Package: hvtiRutilities 1.5.11

hvtiRutilities: A Collection of Utilities for Use by HVTI CORR Group at the Cleveland Clinic

R utilities for the clinical investigations statistics group within The Heart & Vascular Institute at the Cleveland Clinic.

Authors:John Ehrlinger [aut, cre, cph]

hvtiRutilities_1.5.11.tar.gz
hvtiRutilities_1.5.11.zip(r-4.7-any)hvtiRutilities_1.5.11.zip(r-4.6-any)hvtiRutilities_1.5.11.zip(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hvtiRutilities/json (API)

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

Bug tracker:https://github.com/ehrlinger/hvtirutilities/issues

Pkgdown/docs site:https://ehrlinger.github.io

On CRAN:

Conda:

quarto

6.77 score 2 packages 149 scripts 88 exports 40 dependencies

Last updated from:5e886d357c. Checks:6 OK, 3 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK227
source / vignettesOK552
linux-releaseOK253
macos-releaseOK347
macos-oldrelOK387
windows-develERROR757
windows-releaseERROR724
windows-oldrelERROR731
wasm-releaseOK134

Exports:add_abbreviationadd_labelsadopt_data_updateapply_label_overridesapply_value_labelsassert_cohortbuilt_manifestbuilt_pathcache_fitcache_would_fitcapture_provenancecheck_data_updatesclean_labelscohort_countscompare_datasetscompare_parityconcept_mapconcept_ofcovariate_auditcovariates_to_numericdata_dictionarydataset_schemadeclare_datafollowup_checkgenerate_survival_dataget_labelget_labelsguard_snapshothvti_non_prefixeshvti_prefix_foldshvti_taxonomyhvtiRutilities.newsimputed_levelsjob_censusjob_fileslabel_maplevel_mapparity_headlineparity_tolerancePOOL_AFFIXESpool_collinear_pairsPOOL_MIN_STEMPOOL_PLAIN_SUFFIXpreflight_reportproc_contentsproc_freqproc_meansproc_univariateprovenance_artifactprovenance_dataprovenance_pathprune_to_one_formpublish_provenancer_data_typesr_dir_impuritiesread_builtread_clinical_datarecord_provenanceregister_datareview_builtreview_data_updatesample_datasas_macro_defssas_macro_signaturesas_pathsas_triagesas_variable_blockselection_crowdingstrip_level_prefixstudy_abbreviationsstudy_checkliststudy_checkpointstudy_checkpoint_pushstudy_closestudy_configstudy_declarestudy_dirstudy_needstudy_reopenstudy_rootstudy_setupstudy_statusstudy_update_identitytype_conversion_reportupdate_manifestverify_manifestwrite_collision_reportwrite_macro_manifest

Dependencies:bitbit64cellrangerclicliprcpp11crayondigestdplyrforcatsgenericsgluehavenhmsjsonlitelabelledlifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6readrreadxlrematchrlangstringistringrtibbletidyrtidyselecttzdbutf8uuidvctrsvroomwithryaml

Registered Datasets: What an Analyst Needs to Know
The worked example | What Does Registering a Dataset Do? | Why Is It Named That Way? | Which File Does My Job Read? | Which Version Did a Report Use? | What If the SAS File Changes and Nobody Registers It? | Where Do the Older Versions Go? | In Short

Last update: 2026-10-24
Started: 2026-10-23

Dataset Version Tracking with manifest.yaml
The Problem: Datasets Drift | In a Study: Rebuild, Then Update | Setup | Registering Datasets | CSV — automatic row count | Inspecting the manifest | SAS datasets — automatic row count | Excel workbooks — automatic row count | Other formats — supply n_rows explicitly | Verifying Before Every Analysis | Typical script header | What Happens When Data Changes | Collecting all failures at once | Correcting a file | Looking at a Rebuild Before Registering It | Running a Job on the Working File | How a Version Was Produced | A New Pull for a Different Project | What Changed Inside the File? | Policy Recommendations | Session Information

