Package {ERBioR}

Type:	Package
Title:	Reproducible Occupational Biological Risk Assessment with the ERBio Method
Version:	0.9.0
Description:	A source-traceable computational implementation of the ERBio method for occupational biological risk assessment. It provides deterministic risk calculation, versioned questionnaires, a scientifically audited regulatory biological-agent registry, workplace-level assessment, preventive planning outputs, bilingual Spanish-English functionality and reproducible reports. The software preserves a single language-neutral calculation core and keeps method-faithful components distinct from explicit computational extensions. The underlying ERBio method was developed by Aguilar-Elena and is described in Aguilar-Elena (2015) <doi:10.5281/zenodo.22107465>.
License:	GPL (≥ 3)
Encoding:	UTF-8
Depends:	R (≥ 4.1.0)
Imports:	utils
Suggests:	testthat (≥ 3.0.0), shiny, DT, readxl, openxlsx
Config/testthat/edition:	3
NeedsCompilation:	no
Packaged:	2026-08-27 15:21:38 UTC; okashi
Author:	Raúl Aguilar-Elena [aut, cre], Ana Delgado-García [aut]
Maintainer:	Raúl Aguilar-Elena <raguilar@universidadviu.com>
Repository:	CRAN
Date/Publication:	2026-09-09 14:50:26 UTC

ERBioR: Reproducible Occupational Biological Risk Assessment

Description

A source-traceable computational implementation of the ERBio method for occupational biological-risk assessment.

Details

ERBioR separates four layers: the original ERBio deterministic method, versioned questionnaire instruments, regulatory biological-agent data, and technical enrichment. Explicit computational extensions are labelled as such and are not silently treated as source rules.

The underlying ERBio method is described by Aguilar-Elena (2015), doi:10.5281/zenodo.22107465.

References

Aguilar-Elena, R. (2015). Riesgos biológicos laborales: ERBio, un nuevo método de evaluación teórica. Doctoral thesis, Universidad Pública de Navarra. doi:10.5281/zenodo.22107465.

Orden TES/1287/2021, de 22 de noviembre, BOE-A-2021-19371, por la que se sustituye el anexo II del Real Decreto 664/1997.

Directive 2000/54/EC of the European Parliament and of the Council, as updated for Annex III by Commission Directive (EU) 2019/1833 and Commission Directive (EU) 2020/739 for SARS-CoV-2.

See Also

erbio_assess, erbio_assess_questionnaire, erbio_reference_level_from_agent, erbio_assess_workplace

ERBioR Bilingual, Preventive-Action and Shiny Utilities

Description

Utilities supporting the Spanish-English presentation layer introduced in ERBioR 0.9, including language selection, approved scientific translations, preventive-action text, questionnaire internationalisation and the bundled Shiny application. Scientific calculations remain language-neutral.

Usage

erbio_set_language(language = c("es", "en"))

erbio_get_language()

erbio_load_translation_registry(path = NULL)

erbio_validate_translation_registry(path = NULL)

erbio_load_preventive_action_registry(path = NULL)

erbio_validate_preventive_action_registry(path = NULL)

erbio_load_ui_dictionary(path = NULL)

erbio_translate_ui(key, language = erbio_get_language(), path = NULL)

erbio_get_questionnaire_i18n(
  questionnaire_id,
  language = erbio_get_language(),
  version = NULL,
  path = NULL
)

erbio_bilingual_invariance_check(
  questionnaire_id,
  responses,
  version = NULL,
  scoring = "default",
  path = NULL
)

erbio_preventive_action(
  item_id,
  language = erbio_get_language(),
  path = NULL
)

erbio_run_app(launch.browser = TRUE, ...)

erbio_shiny_build_id()

Arguments

Details

The bilingual layer changes presentation text only. Questionnaire identifiers, item identifiers, scoring rules, probability and risk calculations remain language-neutral.

The translation and preventive-action registries are versioned package data. Their validation functions report structural and approval-state checks without changing the underlying ERBio scientific logic.

erbio_bilingual_invariance_check() is intended to verify that equivalent Spanish and English presentations yield the same scientific result.

erbio_run_app() launches the Shiny application bundled with ERBioR.

Value

erbio_set_language() sets the active presentation language.

erbio_get_language() returns the active language.

Registry loading functions return data frames. Registry validation functions return structured validation results.

erbio_translate_ui() returns translated interface text.

erbio_get_questionnaire_i18n() returns a questionnaire with the selected presentation language.

erbio_bilingual_invariance_check() returns the result of the cross-language scientific invariance check.

erbio_preventive_action() returns the approved preventive-action information associated with an ERBioR item.

erbio_run_app() launches the bundled Shiny application.

erbio_shiny_build_id() returns the identifier of the bundled Shiny build.

References

Aguilar-Elena, R. (2015). Riesgos biológicos laborales: ERBio, un nuevo método de evaluación teórica. doi:10.5281/zenodo.22107465.

