Package: PhysioClinical 0.7.0

Yusuke Matsui

PhysioClinical: Clinical Outcome Measures and Responder Analysis

Validated clinical outcome-measure scoring (FMA, Berg, ARAT, TUG, 6MWT, Barthel, Katz, Lawton-Brody IADL, ...), MDC/MCID responder classification, ICF tagging, interval (Rasch) analysis of ordinal ADL/IADL instruments, and normative deviation scoring for the x-biosignal rehabilitation ecosystem.

Authors:Yusuke Matsui [aut, cre]

PhysioClinical_0.7.0.tar.gz
PhysioClinical_0.7.0.zip(r-4.7-any)PhysioClinical_0.7.0.zip(r-4.6-any)PhysioClinical_0.7.0.zip(r-4.5-any)
PhysioClinical_0.7.0.tgz(r-4.6-any)PhysioClinical_0.7.0.tgz(r-4.5-any)
PhysioClinical_0.7.0.tar.gz(r-4.7-any)PhysioClinical_0.7.0.tar.gz(r-4.6-any)
PhysioClinical_0.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PhysioClinical/json (API)

# Install 'PhysioClinical' in R:

install.packages('PhysioClinical', repos = c('https://x-biosignal.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/x-biosignal/physioexperiment/issues

Pkgdown/docs site:https://x-biosignal.github.io

On CRAN:

2.70 score 69 exports 23 dependencies

Last updated from:5a301f33e9. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	NOTE	170
source / vignettes	OK	179
linux-release	NOTE	150
macos-release	NOTE	128
macos-oldrel	NOTE	117
windows-devel	NOTE	116
windows-release	NOTE	117
windows-oldrel	NOTE	119
wasm-release	OK	104

Exports:applyEquating classifyResponder ClinicalInstrument defineGoal equateScores estimateMCID_anchor estimateMCID_distribution estimateMDC fromFHIR gasSummary getClinimetric getInstrument getNormative GovernedNormativeReference listClinimetrics listInstruments listNormative masLevelLabel matchStratum mdcResponder normativeDeviation normativeZScore promisRawToT raschAnalyze raschRecode raschResponder registerInstrument registerNormative romNormalcy romReference score10MWT score6MWT scoreARAT scoreBarthel scoreBerg scoreBPI scoreCohort scoreEQ5D5L scoreFAM scoreFIM scoreFMALE scoreFMAUE scoreFSS scoreGAS scoreInstrument scoreKatz scoreLawton scoreMAS scoreMFIS scoreMMSE scoreMoCA scoreMRCSum scoreMRS scoreNIHSS scorePainNRS scorePROMIS scoreSF36 scoreTUG scoreWMFT show toADaM_ADQS toCDISC_QS toFHIRObservation toOMOP validateFHIRObservation validateNormativeManifest wmftMedianTime writeFHIRBundle writeOMOPTables

Dependencies:abind Biobase BiocGenerics cli DelayedArray digest generics GenomicRanges IRanges lattice lifecycle Matrix MatrixGenerics matrixStats PhysioExperiment rlang S4Arrays S4Vectors Seqinfo SparseArray SummarizedExperiment XVector yaml