Last update: 2026-10-23
Started: 2026-04-01

PROC CONTENTS, MEANS, FREQ and UNIVARIATE in R
Four Procedures You Already Run | What Arrived? proc_contents() | Reading the Extra Columns | Where the SAS Original Has More | Type Is Two-Valued, and That Hides Things | Do the Numbers Look Right? proc_means() | Stratifying with class | The Quartile Trap | Logical Columns | Do the Categories Look Right? proc_freq() | Missing Values | The Denominator Trap | Weighted Percentiles and Tests: proc_univariate() | Weighted Quantiles Follow a Different Rule | VARDEF Changes More Than the Variance | Tests for Location and Normality | Did the Extract Change? compare_datasets() | Where the R Version Differs | Checklist | See Also

Last update: 2026-10-06
Started: 2026-08-14

Simulating Cardiac Surgery Survival Data
Overview | Generating the Dataset | Data Structure | Outcome Summary | Integration with r_data_types() and label_map() | Extracting Variable Labels | Preparing Data for Survival Analysis | Reproducibility | Session Information

Last update: 2026-09-17
Started: 2026-04-01

Getting Started with hvtiRutilities
Introduction | Main Functions | Installation | Basic Usage | Automatic Type Conversion with r_data_types() | Transformation Rules | Working with Real Data | Example: mtcars Dataset | Controlling Factor Conversion | Skipping Specific Variables | Binary Variables as Factors | Working with Variable Labels | Extracting and Looking Up Labels | Labeling Derived Variables | Labels Persist Through Transformations | Complete Workflow Example | Handling Missing Data | Advanced Usage | Custom Workflows for Specific Data Types | Integration with Data Import | Best Practices | When to Use r_data_types() | Recommended Settings by Use Case | Checking Results | Summary | Session Information

Last update: 2026-08-26
Started: 2026-04-01

Data Label Handling Best Practices
Why Labels Matter | The Label Lifecycle | Phase 1: Extracting Labels at Ingestion | Detecting Missing Labels | Phase 2: Labeling Derived Variables | Method A: Label the data directly (preferred) | Method B: Update the label map (for reporting) | Which method should I use? | Phase 3: Study-Specific Overrides | Example labels_overrides.yml | Phase 4: Using Labels in Output | Safe single-variable lookup with get_label() | Building a data dictionary | Labels in summary tables | Labels in plots | Complete Workflow | Labels and r_data_types() | Anti-Patterns to Avoid | 1. Hard-coded label replacements in shared code | 2. Creating derived variables without labels | 3. Using match() without error checking | 4. Labeling the map instead of the data | Function Reference | Session Information

Last update: 2026-04-01
Started: 2026-04-01

Reproducible Seeds in R and SAS
The Problem: Scattered Seeds | The Fix: One Seed, One Place | Create a config.yml | Read it in R | Using the Seed with randomForestSRC | Using the Seed with varPro | Read it in SAS | Keeping R and SAS in Sync | How Seeds Work | R | SAS | randomForestSRC / varPro | Implications for Multi-Script Projects | Checklist

