{
 "id": "cup2016",
 "title": "WCRF/AICR CUP 2016/2017 (SLR 2016, Figs. 125/132/139): red meat per 100 g/day",
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   "name": "Colon – corrected: errors only (model choices as published)",
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     1.4207243203243667
    ],
    "larsson2005": [
     1.14637310753022,
     0.9022038291858254,
     1.4566235025342762
    ],
    "norat2005": [
     1.063640728032427,
     0.8581180754977425,
     1.3183868638044174
    ],
    "english2004": [
     1.0464906104472864,
     0.8344441893235878,
     1.3124216235984245
    ],
    "wei2004": [
     1.16080785450603,
     0.9247884438038438,
     1.4570628386536204
    ],
    "jarvinen2001": [
     1.1014137226829976,
     0.8713980554553571,
     1.3921447046155
    ]
   }
  },
  {
   "name": "Rectum – corrected: all classes",
   "k": 6,
   "re": [
    1.1052943016187926,
    0.8711526541537554,
    1.4023667234047743
   ],
   "fe": [
    1.105738145030306,
    0.8878767584691376,
    1.3770569324093433
   ],
   "I2": 12.94089520889021,
   "Q": 5.743224688557313,
   "tau2": 0.011577034919202518,
   "published": null,
   "comment": "",
   "rows": [
    {
     "label": "takachi2011",
     "cohort": "jphc",
     "rr": 0.9548993969806616,
     "lo": 0.6324995505698258,
     "hi": 1.4416340020045089,
     "w": 26.46090732380535,
     "note": "dose: paper's red-meat medians"
    },
    {
     "label": "lee2009",
     "cohort": "lee2009",
     "rr": 0.74,
     "lo": 0.33,
     "hi": 1.66,
     "w": 8.131193774857882,
     "note": "CUP: red meat (undefined)"
    },
    {
     "label": "larsson2005",
     "cohort": "larsson2005",
     "rr": 0.98,
     "lo": 0.55,
     "hi": 1.72,
     "w": 15.337774689351674,
     "note": "CUP: unprocessed red meat"
    },
    {
     "label": "norat2005",
     "cohort": "epic",
     "rr": 1.75,
     "lo": 0.93,
     "hi": 3.3,
     "w": 12.720756589830206,
     "note": "model: calibrated"
    },
    {
     "label": "english2004",
     "cohort": "mccs",
     "rr": 1.4839,
     "lo": 0.9431,
     "hi": 2.3769,
     "w": 21.956349512254658,
     "note": "model: adjusted for processed meat"
    },
    {
     "label": "wei2004",
     "cohort": "wei2004",
     "rr": 0.89,
     "lo": 0.5,
     "hi": 1.56,
     "w": 15.39301810990023,
     "note": "CUP: red meat as main dish"
    }
   ],
   "loo": {
    "takachi2011": [
     1.159401128680262,
     0.8627015077721076,
     1.5581414487803977
    ],
    "lee2009": [
     1.1454763654544204,
     0.8922298473275408,
     1.4706032394509063
    ],
    "larsson2005": [
     1.12902371919441,
     0.8468803018217689,
     1.5051649634092508
    ],
    "norat2005": [
     1.0385871045972208,
     0.8219561204185488,
     1.3123123571199542
    ],
    "english2004": [
     1.01502265161651,
     0.7910319775669933,
     1.30243910804144
    ],
    "wei2004": [
     1.1499625943327383,
     0.8741243686757431,
     1.5128441852820975
    ]
   }
  },
  {
   "name": "Rectum – corrected: errors only (model choices as published)",
   "k": 6,
   "re": [
    1.125539157219543,
    0.9426309863040071,
    1.3439388401623282
   ],
   "fe": [
    1.125539157219543,
    0.9426309863040071,
    1.3439388401623282
   ],
   "I2": 0.0,
   "Q": 4.9376059837648985,
   "tau2": 0.0,
   "published": null,
   "comment": "",
   "rows": [
    {
     "label": "takachi2011",
     "cohort": "jphc",
     "rr": 0.9548993969806616,
     "lo": 0.6324995505698258,
     "hi": 1.4416340020045089,
     "w": 18.534741760067472,
     "note": "dose: paper's red-meat medians"
    },
    {
     "label": "lee2009",
     "cohort": "lee2009",
     "rr": 0.74,
     "lo": 0.33,
     "hi": 1.66,
     "w": 4.8203953834430155,
     "note": "CUP: red meat (undefined)"
    },
    {
     "label": "larsson2005",
     "cohort": "larsson2005",
     "rr": 0.98,
     "lo": 0.55,
     "hi": 1.72,
