[
 {
  "from": "prereg:14d63d842044a2f68444746e488077c35a7bb4869c7006646f8e1d69782e7012",
  "kind": "changed",
  "detail": "Added code/summarize.py, which reads the registered outputs results/R1.json to R6.json and, in this version, results/V.json, and writes results/S.json, the same values rounded for display (ratios and intervals to two decimals, p- and q-values to two significant digits or '< 0.001'), and results/outcomes.csv, every registered family A and B estimate in one table. code/run calls it last. The registered analysis (code/analyze.py), its data and its parameters are unchanged, so R1.json to R6.json are exactly what the registered plan produces.",
  "claims": [
   "C1",
   "C2",
   "C3",
   "C4",
   "C5",
   "C6",
   "C7",
   "C8",
   "C9"
  ]
 },
 {
  "from": "prereg:14d63d842044a2f68444746e488077c35a7bb4869c7006646f8e1d69782e7012",
  "kind": "changed",
  "claims": [
   "C1",
   "C2",
   "C3",
   "C4",
   "C5",
   "C7",
   "C8"
  ],
  "detail": "The plan calls an outcome's count participants affected. For an outcome of several terms it is the sum of the terms' counts, in which a participant with two of the terms counts twice, so this version calls those counts reports and their ratios ratios of reports per participant, and keeps 'participants' for single preferred terms, deaths and any serious event (V.json, outcomes.*.counts). The counts themselves are unchanged."
 },
 {
  "from": "prereg:14d63d842044a2f68444746e488077c35a7bb4869c7006646f8e1d69782e7012",
  "kind": "changed",
  "claims": [
   "C1",
   "C2",
   "C3",
   "C4",
   "C5",
   "C6",
   "C7",
   "C8",
   "C9"
  ],
  "detail": "The plan uses the Greenland-Robins variance and calls an outcome robust when q < 0.05 and p < 0.05 with a conservative variance, under random effects, and with every single trial left out; its scans give organ systems the conservative variance. Reviews showed the conservative variance is not a bound (it caps an outcome's overcount at the all-events factor, which one outcome can exceed). This version adds a variance clustered by trial (code/revised.py), uses the wider of it and the Greenland-Robins variance for every interval, p- and q-value in the claims and in a repeat of both scans, and calls an outcome robust when q < 0.05 and every leave-one-out p < 0.05 on that variance and the registered random-effects p < 0.05. The random-effects, Peto, single-term, selective-agonist and population estimates stay as registered, on binomial variances. The registered estimates, rule and scans stay in R2.json to R5.json; no claim rests on the conservative variance."
 },
 {
  "from": "prereg:14d63d842044a2f68444746e488077c35a7bb4869c7006646f8e1d69782e7012",
  "kind": "changed",
  "claims": [
   "C2"
  ],
  "detail": "Added after review: bounds on the participants with an outcome from each adverse-event group's reported rows; each comparison arm's count divided by that arm's own serious terms per participant with a serious event, and the same with factors pooled over all comparisons, which the stratified comparison does not use; the uniform ratio of the arms' terms per participant at which the unadjusted interval reaches one, its width held fixed; and each preferred term within bacterial infections and pneumonia with at least 20 participants, estimated alone, with the groups that report it in more than one row. None of these is in the plan."
 },
 {
  "from": "prereg:14d63d842044a2f68444746e488077c35a7bb4869c7006646f8e1d69782e7012",
  "kind": "changed",
  "claims": [
   "C4",
   "C5"
  ],
  "detail": "The plan's categories set the trials' interval against the atlas's point estimate without its uncertainty or a correction for the 44 outcomes tested. Added after review: the ratio of the trials' estimate to the atlas's hazard ratio with an interval from both variances, Benjamini-Hochberg over the outcomes tested, and categories built on it (consistent, meaning significant in the trials in the atlas's direction with no difference detected, which is not a test of equivalence; same direction but different in size; opposite; different; inconclusive; too few events), and a table of how the atlas and the trials differ. Acute pancreatitis is marked not comparable in kind, since the atlas's outcome is drug-induced pancreatitis (data/revised.json), with the largest share of cases a subtype rising by the atlas's factor could make up within the trials' upper limit, the rest unchanged. The registered categories stay in R2.json and R6.json; under them arthritis, gastritis and deep vein thrombosis excluded the atlas's estimate, and here they are inconclusive."
 },
 {
  "from": "prereg:14d63d842044a2f68444746e488077c35a7bb4869c7006646f8e1d69782e7012",
  "kind": "changed",
  "claims": [
   "C9"
  ],
  "detail": "Added after review: two blind coders and a third reader classified how long each eligible trial recorded serious events, from its adverse-event time frame and description alone (data/ae_window/), as on treatment, in trial, the trial's calendar, or unstated, and every estimate is repeated in each group and in all trials not coded as on treatment, with a test of the difference between those and the on-treatment trials. A calendar period may hide recording that stops with treatment, and only three trials are coded in trial. The coding was done after the results were known; the coders saw no counts."
 },
 {
  "from": "prereg:14d63d842044a2f68444746e488077c35a7bb4869c7006646f8e1d69782e7012",
  "kind": "changed",
  "detail": "Added after seeing that COVID-19 pneumonia was a large share of pneumonia reports: pneumonia estimated without the preferred terms naming a coronavirus (data/revised.json). Chosen after seeing the terms."
 },
 {
  "from": "prereg:14d63d842044a2f68444746e488077c35a7bb4869c7006646f8e1d69782e7012",
  "kind": "changed",
  "claims": [
   "C3"
  ],
  "detail": "The plan calls the second half's check a replication and gives organ systems the conservative variance. Both halves share the registry, the coding and the event threshold that chose the items, so this version calls it a check in the held-out half, not an outside replication, and repeats both scans with the wider variance (V.json scans), on which C3 rests: hepatobiliary disorders, which missed the second half under the conservative variance, is found again there, higher on the drugs. The registered scans stay in R4.json and R5.json."
 }
]