Last update: 2026-04-01
Started: 2026-04-01

Readme and manuals

Help Manual

Help pageTopics
hvtiRutilities: Utilities to work with SAS data in R.hvtiRutilities-package
Add a phrase to a study's abbreviation listadd_abbreviation
Add or update labels in a label mapadd_labels
Adopt one published dataset releaseadopt_data_update
Apply label overrides from a YAML fileapply_label_overrides
Declare value labels for coded variables from a YAML fileapply_value_labels
Assert the cohort matches a job-level expectationassert_cohort
Record the state of the built datasetbuilt_manifest
Path to the study's built datasetbuilt_path
Cache an expensive computation, strictlycache_fit
Would cache_fit() compute, or load?cache_would_fit
Capture an explicit job provenance payloadcapture_provenance
Check a study for published dataset updatescheck_data_updates
Apply label overrides from a YAML file (deprecated)clean_labels
Count the analysable cohortcohort_counts
Compare two versions of a datasetcompare_datasets
Compare one R quantity against its SAS referencecompare_parity
Map a candidate pool to conceptsconcept_map
The concept a candidate variable belongs toconcept_of
Audit what would happen to each covariate in a modelcovariate_audit
Apply what covariate_audit() reportscovariates_to_numeric
Build a data dictionary from a labeled datasetdata_dictionary
Column-level schema of a datasetdataset_schema
Name a study's working dataset without registering itdeclare_data
Check recorded follow-up before a time-related analysisfollowup_check
Generate Synthetic Cardiac Surgery Survival Datagenerate_survival_data
Look up the label for a single variableget_label
Look up labels for multiple variables at onceget_labels
Refuse a renv snapshot taken from the wrong Rguard_snapshot
Second fields that are not analysis prefixeshvti_non_prefixes
Legacy prefixes folded into a taxonomy prefixhvti_prefix_folds
Analysis prefix taxonomyhvti_taxonomy
Display the NEWS filehvtiRutilities.news
Levels of a column that are not clean integersimputed_levels
Roll a job-file inventory up to studies and prefixesjob_census print.hvti_job_census
Inventory the job files under one or more corpus rootsjob_files
Build a lookup map of data labelslabel_map
Report what stripping a code prefix would do to a dataset's levelslevel_map
Summarise a parity table as one reviewer-facing claimparity_headline
Tolerance classes for SAS parity comparisonparity_tolerance
Affix conventions for grouping a SAS candidate pool into conceptsPOOL_AFFIXES POOL_MIN_STEM POOL_PLAIN_SUFFIX
Candidate pairs carrying the same information under unrelated namespool_collinear_pairs
Audit the analysis environment before running an analysispreflight_report
Describe a dataset's variables, in the style of SAS PROC CONTENTSproc_contents
Frequency tables, in the style of SAS PROC FREQproc_freq
Summarise numeric variables, in the style of SAS PROC MEANSproc_means
Summarise and test numeric variables, in the style of SAS PROC UNIVARIATEproc_univariate
Snapshot an input artifact for provenanceprovenance_artifact
Snapshot a registered data file for provenanceprovenance_data
Name the provenance sidecar for an outputprovenance_path
Prune a candidate pool to one form per conceptprune_to_one_form
Publish captured provenance beside a completed outputpublish_provenance
Automatically infer and convert data typesr_data_types
Report top-level executable code in an R directoryr_dir_impurities
Read the study's built datasetread_built
Read and prepare a clinical dataset in one stepread_clinical_data
Capture and publish provenance for an existing outputrecord_provenance
Register a study datasetregister_data
Review a rebuilt study dataset before registering itreview_built
Review one published dataset releasereview_data_update
Generate a sample dataset for testingsample_data
Extract every macro definition from a SAS filesas_macro_defs
Parse the documentation header of a legacy SAS macro filesas_macro_signature
Build a path under the study rootsas_path
Triage a directory of legacy SAS macro filessas_triage
Read a variable list out of a SAS jobsas_variable_block
Concepts represented more than once among selected covariatesselection_crowding
Strip a leading code prefix from level textstrip_level_prefix
The abbreviation list a study's labels usestudy_abbreviations
Render a study audit as a markdown checkliststudy_checklist
Record a study checkpointstudy_checkpoint
Push pending study checkpointsstudy_checkpoint_push
Close or reopen a studystudy_close study_reopen
Read the study manifeststudy_config
Declare the packages a study needsstudy_declare
Resolve a directory in the study layoutstudy_dir
Install a package a study needs, or say howstudy_need
Locate the study rootstudy_root
Set up study identity and directoriesstudy_setup
Audit a study's reproducibility readinessstudy_status
Record a verified study identitystudy_update_identity
Read the per-column type-conversion reporttype_conversion_report
Create or update a dataset manifest fileupdate_manifest
Verify all datasets listed in a manifestverify_manifest
Write the macro name-collision reportwrite_collision_report
Write the canonical macro manifestwrite_macro_manifest