Code

add more flexibility with delays#305

Code

Merged

sbfnk merged 42 commits intodevelopepiforecasts/EpiNow2:developfrom

flexible-delaysepiforecasts/EpiNow2:flexible-delaysCopy head branch name to clipboard

Nov 18, 2022

Commits

Commits on Oct 31, 2022

• add more flexibility with delays

  sbfnk

  committed
  a94f753

  Copy full SHA for a94f753

• update man pages

  sbfnk

  committed
  404d04c

  Copy full SHA for 404d04c

• check if truncation mean is uncertain

  sbfnk

  committed
  7bcf7a6

  Copy full SHA for 7bcf7a6

• start on static delays

  sbfnk

  committed
  3553b49

  Copy full SHA for 3553b49

• add generation time and truncation opts

  sbfnk

  committed
  f075f1d

  Copy full SHA for f075f1d

• update trunc_opts docs

  sbfnk

  committed
  2c51993

  Copy full SHA for 2c51993

• add NEWS

  sbfnk

  committed
  0479e32

  Copy full SHA for 0479e32

• run documentation update

  sbfnk

  committed
  381ed5a

  Copy full SHA for 381ed5a

• mention doc update in NEWS

  sbfnk

  committed
  c8f9c71

  Copy full SHA for c8f9c71

• optimise discrete pmfs

  sbfnk

  committed
  8e9c79d

  Copy full SHA for 8e9c79d

• explicit zero for first element of gt

  sbfnk

  committed
  cc31fc9

  Copy full SHA for cc31fc9

• remove deprecated discretised gamma pmf

  sbfnk

  committed
  564ac99

  Copy full SHA for 564ac99

• fix link

  sbfnk

  committed
  e01a7a4

  Copy full SHA for e01a7a4

• only revert after delta pmf

  sbfnk

  committed
  84dd939

  Copy full SHA for 84dd939

• simplify discrete delta pmf

  sbfnk

  committed
  33277f4

  Copy full SHA for 33277f4

• implement fixed delays in stan model

  sbfnk

  committed
  ec536c5

  Copy full SHA for ec536c5

• clarify NEWS

  sbfnk

  committed
  d2c00b7

  Copy full SHA for d2c00b7

• fix check for gt uncertainty

  sbfnk

  committed
  56c33ec

  Copy full SHA for 56c33ec

• create `gt_fixed` with the correct type

  sbfnk

  committed
  8ae1cbf

  Copy full SHA for 8ae1cbf

• update simulation model for flexible delays

  sbfnk

  committed
  63ba0ed

  Copy full SHA for 63ba0ed

• only calculate max fixed delay if we can

  sbfnk

  committed
  93aa345

  Copy full SHA for 93aa345

• use correct sd in gt

  sbfnk

  committed
  f922fcf

  Copy full SHA for f922fcf

• work out pmf parameters

  sbfnk

  committed
  c9b52d2

  Copy full SHA for c9b52d2

• don't reverse delay pmf

  sbfnk

  committed
  35a5838

  Copy full SHA for 35a5838

• update docs

  sbfnk

  committed
  f49443d

  Copy full SHA for f49443d

• use log parameters in lognormal

  Show description for 8a0b944
  sbfnk

  committed
  8a0b944

  Copy full SHA for 8a0b944

• fix truncation parameters

  sbfnk

  committed
  32ba0b0

  Copy full SHA for 32ba0b0

• fix no delay case

  sbfnk

  committed
  243cd99

  Copy full SHA for 243cd99

• document missing options

  sbfnk

  committed
  0f79151

  Copy full SHA for 0f79151

• adapt test to new function syntax

  sbfnk

  committed
  0361d02

  Copy full SHA for 0361d02

• change expected tests results (rounding differences)

  sbfnk

  committed
  ed003a8

  Copy full SHA for ed003a8

• simplify treatment of delay distributions

  sbfnk

  committed
  3f01a21

  Copy full SHA for 3f01a21

Commits on Nov 1, 2022

• fixes following more thorough testing

  sbfnk

  committed
  7c6bfa3

  Copy full SHA for 7c6bfa3

Commits on Nov 15, 2022

• more sensible default for max of distribution

  sbfnk

  committed
  20593d0

  Copy full SHA for 20593d0

• fix tests

  sbfnk

  committed
  c3fc270

  Copy full SHA for c3fc270

• flexible generation time weights

  sbfnk

  committed
  6b25de6

  Copy full SHA for 6b25de6

• size -> linewidth

  sbfnk

  committed
  91a006c

  Copy full SHA for 91a006c

• doc update

  sbfnk

  committed
  c353f3a

  Copy full SHA for c353f3a

• bring size back for geom_point

  sbfnk

  committed
  6d031ed

  Copy full SHA for 6d031ed

• update snaps

  sbfnk

  committed
  3d07292

  Copy full SHA for 3d07292

• update documentation

  sbfnk

  committed
  aaf2d1e

  Copy full SHA for aaf2d1e

Commits on Nov 16, 2022

• fix examples

  sbfnk

  committed
  0ede0b4

  Copy full SHA for 0ede0b4