     "w": 9.677281403962205,
     "note": "CUP: unprocessed red meat"
    },
    {
     "label": "norat2005",
     "cohort": "norat2005",
     "rr": 1.23,
     "lo": 0.94,
     "hi": 1.62,
     "w": 42.46262207817418,
     "note": "CUP: red meat"
    },
    {
     "label": "english2004",
     "cohort": "english2004",
     "rr": 1.57,
     "lo": 0.99,
     "hi": 2.49,
     "w": 14.788033193514527,
     "note": "CUP: fresh red meat"
    },
    {
     "label": "wei2004",
     "cohort": "wei2004",
     "rr": 0.89,
     "lo": 0.5,
     "hi": 1.56,
     "w": 9.716926180838598,
     "note": "CUP: red meat as main dish"
    }
   ],
   "loo": {
    "takachi2011": [
     1.1635362233619404,
     0.9475853041125187,
     1.428701497585289
    ],
    "lee2009": [
     1.1497001093917723,
     0.9586044539712062,
     1.378890256622109
    ],
    "larsson2005": [
     1.130244290025842,
     0.9150615500532749,
     1.3960286661172094
    ],
    "norat2005": [
     1.0521440077271818,
     0.8262274349089466,
     1.339833278615606
    ],
    "english2004": [
     1.0623722347839262,
     0.876681730379513,
     1.2873939608062905
    ],
    "wei2004": [
     1.1506718946951229,
     0.9468604177390502,
     1.3983537429971689
    ]
   }
  }
 ],
 "deviations": [
  {
   "study": "ollberding2012",
   "class": "exposure",
   "text": "CUP used MEC's 'total red meat' row, which includes processed meat; the paper prints 'red meat excluding processed' in the same table",
   "page": "SLR 2016 T79 p341–342; Ollberding 2012 Table 2",
   "alternative": [
    0.9665,
    0.8292,
    1.1264
   ],
   "alt_note": "paper's unprocessed row, GL with the SLR's energy conversion",
   "outcome": "colorectal"
  },
  {
   "study": "norat2005",
   "class": "model",
   "text": "CUP used the observed estimate; EPIC also prints the measurement-error-calibrated estimate 1.49 (0.91–2.43) per 100 g",
   "page": "SLR 2016 T79; Norat 2005 Table 4",
   "alternative": [
    1.49,
    0.91,
    2.43
   ],
   "alt_note": "calibrated estimate, Table 4",
   "outcome": "colorectal"
  },
  {
   "study": "english2004",
   "class": "model",
   "text": "CUP used the model not adjusted for processed meat; the paper also gives the mutually adjusted estimate (1.12 per 100 g after ×5.83)",
   "page": "SLR 2016 T79; English 2004 text/Table 3",
   "alternative": [
    1.1225,
    0.8888,
    1.5666
   ],
   "alt_note": "model adjusted for processed meat, per serving/week × 5.83",
   "outcome": "colorectal"
  },
  {
   "study": "english2004",
   "class": "cases",
   "text": "452 tumours entered as cases; 451 persons; contrast '<3' not '≤3'",
   "page": "SLR 2016 T79; English 2004 Table 1",
   "alternative": null,
   "alt_note": "",
   "outcome": "colorectal"
  },
  {
   "study": "jarvinen2001",
   "class": "exposure",
   "text": "Järvinen's row is labelled 'Red meat' (Table 3), but its quartile cut-points are 91–94 % of those for 'Meat, all', i.e. near-total meat; SLR 2010 itself flagged Järvinen, Lee and Nöthlings as undefined and ran without them (1.21, 1.06–1.37, p156)",
   "page": "SLR 2016 T79; Järvinen 2001 Table 2",
   "alternative": "remove",
   "alt_note": "no red-meat row in the paper",
   "outcome": "colorectal"
  },
  {
   "study": "jarvinen2001",
   "class": "cases",
   "text": "CUP's colorectal case count includes the 63 colon cases twice in its total",
   "page": "SLR 2016 T79",
   "alternative": null,
   "alt_note": "",
   "outcome": "colorectal"
  },
  {
   "study": "lee2009",
   "class": "transcription",
   "text": "2010 extraction 0.80 (0.52–1.23); 2016 re-extraction 0.81 (0.50–1.29) from the same table",
   "page": "SLR 2010 Fig 70; SLR 2016 Fig 125",
   "alternative": null,
   "alt_note": "",
   "outcome": "colorectal"
  },
  {
   "study": "takachi2011",
   "class": "dose",
   "text": "CUP's men's doses (20–117 g) are the medians for total meat; red meat medians are 15–102 g (Table 2)",
