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* Documentation of the visualisation and modelling modules * automatic documentation of the visualisation and modeling modules * minor changes to the documentation. Typos and minor bugs corrected. * feat: define a preliminar version of the minimal dataset needed to use the library, now stored in data/data.RDS (data/data_bu.RDS is backup of the old dataset). The prepare_data() function in seroprevalence_data process the dataset creating 5 columns needed for the analysis (age_mean_f, sample_size, prev_obs, prev_obs_lower and prev_obs_upper). This function is tested in test/test_minimal_data and implemented in test_individual_models. * fix: remove unused functions from all modules in preparation for a compiltation test. Remove the corresponding documentation files. Remove the folder R/stantmodels (it's redundant with inst/extdata/stanmodels). Update dependencies in DESCRIPTION (epitrix and cowplot removed). * fix: prepare data_test for compilation of the package * Dev compilation test nicolas (#10) * minor changes in how the summary is shown * change summary message * minor change in extract_summary_model * create template of vignette * delete temporary files * testing vignette * vignette's test * adding workflows sca and r-cmd-check * adding workflows sca and r-cmd-check (#11) * Static code review with lintr in package modules * changing descriotion * adding info into run-model function * adding a script for model comparison * adding a script for model comparison * adding a script for model comparison * adding a script for model comparison * adding a script for model comparison * adding a script for model comparison * adding a script for model comparison * returning logo * adding a script for model comparison * adding a script for model comparison * changing README.Rmd file * changing README.Rmd file * changing README.Rmd file * changing README.Rmd file * adding plots to the readme file * adding plots to the readme file * adding function for plotting raw seroprevalence data * adding the packages name standart * adding data reference for dplyr * update function documentation * Static code analysis for package modules * Static code analysis for the modeling module * Clean test/test_comparison.R. Add a warning for first compilation of the models. Minor sintaxis changes. Change slightly the name of the visualization module. * fix: Calculate the binomial confidence interval from the raw seroprevalence data in function plot_seroprev. The function is tested in test_plot_functions.R. Add compilation line to test_individual models.R. * Compilation test in test_plot_functions.R * minor changes before merging with dev * feat: Add function prepare_bin_data to seroprevalence_data module. This function prepares the data to plot the binomial confidence intervals and allows to remove redundant code in the visualization and modelling modules. * minor changes before merging with dev * fix: corrects the bin size in plot_seroprev(). Minor syntax changes. * doc: Add the corresponding documentation for plot_seroprev() to README.Rmd and README.md including the example image file man/figures/plot_seroprev_example.png * Dev docu mg (#16) * Added examples in core functions documentation * Example of the functions in the documentation * updating links of R-CMD check and Codecov test * Dev doc nicolas (#18) * doc: Update documentation for run_model, save_or_load_model and fit_model. The name of some functions and parameters were changed for the sake of clarity (make_yexpo -> get_exposure_years, save_or_read_model -> save_or_load_model, yexpo -> exposure_years, ). The order of functions definitions were in the modeling module were changed; now they appear in hierarchical order starting from run_model, since this is the most important function in the module. * refac: fit_model_log function removed. Now the function fit_model has an exception that implements the logarithmic model as the removed function used to. fit_model documentation updated. Minor changes in the name of the objects returned by the functions. * doc: modelling module documentation updated. get_posterior_summary function removed (unused). * updating package version and contributors * Dev doc nicolas (#20) * doc: Update documentation for run_model, save_or_load_model and fit_model. The name of some functions and parameters were changed for the sake of clarity (make_yexpo -> get_exposure_years, save_or_read_model -> save_or_load_model, yexpo -> exposure_years, ). The order of functions definitions were in the modeling module were changed; now they appear in hierarchical order starting from run_model, since this is the most important function in the module. * refac: fit_model_log function removed. Now the function fit_model has an exception that implements the logarithmic model as the removed function used to. fit_model documentation updated. Minor changes in the name of the objects returned by the functions. * doc: modelling module documentation updated. get_posterior_summary function removed (unused). * doc: minor changes to the modelling module. Quotation marks added for string variables in the documentation and some minor errors fixed. * Dev docker tests (#22) * 1st version of Dockerfile * Addedd auto dep install for docker container * Refactor docker folder * Changed process to obtain path of stan and RDS files to make it compatible with testhat * First version of tests * Factored testing functions * config.yml now only stores the base path of stan models * Added automated test tasks for vscode * Added more tests * misc changes to vscode tasks * Misc improvements to containers * small fixes to container * misc docker refactor * moved docker scripts to an R file (tested only on Linux) * Temporary change to test github actions on this branch * added testthat to deps * Added devtools to deps * removed erroneous code in unit test * moving config.yml to inst * same * temp changes to github actions files for testing * doc: Update documentation for run_model, save_or_load_model and fit_model. The name of some functions and parameters were changed for the sake of clarity (make_yexpo -> get_exposure_years, save_or_read_model -> save_or_load_model, yexpo -> exposure_years, ). The order of functions definitions were in the modeling module were changed; now they appear in hierarchical order starting from run_model, since this is the most important function in the module. * Added R CMD Check to Docker * refac: fit_model_log function removed. Now the function fit_model has an exception that implements the logarithmic model as the removed function used to. fit_model documentation updated. Minor changes in the name of the objects returned by the functions. * Added more files to rbuildignore * more testing of github actions * misc fixes * testing windows * adding BH dep * Added linking deps for rstan * added suggest deps for rstan * doc: modelling module documentation updated. get_posterior_summary function removed (unused). * Add LinkingTo field (#19) * Add LinkingTo field * Add roxygen comments from rstantools::use_rstan() * temporarily removed some deps * temp remove of this branch from yaml * added vscode configs * Fixes linking errors in R CMD CHeck * Fixed examples * Fixed tests for latest changes in function and var names * added missing deps --------- Co-authored-by: Nicolas Torres <[email protected]> Co-authored-by: Hugo Gruson <[email protected]> * Now most examples run without errors. Those that not are temporarily enclosed in \dontrun * Documentation of the seroprevalence_data and visualisation modules (#24) Co-authored-by: Nicolás Torres Domínguez <[email protected]> * Added test functions for plots * doc: Update author's information in DESCRIPTION. * Added myself to contributors * Removed test/ folder * Added a TODO * More automatic tests * Update .gitignore Added dataframes actual test folder * Fixed save_or_load_model to avoid DLL Bug * same * dontrun some examples * same * misc changes * Some corrections to the documentation * R CMD Check now seems to be working without errors (hopefully :) * Some fixes to module documentation * R CMD Check works without errors (locally) * doc: review and correct visualization module documentation. * doc: minor changes to seroprevalence_data module documentation. * Add function to generate comparative plot of the models (#29) * test: Add plot tests for each model to test_plot_functions. * fix: Change GridExtra dependencie for cowplot (visualization module). Add plots for the 3 models to test_plot_functions. * feat: Add function plot_models_list to the visualization module. This function plots a grid arrange by means of cowplot::plot_grid. A change that is still needed is to add proper default values for n_row and n_col or an exception for the case when they're passed as NULL. An example of the use of this function can be found at the end of test_plot_functions and the corresponding result can be visualized in plot-arrange-models. * Minor changes to individual_models .svg files. * Testing all platforms in github actions * testing coverage * added missing BH dep to make it work on windows * added more missing deps * doc: minor change to fit_model function documentation. * add back the data folder to use mydata object when importing the library. * doc: generate documentation with devtools::document(). * updated RMD Check tasks for vscode and docker to make them more similar to github actions' * Added some deps to avoid warnings in R CMD Check * Updated man pages with roxygen2 * Added dep to TBB to hopefully fix compilation problems in windows * Upgraded rstan to v2.26.11. Added required TBB dep * Updated SVGs and CSVs to match results from rstan v2.26.11 * Added mc-stan as extra repo to support rstan 2.26.11 * Misc fixes * Rename plot_models_list to plot_seroprev_models_grid. * doc: add documentation for plot_seroprev_models_grid function. * Added more docker-related funcionality * Added script to clean SVGs and CSVs when there rstan needs to be updated and tests fail * misc changes * Dev webrd (#32) * test epidemics * changes to vignette * testing epidemics * testing site * improved vignette * improved vignette * improved vignette * improved vignette with contributions * improved vignette with contributions * improved vignette with refernces * improved vignette with references * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * use cases * use cases * update preloaded package datasets. mydata and serodata contain a copy of the same dataset for the time being. * add additional changes to add multiple datasets to the package. * doc: add datasets documentation files. * use cases * adding veev panama * adding chik 2015 * adding chik 2015 * removing unnecesary data * correcting chik data for nicaragua * correcting chagas data for Colombia * correcting chagas data for Colombia * doc: add mydata and serodata documentation and .R files. * doc: add documentation files for the additional incorporated datasets chagas2012, chik2015 and veev2012. * doc: add documentation files for the additional incorporated datasets chagas2012, chik2015 and veev2012. --------- Co-authored-by: Zulma Cucunubá <[email protected]> Co-authored-by: Zulma M Cucunubá <[email protected]> * dependencie rstan (>= 2.26.11) changed to rstan (>= 2.21.1). 