Examples

old_lang <- erbio_get_language()
erbio_set_language("en")
erbio_get_language()
erbio_set_language(old_lang)

dict <- erbio_load_ui_dictionary()
head(dict)

tr <- erbio_load_translation_registry()
head(tr)

Biological-Agent Registry and ERBio Reference Levels

Description

Query the regulatory biological-agent registry, inspect source rules and derive ERBio reference levels without silently treating unlisted agents as group 1.

Usage

erbio_load_agent_registry(path = NULL)
erbio_load_basebio_index(path = NULL)
erbio_agent_rules(rule_id = NULL, path = NULL)
erbio_validate_agent_registry(path = NULL)
erbio_agent_lookup(query, type = NULL, exact = TRUE, path = NULL)
erbio_reference_level_from_agent(agent, path = NULL, allow_partial = FALSE)
erbio_unclassified_human_virus(agent_name)
erbio_reference_level_from_agents(agents,
  policy = c("report_all", "explicit_max_group"), path = NULL)
erbio_assess_agent_questionnaire(agent, questionnaire_id, responses, exposure,
  version = NULL, scoring = NULL, path = NULL,
  compliance_boundary_policy = c("prose_2015", "table45_intervals", "strict"),
  full_compliance_rule = c("flag_only", "thesis_override"))

Arguments

Details

The legal group is taken from the Spanish regulatory layer. In the v0.7 audited data layer, the primary row source is Order TES/1287/2021 (BOE-A-2021-19371), which replaced Annex II of Real Decreto 664/1997. The consolidated real decree is retained as a secondary convenience reference. BASEBiO is retained as a technical enrichment layer and does not override the legal group. Agents not present in the classified list are not implicitly assigned to group 1. Independent row-by-row EUR-Lex concordance is not claimed until the dedicated EU audit is completed.

Value

Registry functions return data frames or QA lists. Reference-level functions return structured agent-reference objects or multi-agent result lists. erbio_assess_agent_questionnaire() returns an integrated agent and questionnaire assessment.

References

Orden TES/1287/2021, de 22 de noviembre, BOE-A-2021-19371, Annex II replacement.

Real Decreto 664/1997, de 12 de mayo, consolidated reference.

Commission Directive (EU) 2019/1833, Annex III update, and Commission Directive (EU) 2020/739 for SARS-CoV-2.

INSST BASEBiO biological-agent database.

Examples

erbio_agent_lookup("Bacillus anthracis")
erbio_reference_level_from_agent("Mycobacterium tuberculosis")
erbio_reference_level_from_agents(
  c("Bacillus anthracis", "Coxiella burnetii")
)

Core ERBio Calculation Functions

Description

Functions implementing the deterministic ERBio calculation layer: exposure, control compliance, probability, risk score (GRB), risk class and source-aware assessment aggregation.

Usage

erbio_probability_matrix()
erbio_risk_matrix()
erbio_risk_actions()
erbio_exposure_from_cadence(cadence)
erbio_exposure_level(exposure = NULL, time_percent = NULL,
  boundary_policy = c("strict", "upper_category", "lower_category"))
erbio_compliance_binary(responses)
erbio_compliance_audit_0_4(scores)
erbio_compliance_class(percent,
  boundary_policy = c("prose_2015", "table45_intervals", "strict"))
erbio_probability(compliance_class, exposure)
erbio_risk_score(probability, reference_level)
erbio_risk_class(score)
erbio_action(risk_class)
erbio_failed_controls(responses, item_text = NULL,
  scoring = c("binary", "audit_0_4"))
erbio_assess(reference_level, exposure, compliance_percent = NULL,
  responses = NULL, scoring = c("binary", "audit_0_4"), item_text = NULL,
  compliance_boundary_policy = c("prose_2015", "table45_intervals", "strict"),
  full_compliance_rule = c("flag_only", "thesis_override"))
erbio_assess_set(assessments,
  aggregation_rule = c("unresolved", "max_risk_extension"))

Arguments

Details

ERBioR preserves documented ambiguities rather than silently resolving them. In particular, the default aggregation policy does not invent a global risk class when questionnaire-level classes disagree.

Value

Matrix/reference functions return data frames or lookup values. Scoring functions return numeric or structured results. erbio_assess() returns an erbio_assessment object. erbio_assess_set() returns a structured list that preserves source-defined and unresolved aggregation status.

References

Aguilar-Elena, R. (2015). Riesgos biológicos laborales: ERBio, un nuevo método de evaluación teórica. doi:10.5281/zenodo.22107465.

Examples

erbio_probability("Aceptable", "Frecuente")
erbio_risk_score(probability = 2, reference_level = 3)
erbio_risk_class(6)

a <- erbio_assess(
  reference_level = 3,
  exposure = "Muy frecuente",
  compliance_percent = 82.5
)
a

Integral Workplace-Level ERBio Assessment

Description

Validate the required questionnaire set, evaluate one or more biological agents, preserve questionnaire and agent-level results, and build preventive planning candidates.

