3.2

support for ORACLE databses using RODBC as oracle() and methods

changed .dict -> .desc for sql() methods

- R
Published by joshkenney 8 months ago

wizaRdry - wizaRdry 0.3.1

wizaRdry 0.3.1

re-engineered sql() to use DBI and follow design patterns sql.index() and sql.dict() renamed mongo.collection -> mongo.database in config.yml and scry

- R
Published by joshkenney 9 months ago

wizaRdry - wizaRdry 0.3.0

added sql() functions and updated SecretsEnv and ConfigEnv for alpha testing

- R
Published by joshkenney 9 months ago

wizaRdry - wizaRdry 0.2.9

wizaRdry 0.2.9

fix: convert empty strings to NA in character columns

Add preprocessing step in apply_type_conversions to systematically replace
empty strings with NA values across all character columns, improving data
consistency and preventing conversion errors in downstream processing.

- R
Published by joshkenney 9 months ago

wizaRdry - wizaRdry 0.2.7

wizaRdry 0.2.7

added transformvaluefields to ndaValidator() which uses ValueRange field to auto-transform value ranges bi-directionally

- R
Published by joshkenney 9 months ago

wizaRdry - wizaRdry 0.2.8

wizaRdry 0.2.8

in redcap() 2 is raw value for complete param

- R
Published by joshkenney 9 months ago

wizaRdry - wizaRdry 0.2.6

wizaRdry 0.2.6

0.2.6 fixes hardcoded checks to primary keys other than record_id in redcap()

- R
Published by joshkenney 9 months ago

wizaRdry - wizaRdry 0.2.5

wizaRdry 0.2.5

fixed config not defined error in redcap()

- R
Published by joshkenney 9 months ago

wizaRdry - wizaRdry 0.2.4

wizaRdry changelog

Version 0.2.4 (June 13, 2025)

• Enhancement
  • Added configurable primary_key in config.yml for REDCap instances using something alternate to record_id
  • Added placeholder for SQL cleaning scripts for testing workflow
  • Added CSV path for nda()and clean()

- R
Published by joshkenney 9 months ago

wizaRdry -

wizaRdry changelog

Version 0.2.4 (June 13, 2025)

• Enhancement
  • Added configurable primary_key in config.yml for REDCap instances using something alternate to record_id
  • Added placeholder for SQL cleaning scripts for testing workflow

- R
Published by joshkenney 9 months ago

wizaRdry - wizaRdry 0.2.3

wizaRdry changelog

Version 0.2.3 (June 6, 2025)

• Bug Fixes
  • Implemented invalid response catching during prompts when using nda(). Responses outside of valid options are now not accepted.
• Enhancement
  • Updated logic for saving and updating .wizaRdry_prefs
    • Includes changes in functions to.csv(), to.rda(), to.sav(), nda(), clean() and scry().
    • All file creation functions now save user preference (for file creation) as yes when y option is selected during y/n prompts. No change when 'n' is selected.
    • Default behavior for skip_prompt parameters now set to TRUE to make prompting and preference logic cleaner.
    • Removed extra question asking if users want to save preferences for next time.
    • Cleaned up extra message text.
  • Changed nda() prompting logic to now use Enter to skip instead of 0.
  • Updated safe_readline() so users can now use ctrl + c to exit gracefully during NDA validation prompts when using nda().

- R
Published by christian-horgan 9 months ago

wizaRdry - wizaRdry 0.2.2

wizaRdry changelog

missing-data-codes

Version 0.2.2 (May 21, 2025)

• Breaking
  • Support for the api/ submodule offically dropped
• Feature
  • missing_data_codes may now be defined in config.yml to allow dynamic interpolation when using nda()
  • Added complete parameter to redcap() to work with raw and label
  • Added redcap.rune() currently in beta
  • Changed behavior of getters to select only TRUE dates when interview_date parameter is filled
  • Added ... as second parameter to all getters to return columns from named row *args
• Bug Fix
  • Fixed qualtrics.rune() function call
  • Fixed processNda where extraneous Qualtrics fields were not removed by default
  • Fixed ndaValidator where renaming and dropping of fields was not taking place
• Enhancement
  • Added missing values support, increased flexibility in fix_na_values
  • Improved separation of concerns by moving drop/rename operations to find_and_replace_fields
  • Added processNda section to remove jsPsych Mongo fields
  • The validate_structure no longer prompts user, all violations now cause failure

