Risk Management with r4subrisk • r4subrisk

Clinical submissions require a systematic approach to identifying, scoring, and mitigating risks. The r4subrisk package implements an FMEA (Failure Mode and Effects Analysis) based risk framework aligned with ICH Q9 quality risk management principles.

library(r4subrisk)

Default configuration

risk_config_default() defines the RPN (Risk Priority Number) band thresholds and scoring scales:

cfg <- risk_config_default()
cfg$rpn_bands
#> $critical
#> [1]  80 125
#> 
#> $high
#> [1] 40 79
#> 
#> $medium
#> [1] 15 39
#> 
#> $low
#> [1]  1 14
cfg$required_origins
#> NULL

Creating a risk register

A risk register is built from a data frame with at minimum risk_id, description, probability, impact, and detectability — each scored 1–5. The RPN is computed as probability * impact * detectability.

risks <- data.frame(
  risk_id       = paste0("RISK-00", 1:5),
  description   = c(
    "Missing required variables in ADSL",
    "Incomplete derivation documentation for ADTTE",
    "Independent QC not completed for ADRS",
    "Define-XML missing codelist references",
    "ADRG not included in submission package"
  ),
  category      = c("data_quality", "traceability", "process",
                    "documentation", "regulatory"),
  probability   = c(3L, 4L, 2L, 2L, 1L),
  impact        = c(4L, 5L, 5L, 3L, 5L),
  detectability = c(2L, 3L, 4L, 2L, 1L),
  owner         = c("Data Mgmt", "Stats", "Stats", "Programming", "Regulatory"),
  stringsAsFactors = FALSE
)

rr <- create_risk_register(risks)
print(rr)
#> ℹ Risk Register: 5 risk(s), 5 open
#> ℹ   Critical: 0, High: 2, Mean RPN: 28.2
#> # A tibble: 5 × 11
#>   risk_id description category probability impact detectability owner mitigation
#> * <chr>   <chr>       <chr>          <dbl>  <dbl>         <dbl> <chr> <chr>     
#> 1 RISK-0… Missing re… data_qu…           3      4             2 Data… NA        
#> 2 RISK-0… Incomplete… traceab…           4      5             3 Stats NA        
#> 3 RISK-0… Independen… process            2      5             4 Stats NA        
#> 4 RISK-0… Define-XML… documen…           2      3             2 Prog… NA        
#> 5 RISK-0… ADRG not i… regulat…           1      5             1 Regu… NA        
#> # ℹ 3 more variables: status <chr>, rpn <dbl>, risk_level <chr>

Computing risk scores

compute_risk_scores() returns aggregate metrics including overall risk score (normalized 0-1), mean RPN, and per-category breakdown:

rs <- compute_risk_scores(rr)
rs$overall_risk_score
#> [1] 0.2256
rs$mean_rpn
#> [1] 28.2
rs$risk_distribution
#> # A tibble: 3 × 2
#>   risk_level     n
#>   <chr>      <int>
#> 1 high           2
#> 2 low            2
#> 3 medium         1
rs$category_summary
#> # A tibble: 5 × 3
#>   category          n mean_rpn
#>   <chr>         <int>    <dbl>
#> 1 data_quality      1       24
#> 2 documentation     1       12
#> 3 process           1       40
#> 4 regulatory        1        5
#> 5 traceability      1       60

Applying mitigations

apply_mitigations() updates the register with post-control scores to show residual risk after mitigations are applied:

controls <- data.frame(
  risk_id               = c("RISK-001", "RISK-002", "RISK-003"),
  mitigation            = c(
    "Automated variable check implemented in CI pipeline",
    "Derivation review added to QC checklist",
    "QC sign-off required before dataset lock"
  ),
  probability_residual  = c(1L, 2L, 1L),
  impact_residual       = c(4L, 5L, 5L),
  detectability_residual = c(1L, 1L, 1L),
  stringsAsFactors = FALSE
)

rr_mitigated <- apply_mitigations(rr, controls)

Comparing registers

compare_risk_registers() shows the RPN change before and after mitigations:

comparison <- compare_risk_registers(rr, rr_mitigated)
comparison
#> $rpn_changes
#> # A tibble: 5 × 4
#>   risk_id  rpn_before rpn_after rpn_delta
#>   <chr>         <dbl>     <dbl>     <dbl>
#> 1 RISK-001         24        24         0
#> 2 RISK-002         60        60         0
#> 3 RISK-003         40        40         0
#> 4 RISK-004         12        12         0
#> 5 RISK-005          5         5         0
#> 
#> $new_risks
#> character(0)
#> 
#> $resolved_risks
#> character(0)
#> 
#> $level_transitions
#> # A tibble: 5 × 4
#>   risk_id  level_before level_after changed
#>   <chr>    <chr>        <chr>       <lgl>  
#> 1 RISK-001 medium       medium      FALSE  
#> 2 RISK-002 high         high        FALSE  
#> 3 RISK-003 high         high        FALSE  
#> 4 RISK-004 low          low         FALSE  
#> 5 RISK-005 low          low         FALSE  
#> 
#> $delta_mean_rpn
#> [1] 0

Integration with r4subcore evidence

evidence_to_risks() converts an evidence table with indicator_domain == "risk" into a risk register format, allowing automation of risk identification from evidence outputs:

# Requires r4subcore
ctx <- r4subcore::r4sub_run_context(study_id = "STUDY01")
ev <- r4subcore::as_evidence(
  data.frame(
    asset_type = "program", asset_id = "prod_adrs.R",
    source_name = "r4subrisk", source_version = "0.1.0",
    indicator_id = "R-001", indicator_name = "Program Validation",
    indicator_domain = "risk", severity = "high",
    result = "fail", metric_value = 0, metric_unit = "score",
    message = "DVP not submitted", location = "prod_adrs.R",
    evidence_payload = "{}", stringsAsFactors = FALSE
  ), ctx = ctx
)
risk_df <- evidence_to_risks(ev)
rr_from_evidence <- create_risk_register(risk_df)