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  "Package": "picMort",
  "Title": "Reproducible Pediatric ICU Mortality Benchmark on PIC V1.1.0",
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  "Authors@R": "c(\nperson(\"Max\", \"Moldovan\", email = \"max.moldovan@adelaide.edu.au\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9680-8474\")),\nperson(\"Usman\", \"Iqbal\", role = c(\"aut\", \"ths\")))",
  "Description": "Tools and pipelines for a calibration-first pediatric ICU\nmortality benchmark on the open-access PIC v1.1.0 database.\nAuthoritative cohort specification, T+24h prediction-window\nfeature extraction, PIM3 reconstruction, calibration and\ndecision-curve evaluation. The package is the methodological\nsubstrate for the companion manuscript, illustrated end to end\nin a worked vignette.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/max578/picMort,\nhttps://max578.github.io/picMort",
  "BugReports": "https://github.com/max578/picMort/issues",
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  "Repository": "https://max578.r-universe.dev",
  "Date/Publication": "2026-05-25 00:14:04 UTC",
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  "Author": "Max Moldovan [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9680-8474>),\nUsman Iqbal [aut, ths]",
  "Maintainer": "Max Moldovan <max.moldovan@adelaide.edu.au>",
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    },
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