   "page": "SLR 2016 T79; Takachi 2011 Table 2",
   "alternative": [
    1.394970580080643,
    1.0751170832467631,
    1.8099823262169192
   ],
   "alt_note": "GL with the paper's red-meat medians, men+women fixed",
   "outcome": "colon"
  },
  {
   "study": "takachi2011",
   "class": "exposure",
   "text": "JPHC 'red meat' includes ham, sausage and bacon; no unprocessed row in the paper",
   "page": "Takachi 2011 Methods",
   "alternative": null,
   "alt_note": "",
   "outcome": "colon"
  },
  {
   "study": "takachi2011",
   "class": "cases",
   "text": "men's colon cases 481, CUP entered 259",
   "page": "SLR 2016 T79; Takachi 2011 Table 2",
   "alternative": null,
   "alt_note": "",
   "outcome": "colon"
  },
  {
   "study": "larsson2005_distal",
   "class": "duplicate",
   "text": "SMC entered twice (distal and proximal colon as separate rows); one cohort, one row",
   "page": "SLR 2016 Fig 128",
   "alternative": [
    1.6851769595085448,
    1.1108464998521765,
    2.556448064819367
   ],
   "alt_note": "distal + proximal combined (fixed) as one SMC row",
   "outcome": "colon"
  },
  {
   "study": "larsson2005_proximal",
   "class": "duplicate",
   "text": "see distal row",
   "page": "SLR 2016 Fig 128",
   "alternative": "remove",
   "alt_note": "",
   "outcome": "colon"
  },
  {
   "study": "jarvinen2001",
   "class": "exposure",
   "text": "near-total meat (see CRC)",
   "page": "Järvinen 2001 Table 3",
   "alternative": "remove",
   "alt_note": "no red-meat row",
   "outcome": "colon"
  },
  {
   "study": "norat2005",
   "class": "model",
   "text": "observed estimate used; calibrated colon estimate 1.36 (0.74–2.50) printed",
   "page": "Norat 2005 Table 4",
   "alternative": [
    1.36,
    0.74,
    2.5
   ],
   "alt_note": "calibrated",
   "outcome": "colon"
  },
  {
   "study": "english2004",
   "class": "model",
   "text": "model not adjusted for processed meat",
   "page": "English 2004",
   "alternative": [
    1.0,
    0.697,
    1.4048
   ],
   "alt_note": "adjusted for processed meat",
   "outcome": "colon"
  },
  {
   "study": "wei2004",
   "class": "exposure",
   "text": "'red meat as main dish' excludes hamburger and mixed dishes; NHS and HPFS combined by CUP",
   "page": "Wei 2004 Table II",
   "alternative": null,
   "alt_note": "",
   "outcome": "colon"
  },
  {
   "study": "bostick1994",
   "class": "exposure",
   "text": "'red meat main dish' includes ham",
   "page": "Bostick 1994 Table 3",
   "alternative": null,
   "alt_note": "",
   "outcome": "colon"
  },
  {
   "study": "jarvinen2001",
   "class": "exposure",
   "text": "near-total meat",
   "page": "Järvinen 2001",
   "alternative": "remove",
   "alt_note": "",
   "outcome": "rectum"
  },
  {
   "study": "takachi2011",
   "class": "dose",
   "text": "men's doses are total-meat medians",
   "page": "Takachi 2011 Table 2",
   "alternative": [
    0.9548993969806616,
    0.6324995505698258,
    1.4416340020045089
   ],
   "alt_note": "paper's red-meat medians",
   "outcome": "rectum"
  },
  {
   "study": "norat2005",
   "class": "model",
   "text": "observed estimate used; calibrated rectum estimate 1.75 (0.93–3.30) printed",
   "page": "Norat 2005 Table 4",
   "alternative": [
    1.75,
    0.93,
    3.3
   ],
   "alt_note": "calibrated",
   "outcome": "rectum"
  },
  {
   "study": "english2004",
   "class": "model",
   "text": "model not adjusted for processed meat (adjusted gives 1.48)",
   "page": "English 2004",
   "alternative": [
    1.4839,
    0.9431,
    2.3769
   ],
   "alt_note": "adjusted for processed meat",
   "outcome": "rectum"
  }
 ],
 "notes": [
  "Assumptions CUP made that are not errors (portion 120 g for Larsson 2005 and Bostick 1994; Tiemersma and Singh open-top doses) are handled in the multiverse (kontroll/multiverse_report.md), not as deviations.",
  "Papadimitriou 2022 (EPIC) reports colorectal only; no colon follow-up for EPIC."
 ]
}