Clinical outcome analysis: an end-to-end pipeline

Rendered fromclinical-outcomes.Rmdusingknitr::rmarkdown

Last update: 2026-10-03
Started: 2026-10-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Apply a score crosswalk to new values	applyEquating
Convert a ClinicalScore to a one-row data.frame	as.data.frame.ClinicalScore
Dual MDC-vs-MCID responder classification	classifyResponder summary.responder_classification
Construct a ClinicalInstrument	ClinicalInstrument
Clinical instrument specification	ClinicalInstrument-class show,ClinicalInstrument-method
Clinical score result	ClinicalScore ClinicalScore-class show,ClinicalScore-method
Define a Goal Attainment Scaling goal	defineGoal
Equate one clinical score scale to another (build a crosswalk)	equateScores
Anchor-based MCID	estimateMCID_anchor
Distribution-based MCID (fraction-of-SD rule)	estimateMCID_distribution
Distribution-based Minimal Detectable Change from test-retest data	estimateMDC
Import a FHIR R4 Observation as a clinical score	fromFHIR
Tabulate a GAS result	gasSummary
Look up a per-instrument clinimetric constant	getClinimetric
Retrieve a registered clinical instrument	getInstrument
Retrieve a normative reference from the registry	getNormative
Construct a governed normative reference	GovernedNormativeReference
Governed normative reference	GovernedNormativeReference-class
List available clinimetric constants	listClinimetrics
List available clinical instruments	listInstruments
List registered normative references	listNormative
Modified Ashworth Scale level label for a value	masLevelLabel
Match the normative stratum for a set of covariates	matchStratum
Classify change scores against the minimal detectable change (MDC)	mdcResponder
Batch normative deviation over a metric table	normativeDeviation
Normative z-score / percentile for an observation	normativeZScore
Convert a PROMIS summed score to a T-score via a lookup table	promisRawToT
Rasch (interval) analysis of a clinical ADL/IADL instrument	raschAnalyze
Recode clinical instrument responses to consecutive Rasch categories	raschRecode
Responder analysis of pre-to-post change on the Rasch interval scale	raschResponder
Register a clinical instrument	registerInstrument
Register a normative reference in the versioned registry	registerNormative
Compare a measured joint ROM to the reference (and the other side)	romNormalcy
Joint range-of-motion reference values (goniometry)	romReference
Score a 10-metre walk test (10mWT)	score10MWT
Score a 6-minute walk test (6MWT)	score6MWT
Score the Action Research Arm Test (ARAT)	scoreARAT
Score the Barthel Index (basic activities of daily living)	scoreBarthel
Score the Berg Balance Scale (BBS)	scoreBerg
Score the Brief Pain Inventory (short form)	scoreBPI
Score a cohort's instrument responses into interop-ready ClinicalScores	scoreCohort
Score the EQ-5D-5L descriptive system (level-sum score)	scoreEQ5D5L
Score the Functional Assessment Measure (FIM+FAM)	scoreFAM
Score the Functional Independence Measure (FIM)	scoreFIM
Score the Fugl-Meyer Assessment, Lower Extremity (FMA-LE)	scoreFMALE
Score the Fugl-Meyer Assessment, Upper Extremity (FMA-UE)	scoreFMAUE
Score the Fatigue Severity Scale (FSS)	scoreFSS
Score Goal Attainment Scaling (GAS T-score)	scoreGAS
Score item responses against a clinical instrument	scoreInstrument
Score the Katz Index of Independence in ADL	scoreKatz
Score the Lawton-Brody IADL scale (instrumental ADL)	scoreLawton
Score a Modified Ashworth Scale (MAS) rating	scoreMAS
Score the Modified Fatigue Impact Scale (MFIS)	scoreMFIS
Score the Mini-Mental State Examination (MMSE)	scoreMMSE
Score the Montreal Cognitive Assessment (MoCA)	scoreMoCA
Score the Medical Research Council (MRC) sum score	scoreMRCSum
Score the modified Rankin Scale (mRS)	scoreMRS
Score the NIH Stroke Scale (NIHSS)	scoreNIHSS
Score a Pain Numeric Rating Scale (0-10)	scorePainNRS
Score a PROMIS (or other GRM) short form by EAP	scorePROMIS
Score the SF-36 / RAND-36 Health Survey	scoreSF36
Score a Timed Up and Go test (TUG)	scoreTUG
Score the Wolf Motor Function Test functional-ability scale (WMFT-FAS)	scoreWMFT
Show a normative reference (surfacing its governance)	show,GovernedNormativeReference-method
Export clinical scores to an ADaM BDS (ADQS) data frame	toADaM_ADQS
Export clinical scores to a CDISC SDTM QS (Questionnaires) domain	toCDISC_QS
Export a clinical score as a FHIR R4 Observation	toFHIRObservation
Export clinical scores to OMOP CDM v5.4 tables	toOMOP
Validate a FHIR Observation against the bundled JSON schema	validateFHIRObservation
Validate a normative-artifact governance manifest	validateNormativeManifest
Median WMFT performance time	wmftMedianTime
Write a FHIR Bundle of clinical-score Observations	writeFHIRBundle
Write OMOP CDM tables to CSV files	writeOMOPTables