NEWS

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pmxdchk 0.0.0.9000

Checks

• Every check now carries a plain-language rule and guidance on what to do when it flags; check_catalogue() lists them and the app shows them next to each finding.
• run_nmpk_checks() returns a title column, and partial thresholds lists fall back to default_thresholds(). New thresholds: outlier_iqr_k and predose_cmax_frac.
• New findings: DV or MDV = 0 on dose records (CORE-OBS-001), DV below LLOQ without a BLQ flag (CORE-OBS-002), non-numeric ID (CORE-STRUCT-002), missing EVID (CORE-STRUCT-003), ID versus USUBJID uniqueness (CORE-INT-001), exclusion reason on a record that is not excluded (CORE-MR-001), ADDL on non-dose records (CORE-DOSE-005), and placeholder RATE values or AMT / RATE / DUR disagreement (CORE-DOSE-006).
• Fewer false positives: outliers are compared within nominal time point and analyte (CORE-OBS-005, CORE-TIME-004), BLQ troughs before the next dose are not "mid-profile" (CORE-OBS-003), ordinary dose levels are not outliers (CORE-DOSE-002), TIME may restart on reset records (CORE-TIME-001), and time-varying covariates are no longer reported as inconsistent fixed covariates (CORE-COV-001, CORE-COV-006).
• Changed rules: predose concentrations are compared with 5% of the subject's Cmax (CORE-OBS-004); covariate outliers use boxplot fences and cover more covariates (CORE-COV-004); missingness is reported by event type and flags only unexpected gaps (CORE-STRUCT-006); duplicates are split into exact rows and conflicting values (CORE-STRUCT-005); cross-study medians are compared from two studies upwards (CORE-INT-003); CORE-MR-003 lists the subjects flagged by other checks.
• USUBJID and VISIT are canonical variables; USUBJID is no longer preferred over a numeric identifier for ID.

App

• Built-in example datasets can be loaded from the Data tab.
• Uploads accept comma-, semicolon-, tab-, and space-delimited text and read ., the NONMEM null value, as missing.
• Findings is the main workspace: it lists the checks to review with triage progress, and for the selected check shows the rule, guidance, the profile of each affected subject, all result tables, and the triage decision, which is saved as it is entered.
• Overview describes the dataset before any check runs: all concentration-time profiles (by time since first dose or after the last dose), dose levels, and missing values by event type.
• The sidebar is replaced by a status line with the dataset, the state of the last run, and a run button; thresholds moved to the Data tab.
• Profiles can be filtered by check; new Check library tab.
• Results are cleared when another dataset is confirmed; a column can no longer be mapped to two variables.
• New compact, neutral theme. The Data tab shows the three steps next to the data preview; the status line stays visible while scrolling; the Findings tab shows the number of checks to review; severity, result, and triage state are shown as badges; plots use a colour-blind safe palette.