Code

Prospective refactor#77

Code

Open

joshwlambert wants to merge 35 commits intoepiforecasts:mainepiforecasts/ringbp:mainfrom joshwlambert:sandboxjoshwlambert/ringbp:sandboxCopy head branch name to clipboard

+795-602

Commits

Commits on Aug 20, 2024

• updated RoxygenNote in DESCRIPTION

  joshwlambert

  committed
  5958c8a

• remove NULL argument defaults from outbreak_model()

  joshwlambert

  committed
  9d8e4c9

• move argument documentation from outbreak_step to outbreak_model and order to match func signature

  joshwlambert

  committed
  bdf064f

• remove NULL argument defaults from outbreak_step

  joshwlambert

  committed
  b29f649

• order outbreak_step arguments to match outbreak_model

  joshwlambert

  committed
  4a862ba

• remove empty line in outbreak_model

  joshwlambert

  committed
  f4d76e6

• linting aux_functions

  joshwlambert

  committed
  2dae23f

• linting outbreak_setup

  joshwlambert

  committed
  4a8c48d

• linting outbreak_model

  joshwlambert

  committed
  3f4f525

• linting test-outbreak_step

  joshwlambert

  committed
  e309b67

• linting test-basicusage

  joshwlambert

  committed
  da27861

• linting test-aux_functions

  joshwlambert

  committed
  6d21935

• linting testthat.R

  joshwlambert

  committed
  7a8afe1

• linting scenario_sim

  joshwlambert

  committed
  d1bfaa2

• linting parameter_sweep

  joshwlambert

  committed
  877e839

• change function arguments to snake case and merge duplicated @param num_initial_cases and prop_asym

  joshwlambert

  committed
  f79eeb2

• update variables to use snake case

  joshwlambert

  committed
  2a0f49d

• instead of manually setting r0subclin default in scenario_sim set argument default in scenario_sim, outbreak_model and outbreak_step

  joshwlambert

  committed
  664d70e

• instead of manually setting disp_subclin to disp_com in scenario_sim, set argument default in scenario_sim, outbreak_model and outbreak_step

  joshwlambert

  committed
  5dd95c6

• merge duplicated @param incfn

  joshwlambert

  committed
  2e38933

• merge duplicated @param delayfn

  joshwlambert

  committed
  dfb6b5b

Commits on Aug 21, 2024

• use scalar logical operators in if statement in outbreak_model

  joshwlambert

  committed
  bf013e6

• add checkmate as dependency

  joshwlambert

  committed
  3f92740

• fix mistake in dist_setup documentation

  joshwlambert

  committed
  5b66708

• add input checking to outbreak_model

  joshwlambert

  committed
  172d01b

• fix test-aux_functions by specifying quarantine

  joshwlambert

  committed
  d328e12

• make outbreak_setup internal (unexport)

  joshwlambert

  committed
  5e887ca

• make outbreak_step interal (unexport)

  joshwlambert

  committed
  66bd548

• update outbreak_model example to actually call outbreak_model

  joshwlambert

  committed
  d94b081

• remove dist_setup function

  joshwlambert

  committed
  7f6a899

• replace delay_shape and delay_scale with onset_to_isolation arg and replace hardcoded incubation period with incubation_period arg

  joshwlambert

  committed
  891f932

• replace instances of delayfn with onset_to_isolation

  joshwlambert

  committed
  e5775b7

• replace instances of incfn with incubation_period

  joshwlambert

  committed
  33226a9

• replace delay_shape and delay_scale args with onset_to_isolation and incubation_period args

  joshwlambert

  committed
  be94d1a

• remove dist_setup from _pkgdown.yml

  joshwlambert

  committed
  5c4be3d