Usage

erbio_sector_questionnaires(path = NULL)
erbio_validate_workplace_questionnaires(questionnaire_responses, path = NULL,
  require_core = TRUE, require_sector = TRUE)
erbio_build_preventive_plan(questionnaire_scores, risk_results,
  priority_policy = c("context_only", "max_observed_extension"))
erbio_workplace_rules(rule_id = NULL, path = NULL)
erbio_assess_workplace(activity, agents, questionnaire_responses, exposure,
  versions = NULL, scoring = NULL, path = NULL, require_core = TRUE,
  require_sector = TRUE,
  questionnaire_aggregation_rule = c("unresolved", "max_risk_extension"),
  workplace_aggregation_rule = c("unresolved", "max_risk_extension"),
  preventive_priority_policy = c("context_only", "max_observed_extension"),
  compliance_boundary_policy = c("prose_2015", "table45_intervals", "strict"),
  full_compliance_rule = c("flag_only", "thesis_override"))

Arguments

Details

The default workplace policy preserves discordant questionnaire classes and multi-agent results rather than manufacturing a single global class. The highest observed risk class is reported separately as a descriptive field. Responsible person, target date and resources in the preventive plan are not inferred automatically.

Value

erbio_assess_workplace() returns an erbio_workplace_assessment containing agent summaries, questionnaire summaries, risk results, unresolved items, warnings, provenance and a deduplicated preventive plan.

References

Aguilar-Elena, R. (2015). Riesgos biológicos laborales: ERBio, un nuevo método de evaluación teórica. doi:10.5281/zenodo.22107465.

Examples

responses <- list(
  audit = rep("Si", 32),
  general = rep("Si", 48),
  workers = rep("Si", 34),
  sec_wastewater = rep("Si", 12)
)

x <- erbio_assess_workplace(
  activity = "Tratamiento de aguas residuales",
  agents = "Mycobacterium tuberculosis",
  questionnaire_responses = responses,
  exposure = "Frecuente"
)
x

Render and Export Reproducible ERBio Workplace Reports

Description

Render a workplace assessment to Markdown or export the full reproducibility bundle to files.

Usage

erbio_render_workplace_report(x, max_plan_rows = 100L)
erbio_write_workplace_report(x, file = "ERBioR_workplace_report.md",
  max_plan_rows = 100L)
erbio_export_workplace_bundle(x, dir, overwrite = FALSE,
  max_plan_rows = 100L)

Arguments

Value

erbio_render_workplace_report() returns a character string; erbio_write_workplace_report() returns the normalized report path; erbio_export_workplace_bundle() returns a named character vector of written artifact paths.

Examples

responses <- list(
  audit = rep("Si", 32),
  general = rep("Si", 48),
  workers = rep("Si", 34),
  sec_wastewater = rep("Si", 12)
)
x <- erbio_assess_workplace(
  "Tratamiento de aguas residuales",
  "Mycobacterium tuberculosis",
  responses,
  "Frecuente"
)
substr(erbio_render_workplace_report(x), 1, 120)

ERBio Questionnaire Data and Assessment

Description

Access, validate, score and assess versioned ERBio questionnaires while preserving item identifiers, source provenance and validation status.

Usage

erbio_load_question_bank(path = NULL)
erbio_load_questionnaire_registry(path = NULL)
erbio_questionnaire_catalog(path = NULL)
erbio_get_questionnaire(questionnaire_id, version = NULL, path = NULL)
erbio_validate_question_bank(path = NULL)
erbio_score_questionnaire(questionnaire_id, responses, version = NULL,
  scoring = c("default", "binary", "audit_0_4"), path = NULL,
  language = erbio_get_language())
erbio_assess_questionnaire(questionnaire_id, responses, reference_level,
  exposure, version = NULL,
  scoring = c("default", "binary", "audit_0_4"), path = NULL,
  compliance_boundary_policy = c("prose_2015", "table45_intervals", "strict"),
  full_compliance_rule = c("flag_only", "thesis_override"))
erbio_questionnaire_rules(questionnaire_id = NULL)

Arguments

Details

Not-applicable items are excluded from the compliance denominator. Core and sector-specific questionnaires retain their documented validation status rather than being labelled uniformly.

Value

Load/catalog functions return data frames. Validation returns a structured QA list. erbio_score_questionnaire() returns an erbio_questionnaire_score; erbio_assess_questionnaire() returns an erbio_questionnaire_assessment including failed controls and source warnings.

References

Aguilar-Elena, R. (2015). Riesgos biológicos laborales: ERBio, un nuevo método de evaluación teórica. doi:10.5281/zenodo.22107465.

Examples

cat <- erbio_questionnaire_catalog()
head(cat)

general <- erbio_get_questionnaire("general")
nrow(general)

score <- erbio_score_questionnaire("general", rep("Si", 48))
score

assessment <- erbio_assess_questionnaire(
  "general", rep("Si", 48), reference_level = 3, exposure = "Frecuente"
)
assessment

ERBioR Version Information

Description

Return the ERBioR development version and frozen report-layer identifier.

Usage

erbio_version()
erbio_report_patch_version()

Value

A length-one character string.

Examples

erbio_version()
erbio_report_patch_version()