- R
Published by joshkenney 10 months ago

wizaRdry - wizaRdry 0.2.1

wizaRdry changelog

reacher

Version 0.2.1 (April 28, 2025)

• Bug Fix
  • Fixed parallelization issue in mongo() which broke concurrency in smaller datasets like sing
  • Script creation in clean() nda() and to.()* now stop if no is selected and produce helpful message

- R
Published by joshkenney 10 months ago

wizaRdry - wizaRdry 0.2.0

wizaRdry changelog

hail-mary

Version 0.2.0 (April 24, 2025)

• API Integration

  • Added interview_date parameter to redcap(), mongo(), and qualtrics() functions
  • Optimized mongo() for performance while maintaining date checking functionality
  • Added code to rename fields without dropping them in nda()

• Improvements

  • Improved rune() and .rune() to no longer exclude NDA required variables

• Maintainer Fixes

  • Resolved Globalenv issue in ndaValidator
  • Removed import in src/createSpss
  • Removed options(warn = -1) from getSurvey and getTask
  • Unwrapped examples for sift() and rune()

• User Experience

  • Added notification that .wizaRdry_prefs will be added to .gitignore in scry

- R
Published by joshkenney 10 months ago

wizaRdry - wizaRdry 0.1.9

wizaRdry changelog

no-default-writes

Version 0.1.9 (April 22, 2025)

Improvements

• Configuration Management

  • Updated .wizaRdry_prefs to store skips for all output functions
  • Added .wizaRdry_prefs to .gitignore

• Documentation and Descriptions

  • Added more specificity to rune descriptions
  • Improved descriptions for clean() and nda() functions
  • Homogenized language descriptions of exported functions

• Function Exports

  • Made to.nda() and createNda() non-exported functions as they require information from the flow of nda()

• User Experience

  • Added readline responses to provide user input for all to.* functions scry() clean() and nda() for writing to space

- R
Published by joshkenney 11 months ago

wizaRdry - wizaRdry 0.1.8

wizaRdry changelog

shine

Version 0.1.8 (April 16, 2025)

Bug Fixes

Refined Config and Secrets Validation - users can now leave blank the secrets and config for apis they wont use and won't be thrown unnecessary errors - scry() now creates config.yml with commented out survey_ids, superkey, and collection to support this

Improvements

sift() - renamed columns to cols argument for brevity

- R
Published by joshkenney 11 months ago

wizaRdry - wizaRdry 0.1.7

wizaRdry changelog

wax-on-wax-off

Version 0.1.7 (April 16, 2025)

New Features

1. Enhanced Data Handling

• Added support for improved parameter handling in sift() function

Data Structure Improvements

1. Better Data Organization
   • Reorganized output data frames to prioritize superkey fields

Function Enhancements

1. sift() Improvements
   • Renamed parameters for better clarity (rowsofinterest → rows, columnsofinterest → columns)
   • Added support for single values and vectors for all filter parameters
   • Special handling for fields with variant names (state/status, losttofollowup/losttofollow-up variants)
   • Added support for boolean TRUE with interview_date to filter non-NA values
   • Improved date format handling with support for ISO, US, European and other common formats

redcap() Improvements

1. Advanced Edge-Case Handling
   • Added allowed_superkey_cols parameter to handle extraneous fields in RedCap superkeys
   • New parameter exclude_pii which removes fields marked in RedCap as identifiers (defaults to TRUE)
   • Fixed bug where multiple redcapeventnames were not populated correctly in merge
   • Removed study-specific processing for impact in redcap()

User Experience

1. Workflow Enhancements
   • Running clean() or nda() now opens cleaning script in new RStudio tab (only if it's a new script)
   • Enhanced scry() to autodetect study_alias from *.Rproj files
   • Added study_alias as first argument to scry()
   • Improved .gitignore handling in scry() to include *.pem files

Improvements

1. Date Handling
   • Added parse_dates_to_iso() to better convert dates to ISO format in qualtrics() and mongo()
   • Implemented standardized date formatting with default YMD ISO format in redcap()

- R
Published by joshkenney 11 months ago

wizaRdry - wizaRdry 0.1.6

wizaRdry changelog

quite a bit of elbow grease

Version 0.1.6 (April 14, 2025)

