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Simulation functions and vignette plus other things #199

Merged
merged 43 commits into from
Jul 31, 2024
Merged

Simulation functions and vignette plus other things #199

merged 43 commits into from
Jul 31, 2024

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ben18785
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  • creates a vignette
  • corrects lambda_over_both to handle foi=0 in three places
  • makes a public-facing probability simulation function
  • validates age bins in survey features

ben18785 and others added 30 commits May 15, 2024 14:08
@ben18785
#169 move probability functionality
e4d7f01
@ben18785
#169 corrections to exposure matrix and simulating time models first …
e3391df 
…draft
@ntorresd
fix(i169): minor corrections to simulation functionalities
d33282c
@ben18785
#169 chatgpt gave a useful tip about refactorising
e577a40
@ben18785
#169 removed redundant functions
1f14a31
@ben18785
#169 added all tests for simulate_serosurvey_time_model
0ad6e1b
@ben18785
#169 started to include docstrings
a480a7c
@ben18785
#169 added further docstrings and more tests incl seroreversion
f1fa164
@ben18785
#169 first draft of time-varying foi model with comprehensive unit tests
2ccf6ee
@ben18785
#169 started to add in age-varying simulation but there's an error wi…
338c6d1 
…th the age-varying probs
@ben18785
#169 tests corrected for probability exact calcs
d4a3f37
@ben18785
#169 first draft of age-varying simulation model with full tests
2c31fb8
@ben18785
#169 added master simulate function. Bug for sample_size_by_individua…
b15dae2 
…l_age_random needs sorting
@ben18785
added tests for master simulate function
618ea70
@ben18785
#169 corrected probability_exact_time_varying function (which now doe…
30cef67 
…s not use an exposure matrix)
@ben18785
#169 removed redundant age-varying probability calculator
bc5c705
@ben18785
#169 added validation functions for serosurveys
260d6bd
@ntorresd
fix(i169): correct age binning for data simulation function
ae2283a 
- Correct tests accordingly
- Avoids using `cut`
@ntorresd
test(i169): adds test draft for time-age model
fb24513
@ben18785
#169 corrected mistake which meant (previously) age and time model se…
445baa1 
…ropositivities were the same
@ben18785
Update simulate_serosurvey.R
2315e0b
@ben18785
#169 working draft of age and time model
3ce4bbf
@ben18785
#169 now passing all tests for simulate_serosurvey
29981ec
@ben18785
#169 added tidyr calls to expand_grid
af6633b
@ben18785
#169 corrected partial argument match
8bb65e5
@ntorresd
i169: remove old data simulation functions
3c3991a
@ben18785
#169 added validation error for simulation
ef6b796
@ntorresd
test(i169): remove old data simulation functions tests
c5b9f91
@ntorresd
update NAMESPACE
7a154f9
@ntorresd
fix: minor correction to simulate_serosurvey foi specification
3622401
@ben18785 ben18785 linked an issue Jul 19, 2024 that may be closed by this pull request
Changes to generate_sim_data #169
Closed
@ben18785 ben18785 requested a review from ntorresd July 19, 2024 16:54
@ntorresd ntorresd changed the base branch from main to dev July 19, 2024 22:31
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This pull request:

  • Adds 1 new dependencies (direct and indirect)
  • Adds 1 new system dependencies
  • Removes 0 existing dependencies (direct and indirect)
  • Removes 0 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

@github-actions GitHub Actions
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This pull request:

  • Adds 1 new dependencies (direct and indirect)
  • Adds 1 new system dependencies
  • Removes 0 existing dependencies (direct and indirect)
  • Removes 0 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

@github-actions GitHub Actions
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This pull request:

  • Adds 1 new dependencies (direct and indirect)
  • Adds 1 new system dependencies
  • Removes 0 existing dependencies (direct and indirect)
  • Removes 0 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

@ntorresd
doc: make sure old vignettes work as expected
68153b8 
(provisional) Manually change variable names to use visualization functions.
This will be remove after the refactorization of the package.
@ntorresd
doc: syntax changes to 'simulating_serosurveys.Rmd'
57fa10b 
- Use different names for foi data frames on each example
- Minor text and syntax changes to improve vignette's aesthetics
@ntorresd
doc: use different names for foi data frames on each example
6923235
@ntorresd
doc: add analytical solution line to seroprevalence plots in 'simulat…
617e4ed 
…ing_serosurveys.Rmd'
@ntorresd
doc: changes to code chunks options
b890745 
- Set theme to 'theme_bw()'
- Set 'echo=FALSE' on plotting code chunks
- Set 'fig.align="center"' on plotting code chunks
@github-actions GitHub Actions
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This pull request:

  • Adds 1 new dependencies (direct and indirect)
  • Adds 1 new system dependencies
  • Removes 0 existing dependencies (direct and indirect)
  • Removes 0 existing system dependencies

(Note that results may be inacurrate if you branched from an outdated version of the target branch.)

@ntorresd ntorresd changed the title Simulation vignette plus other things Simulation functions and vignette plus other things Jul 31, 2024
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We'll make sure the R-CMD checks pass in the development branch after cleanly merging the refactorizations in full-refac-test

@ntorresd ntorresd merged commit 941ae9a into dev Jul 31, 2024
1 of 8 checks passed
@ntorresd ntorresd deleted the i169-restructure-simulation-functionality branch July 31, 2024 21:29
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ntorresd commented Jul 31, 2024 •
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This PR:

This was referenced Aug 6, 2024
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@ntorresd ntorresd mentioned this pull request Sep 9, 2024
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Changes to generate_sim_data
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@ben18785 @ntorresd