Package: tidyOhdsiSolutions 0.1.0

tidyOhdsiSolutions: Tidy Utilities for Observational Medical Outcomes Partnership Common Data Model Workflows

Lightweight utilities for working with OMOP (Observational Medical Outcomes Partnership) Common Data Model (CDM) data in the Observational Health Data Sciences and Informatics ecosystem. Provides base-R re-implementations of common 'purrr' functional helpers, tools to convert plain data frames into 'CIRCE' concept set expressions, SQL generators for resolving concept sets against an OMOP vocabulary schema without requiring 'CirceR'.

Authors:Alexander Alexeyuk [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
tidyOhdsiSolutions/json (API)

# Install 'tidyOhdsiSolutions' in R:
install.packages('tidyOhdsiSolutions', repos = c('https://a1exanderalexeyuk.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.00 score 269 downloads 58 exports 1 dependencies

Last updated from:475378df05. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK105
source / vignettesOK167
linux-releaseOK105
macos-releaseOK151
macos-oldrelOK215
windows-develOK68
windows-releaseOK91
windows-oldrelOK83
wasm-releaseOK93

Exports:as_mapperbuildConceptSetQueriesbuildConceptSetQuerycohortFromConceptSetcohortToJsoncollectCsFromCohortcreateConceptSetCohortimapimap_chrimap_dblimap_dfrmapmap_chrmap_dblmap_dfcmap_dfrmap_intmap_lglmap2map2_chrmap2_dblmap2_dfcmap2_dfrmap2_intmap2_lglmsg_abortmsg_blankmsg_bulletmsg_dangermsg_debugmsg_headermsg_infomsg_kvmsg_listmsg_processmsg_progressmsg_rulemsg_spinnermsg_successmsg_timedmsg_todomsg_trymsg_verbosemsg_warnmsg_warningpluckpmappmap_chrpmap_dblpmap_dfcpmap_dfrpmap_intpmap_lglpwalktoConceptSettoConceptSetswalkwalk2

Dependencies:jsonlite

Building Cohorts from Concept Sets
Overview | Typical Workflow | Step 1: Define Concept Sets as Data Frames | Step 2: Convert to Concept Set Expressions | Step 3: Build the Cohort | Parameters | Step 4: Export to JSON | End Strategies | Default: observation period end date | Fixed exit: offset from index | Drug exit: era-based persistence | Event Limits | Source Criteria | Structure of the Output

Last update: 2026-04-15
Started: 2026-04-15

Console Messaging with handyCli
Overview | 1 Basic message levels | 2 Section structure: headers, rules, and blank lines | 3 Structured output: lists and key-value tables | Named list | Key-value table | 4 Iteration patterns | 4a Logging inside a loop | 4b Safe iteration with msg_try() | 4c Verbose mode — conditional logging inside helpers | 5 Timing expressions with msg_timed() | Timing an iteration | 6 Error and warning handling | Raising styled errors with msg_abort() | Raising styled warnings with msg_warning() | msg_try() on_error modes | 7 Debug messages | 8 Progress bar (interactive sessions) | 9 Spinner (interactive sessions) | 10 Putting it all together — annotated pipeline

Last update: 2026-04-15
Started: 2026-04-15

Readme and manuals

Help Manual

Help pageTopics
Convert Input to a Mapping Functionas_mapper
Resolve Multiple Concept Sets to SQLbuildConceptSetQueries
Build SQL to resolve a concept set expression without Java/CirceRbuildConceptSetQuery
Create a CirceR-compatible cohort definition from multiple concept set expressionscohortFromConceptSet
Serialize a Cohort Expression to JSONcohortToJson
Extract Concept Set Expressions from a Cohort DefinitioncollectCsFromCohort
Create a CirceR-compatible cohort definition from a concept set expressioncreateConceptSetCohort
Apply a Function to Each Element with Its Index or Nameimap imap_chr imap_dbl imap_dfr
Apply a Function to Each Element of a List or Vectormap map_chr map_dbl map_dfc map_dfr map_int map_lgl
Apply a Function to Pairs of Elements from Two Listsmap2 map2_chr map2_dbl map2_dfc map2_dfr map2_int map2_lgl
Stop with a styled error messagemsg_abort
Print a blank linemsg_blank
Print a bullet pointmsg_bullet
Print a danger / error message (styled, non-stopping)msg_danger
Print a debug message (only when option is set)msg_debug
Print a section headermsg_header
Print an informational messagemsg_info
Print a two-column key-value tablemsg_kv
Print a named list of itemsmsg_list
Print a process / action messagemsg_process
Simple inline progress countermsg_progress
Print a simple rule / dividermsg_rule
Animated spinner for long-running tasksmsg_spinner
Print a success messagemsg_success
Time a block and report durationmsg_timed
Print a todo itemmsg_todo
Run expr and catch + style any errors/warningsmsg_try
Message only when verbose option is TRUEmsg_verbose
Print a warning message (styled, non-stopping)msg_warn
Warn with a styled warning messagemsg_warning
Extract an Element from a Nested Structurepluck
Apply a Function to Multiple Lists in Parallelpmap pmap_chr pmap_dbl pmap_dfc pmap_dfr pmap_int pmap_lgl
Convert a single data.frame to a concept set expression listtoConceptSet
Convert Concept Set Expression Tibble(s) to Concept Set Expression ListstoConceptSets
Apply a Function for Side Effectspwalk walk walk2