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Dev #207

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Commits on May 9, 2024

  1. doc: use chunks functionality in use_cases.Rmd examples 

    - use same ylim in foi plots for better readability
- add environment cleanup at the end of each example
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  2. doc: replace data(simdata_*) by corresponding code to simulate data 

    - use data simulation functionalities of the package to simulate the
datasets in `foi_models.Rmd` examples
- use same chunk structure in modelling to validate results
- overall cleanup of the vignette
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  3. remove simdata_* datasets from the package (no longer needed)

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  4. doc: add environment cleanup in foi_models vignette examples

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  5. doc: minor spelling correction in foi_models vignette

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  6. doc: update NEWS

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Commits on May 10, 2024

  1. change rhat threshold to <1.01 in extract_seromodel_summary

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  2. refac: add input validation to plot_rhats

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  3. change rhat convergence threshold to <1.01 in plot_rhats

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  4. add input validation and warnings to get_table_rhats

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  5. doc: minor documentation update

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  6. doc: update NEWS and WORDLIST

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  7. feat: add age-varying normal model av_normal 

    - Replace `prob_infected.stan` by two separate files for each
type of model
- Slight change to parameter order in `prob_infected_calculate`
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  8. feat: allow for parameter specification in constant model prior

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  9. feat: modify fit_seromodel to allow for age-varying model implement… 

    …ation

- Change how `stan_data` is constructed depending on type of model
- Specify default behavior by type of model
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  10. fix: use years or ages in plots depending on the type of model 

    - Use `age` for age-varying models and `years` in time-varying
models in
    - `get_foi_central_estimates`
    - `plot_foi`
    - `plot_rhats`
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  11. feat: add age-varying normal model av_normal 

    - Update `R/stanmodels.R`
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  12. doc: update documentation

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  13. doc: update NEWS.md

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Commits on Jul 31, 2024

  1. #169 move probability functionality

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  2. #169 corrections to exposure matrix and simulating time models first … 

    …draft
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  3. fix(i169): minor corrections to simulation functionalities

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  4. #169 chatgpt gave a useful tip about refactorising

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  5. #169 removed redundant functions

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  6. #169 added all tests for simulate_serosurvey_time_model

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  7. #169 started to include docstrings

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  8. #169 added further docstrings and more tests incl seroreversion

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  9. #169 first draft of time-varying foi model with comprehensive unit tests

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  10. #169 started to add in age-varying simulation but there's an error wi… 

    …th the age-varying probs
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  11. #169 tests corrected for probability exact calcs

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  12. #169 first draft of age-varying simulation model with full tests

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  13. #169 added master simulate function. Bug for sample_size_by_individua… 

    …l_age_random needs sorting
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  14. added tests for master simulate function

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  15. #169 corrected probability_exact_time_varying function (which now doe… 

    …s not use an exposure matrix)
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  16. #169 removed redundant age-varying probability calculator

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  17. #169 added validation functions for serosurveys

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  18. fix(i169): correct age binning for data simulation function 

    - Correct tests accordingly
- Avoids using `cut`
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  19. test(i169): adds test draft for time-age model

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  20. #169 corrected mistake which meant (previously) age and time model se… 

    …ropositivities were the same
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  21. Update simulate_serosurvey.R

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  22. #169 working draft of age and time model

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  23. #169 now passing all tests for simulate_serosurvey

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  24. #169 added tidyr calls to expand_grid

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  25. #169 corrected partial argument match

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  26. i169: remove old data simulation functions

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  27. #169 added validation error for simulation

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  28. test(i169): remove old data simulation functions tests

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  29. update NAMESPACE

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  30. fix: minor correction to simulate_serosurvey foi specification

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  31. fix: minor correction to get_cohort_ages

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  32. fix: corrections to plot_foi option to plot foi used to simulate

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  33. test: add value based tests for fit_seromodel using simulated data

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  34. first draft of simulation vignette

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  35. now runs ok

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  36. made vignette nicer

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  37. started to add more general model

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  38. added in general simulation functionality

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  39. doc: make sure old vignettes work as expected 

    (provisional) Manually change variable names to use visualization functions.
This will be remove after the refactorization of the package.
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  40. doc: syntax changes to 'simulating_serosurveys.Rmd' 

    - Use different names for foi data frames on each example
- Minor text and syntax changes to improve vignette's aesthetics
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  41. doc: use different names for foi data frames on each example

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  42. doc: add analytical solution line to seroprevalence plots in 'simulat… 

    …ing_serosurveys.Rmd'
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  43. doc: changes to code chunks options 

    - Set theme to 'theme_bw()'
- Set 'echo=FALSE' on plotting code chunks
- Set 'fig.align="center"' on plotting code chunks
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Commits on Sep 9, 2024

  1. clean R and tests folders

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  2. feat: add constant models with and without seroreversion

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  3. delete old modules

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  4. add config file with default priors and distribution indexes