New Features

1. Rune

   • Thoroughly tested rune() which works with any data frame, detecting prefixes, creating component data frames
   • Added qualtrics.rune() and equivalent mongo.rune() functions for concise processing of composite data

2. Security Enhancements

   • Implemented secure secrets management system for API credentials
   • Secrets are no longer visible as environment variables

3. NDA Submission Improvements

   • Implemented automatic script creation routines in nda()
   • Better detection duplicate scripts through checkDuplicateScripts on wizaRdry startup

Alias System Refinements

1. Finalized Function Names
   • Changed default function names to use magical-themed aliases:
     • redcap() as default for getRedcap()
     • qualtrics() as default for getSurvey()
     • mongo() as default for getMongo()
     • sift() as default for dataFilter()
     • clean() as default for dataRequest()
     • meld() as default for dataMerge()
     • nda() as default for ndaRequest()
     • rune() as default for dataParse()
2. Finalized Method Names
   • .index() to view collections, surveys, and instruments
   • .dict() to view data dictionaries

Bug Fixes

1. Dictionary Access

   • Enhanced redcap.dict() and qualtrics.dict() to handle non-existent variables gracefully
   • Modified qualtrics.dict() to display only QIDs

2. Performance Optimization

   • redcap.dict() and qualtrics.dict() now produce output regardless of whether strings or variable names are presented as args
   • Improved ability to append code to cleaning scripts where user selected columns to be removed in nda()
   • Better script validation through validate_script_names

Improvements

1. User Experience

   • Added interactive mode and case-insensitive removal to more efficiently remediate submission templates using nda()
   • nda() now checks that script name is valid against short names in NDA API
   • Improved and consolidated example script boiler plate instructions
   • Added qualtrics.index() allowing users to view their qualtrics surveys presented by the Qualtrics API

2. Output Management

   • Modified to.nda() to output to ./tmp to avoid nesting

- R
Published by joshkenney 11 months ago

wizaRdry - wizaRdry 0.1.5

wizaRdry changelog

optimizations, improvements, and new aliases

Version 0.1.5 (March 29, 2025)

New Features

1. Enhanced REDCap Integration

   • Added attribute tracking to getRedcap() for improved metadata access
   • Implemented intelligent metadata detection in getRedcapDictionary()
   • Created seamless flow between data retrieval and metadata extraction

2. Expanded Alias System

   • Added comprehensive set of magical-themed aliases for core functions
   • Implemented intuitive naming patterns (e.g., clean, decipher, meld)
   • Created consistent conversion aliases using to.* pattern

3. MongoDB Improvements

   • Added verbose parameter to getMongo() and getMongoData() functions for detailed logging
   • Enhanced collection validation and error handling
   • Added dependency for column prefix functionality required by PRL cleaning scripts

Bug Fixes

1. REDCap Dictionary Access

   • Fixed issue where getRedcapDictionary() couldn't properly access metadata from getRedcap() output
   • Resolved metadata retrieval inconsistencies when accessing dictionary information
   • Improved error handling during REDCap dictionary access

2. Qualtrics Dictionary Access

   • Applied same improvements to getQualtricsDictionary() for consistency
   • Enhanced metadata extraction from Qualtrics survey data
   • Standardized dictionary access patterns across REDCap and Qualtrics

3. Missing Dependency

   • Added addColumnPrefix() as it was used by in clean/prl.R

Improvements

1. Code Quality

   • Enhanced function documentation for API-related functions
   • Added clearer messaging during metadata operations
   • Improved structure for maintaining API compatibility

2. User Experience

   • Standardized function behavior across data sources
   • Balanced magical theming with clear function naming
   • Improved documentation with examples for all aliases

---

wizaRdry Package Aliases

The wizaRdry package provides both standard function names and magical-themed aliases to help researchers work with data from various sources (REDCap, Qualtrics, and MongoDB). The aliases offer an intuitive and memorable alternative way to access core functionality.

Core Function Aliases

| Magical Alias | Standard Function | Description | |----------------|-------------------|--------------------------------------------| | clean | dataRequest | Clean and prepare data | | nda | ndaRequest | Generate NDA submission data | | decipher | dataParse | Parse Qualtrics data into separate dataframes | | meld | dataMerge | Merge datasets together | | sift | dataFilter | Filter data based on criteria |

Data Source Aliases

REDCap Functions

| Alias | Function | Description | |---------------|--------------------|---------------------------------------| | redcap | getRedcap | Retrieve data from REDCap | | redcap.codex | getRedcapDictionary | Extract data dictionary from REDCap | | redcap.index | getRedcapForms | Get available REDCap forms |

Qualtrics Functions

| Alias | Function | Description | |-----------------|----------------------|-----------------------------------------| | qualtrics | getQualtrics | Retrieve survey data from Qualtrics | | qualtrics.codex | getQualtricsDictionary | Extract column mapping from Qualtrics |

MongoDB Functions

| Alias | Function | Description | |----------------|----------------------|----------------------------------------| | mongo | getMongo | Retrieve data from MongoDB | | mongo.index | getMongoCollections | Get available MongoDB collections |

Data Conversion Aliases

| Alias | Function | Description | |-----------|------------------|------------------------------------------------| | to.csv | createCsv | Create CSV file from a dataframe | | to.nda | createNda | Create NDA submission template | | to.rda | createRda | Create RDS file from a dataframe | | to.sav | createSpss | Create SPSS file from a dataframe |

These magical aliases are designed to make your data handling code more intuitive and enjoyable while maintaining compatibility with established naming conventions.

- R
Published by joshkenney 11 months ago

wizaRdry - wizaRdry 0.1.4

I'll update the changelog to address the maintainer's comments and reflect our discussion:

wizaRdry changelog

Addressing CRAN maintainer's manual revision

Version 0.1.4 (March 28, 2025)

CRAN Compliance Updates

1. Examples Improvements

   • Modified examples to use \dontrun{} only when necessary (API access, file creation)
   • Added self-contained examples with sample data for testable functions
   • Fixed directory handling in examples to comply with CRAN policies

2. Code Improvements

   • Removed unnecessary package installations from function bodies
   • Replaced cat() calls with proper message() for user feedback
   • Added missing debug_message function definition
   • Improved error handling throughout the package

3. Documentation

   • Fixed spacing issues in DESCRIPTION field
   • Enhanced documentation clarity across all functions
   • Ensured examples follow CRAN guidelines for execution time

- R
Published by joshkenney 11 months ago

wizaRdry - wizaRdry 0.1.3

wizaRdry changelog

Bug fixes found after meeting with Praveen getQualtrics("rgpts")

Pre-release Version 0.1.3 (March 27, 2025)

Bug Fixes

1. add checkKeys
   • Adding missing checkKeys dependency which is part of testSuite() for qualtrics

- R
Published by joshkenney 11 months ago

wizaRdry - wizaRdry 0.1.2

wizaRdry changelog

Bug fixes found after meeting with Praveen testing scry() and initial setup

Pre-release Version 0.1.2 (March 27, 2025)

Bug Fixes

1. PRL example function typo
   • Fixed reference to lshsr instead of prl in example function in scry()

Breaking Changes

1. dataRequest() task/ -> mongo/
   • dataRequest() now uses the folder for mongo instead of tasks; update necessary to rename tasks -> mongo in existing repos

- R
Published by joshkenney 11 months ago

wizaRdry - wizaRdry 0.1.1

wizaRdry changelog

Bug fixes found after meeting with UWash REDCap integration for IMPACT-MH

Pre-release Version 0.1.1 (March 26, 2025)

Bug Fixes

1. NDA Base URL

   • Fixed known issue in ndaRequest() where lenient parsing in dev/process_file which was causing nda_base_url to become commented out on file sync prior to build cycle

2. RedCap Integration

   • Fixed bug in getRedcap() to ensure ndar_subject01 now populates all events, even where superkey may not be the default REDCap event

3. NDA Validation Enhancements

   • Upgraded dataValidator() to drop columns on user feedback and add to cleaning script
   • Restored .wizaRdry_env to ndaValidator for consistent data handling
   • Added a switch to toggle between .wizaRdry_env and global environment

New Features

1. Added Exports
   • Added getQualtricsDictionary() export
   • Added getRedcapDictionary() export
   • Added createExtract() dependency for dataRequest()

Breaking Changes

1. Function Renaming

   • Renamed getForms() to getRedcapForms()

2. Configuration Changes

   • In config.yml: super_keys renamed to superkey (now identifies ndar_subject01)

- R
Published by joshkenney 11 months ago

wizaRdry - wizaRdry 0.1.0

Initial public release of the wizaRdry R package!

- R
Published by joshkenney 12 months ago