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  5. add input validation utilities

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  6. feat: add working version of fit_seromodel using functional specifi… 

    …cation of priors
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  7. feat: add clean seroprevalence visualisation functions

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  8. feat: add age_seroreversion model

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  9. feat: add foi_index (old chunks) default behavior

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  10. feat: add plot_foi_estimates with option to add foi trend

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  11. change model name for models without seroreversion to *_no_seroreversion

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  12. feat: add age-varying model without seroreversion

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  13. refac: change stan functions names to avoid ambiguity

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  14. feat: add time varying model with and without seroreversion

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  15. remove unnecessary line in probability_exact_time_varying

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  16. doc: add documentation for new functions

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  17. refac: move data simulation validation functions to validation module

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  18. fix: change to extract_central_estimates to deal with 1-time estimates

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  19. feat: add 'plot_rhats' function

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  20. remove unnecessary stan file

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  21. fix: add error message for constant model exceptions in plotting func… 

    …tions
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  22. feat: add summarise_model and plot_summary functions

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  23. feat: add new plot_seromodel function

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  24. fix: change reference to config file

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  25. fix: correct stan models reference

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  26. doc: add export tag to plot_seromodel

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  27. fix: remove uneccessary argument call in plot_seromodel

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  28. feat: introduce 'summarise_loo_estimate' to simplify 'summarise_serom… 

    …odel'

This function allows to extact an specific loo estimate for model parameters
like 'seroreversion_rate' or 'foi'.

This introduce changes in:
- 'summarise_seromodel'
- 'plot_summary'
- 'plot_seromodel'
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  29. refac: move 'summarise_seromodel' to a separate file

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  30. feat: add convergence field to summary in 'summarise_seromodel'

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  31. refac: improve parameter specification in plotting functions

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  32. add comments to config.yml

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  33. fix: add manually null seroprev for age=0 in expanded prevalence

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  34. doc: lintr functions' documentation

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  35. refac: add #nolint to long variable and function names

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  36. refac(lintr): add .data$ where needed in pipes

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  37. refac(lintr): other syntax and lintr corrections

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  38. fix: remove deprecated @docType tag

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  39. doc(lintr): syntax and lintr corrections to data simulation vignette

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  40. doc: update documentation

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  41. update DESCRIPTION

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  42. update WORDLIST

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  43. fix: change append() by c() to append when possible

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  44. fix: improve error messages readability

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  45. fix: replace validation function by checkmate::assert_names() 

    - Remove two validation functions
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  46. feat: add stan time-varying models in log-scale

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  47. feat: modify R modules to allow log-scale model implementation 

    - Add `sf_cauchy()` to set sigma prior in tv log modules
- Add `is_log_foi` parameter to `fit_seromodel`
- Add corresponding defaults
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  48. feat: update stanmodels.R

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  49. fix: correct foi_sigma_rw parameters set up

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  50. feat: set default behavior for sampling initialization 

    - Set different init functions for log and no-log models
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  51. fix: simplify loaded datasets structure and update column NAMESPACE 

    - Change `tsur` to `survey_year`
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  52. fix: change tsur to survey_year in R modules

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  53. update NAMESPACE

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  54. update DESCRIPTION

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  55. feat: enable sigma prior specification for all foi_models 

    - Set defaults in the log and regular scale for sigma statistics
- Use Cauchy distribution for sigma prior in regular scale
- Use normal distribution for sigma prior in log scale
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  56. fix: change default seroreversion prior to sf_normal

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  57. fix: add error whenever a not supported model_type is specified 

    Current available options are:
- `'constant'`
- `'time'`
- `'age'`
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  58. doc: improve fit_seromodel prior parameters documentation

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  59. fix: remove unecessary samples from output stanfit object

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  60. feat: add get_age_intervals function to plot_seromodel module

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  61. feat: enable data binning for plotting in plot_serosurvey

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  62. fix: remove unecessary validation of survey_year in `validate_seros… 

    …urvey`
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  63. fix: minor syntax corrections

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  64. doc: update documentation

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  65. doc: upgrade vignettes accordingly to refactorization

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  66. update WORDLIST

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  67. doc: update serofoi.Rmd

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  68. doc: remove unecessary dependency from simulating_serosurveys vignette

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  69. fix: correct serofoi-package.Rd encoding

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  70. doc: move vignettes to articles

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  71. change version tag to 1.0.0

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  72. fix: remove survey_year from plot_serosurvey()

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  73. doc: add some examples in functions' documentation 

    Add examples for:
- `fit_seromodel`
- `get_foi_index`
- `plot_serosurvey`
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  74. doc: add complementary information to functions' documentation

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  75. doc: update documentation

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  76. refac: change sample_size for n_sample across the package

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  77. doc: update documentation

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  78. change version to 1.0.1

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Commits on Sep 12, 2024

  1. (i208)fix: correct time indexation in time-log-foi model and remove u… 

    …nnecessary lines
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