2.26.11 was generating an error in the installation of the package. * Back to rstan (>= 2.26.11), * Adding multiplatform tests * test: run all tests for the new test dataset. * update plot_functions test figures. * doc: minor change to plot_seroprev_models_grid documentation. * style: Update the name of the functions to specify they refer to seroprevalence models (seroprev sufix). Update the documentation correspondingly. * style: mydata changed to serodata. The current dataset is chagas2012.RDS, but this will be changed to a simulated dataset in the future. * update tdata_test dataset. The dataset now corresponds to chagas2012. This will be changed by a simulated dataset in the future. * removed unused code * Temporarily skipping tests on windows and mac, until we find an efficient way to test in those platforms without worrying about reproducibility * branch change for testing * updated testing snapshots * misch changes * added install deps task for vscode * Added TODOs * Added missing deps * Added missing testthat snapthots * Created new function `expect_similar_dataframes` to test dataframes using snapshots. It is compatible with column_comparation_functions * Increased default tolerance to deal with rstan shenanigans * testing ci * Skipping these tests on CI * Misc changes * Temporary changes while we improve tests * fix: solve minor typo in the name of function prepare_seroprev_data. * Dev zulma vignette (#34) * vignette draft * vignette draft * vignette draft * testing vignette * testing vignette * updating vignette * updating vignette * remove doc of .gitignore --------- Co-authored-by: zmcucunuba <[email protected]> Co-authored-by: GeraldineGomez <[email protected]> * Dev webrd (#35) * test epidemics * changes to vignette * testing epidemics * testing site * improved vignette * improved vignette * improved vignette * improved vignette with contributions * improved vignette with contributions * improved vignette with refernces * improved vignette with references * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * improved vignette with use cases * use cases * use cases * update preloaded package datasets. mydata and serodata contain a copy of the same dataset for the time being. * add additional changes to add multiple datasets to the package. * doc: add datasets documentation files. * use cases * adding veev panama * adding chik 2015 * adding chik 2015 * removing unnecesary data * correcting chik data for nicaragua * correcting chagas data for Colombia * correcting chagas data for Colombia * doc: add mydata and serodata documentation and .R files. * doc: add documentation files for the additional incorporated datasets chagas2012, chik2015 and veev2012. * doc: add documentation files for the additional incorporated datasets chagas2012, chik2015 and veev2012. * changing rstan version from 2.26.11 (non existen) to > 2.21.1 * simulated fake data * refac: test_sim_data is refactorized. I cleaned the code and added a function to plot the simulated datasets obtained for each foi example. * Save selected simulated data for scenarios A,B and D to tests/sim_data. I took all the grouped datasets for n=5. * chik-seroinference-simulations --------- Co-authored-by: Zulma Cucunubá <[email protected]> Co-authored-by: Zulma M Cucunubá <[email protected]> * fix: function get_exposure_years was returning ages that were not consistent with the survey time and the minimal birth_year in the dataset. I changed the name of the function to get_exposure_ages for consistency with the output. * fix: description typo. * change the name of get_exposure_years to get_exposure_ages (for lack of a better name). Update mydata to serodata. Reran all tests (slight changes in the tests results). * fix: updating functions and variables names in the vignettes files. This was causing the R-CMD github checks to fail. * Removed dev from actions scripts * Updated badges in README.Rmd. Updated README.md with latest changes from README.Rmd * fix: add default value for seroprev_data to the prepare_seroprev_data function. * Update prepare_seroprev_data documentation. * doc: minor corrections to simulated_data.Rmd. * webpage publication * fixed bug "recompiling to avoid crashing R session" * Update use_cases.Rmd * Add simulated data generation (#36) * Add conditional to prepare_seroprev_data. In some cases, like when datasets are being simulated, columns age_mean_f and birt_year need to be added prior to the data preparation in order to compute the exposure matrix. * refac: modification of get_exposure_matrix. Now it does not depend on get_exposure_ages explicitely, this was a redundant dependency. * testing changes in extract_seroprev_model_summary. * feat: add functions get_sim_counts, generate_sim_data and generate_sim_data_grouped to module seroprevalence_data. This functions can be used to generate simulated datasets like is shown in test_simdata_caseA.R * add results obtained by running the test test_simdata_caseA.R * delete redundant or unnecessary tests and their corresponding results. * remove old simulated data. * Add simulated data test script (tests/testthat/test_simdata_cases.R) and results for a constant foi (case A) and for a stepwise decreasing foi (case B). * doc: add documentation for the data simulation functions. * Add title identifying the specific case of each simulation for the test test_simdata_cases.R. Update the corresponding figures. * Save simulated data into testthat/exdata/ for cases A and B. They are stored automatically on running test_simdata_cases. * remove unused man files. * refac: Removed functions still in developing stage that will be added in a future version. In particular all functions for data simulation are removed. The function plot_seroprev_models_grid can be replaced in its current state by cowplot::plot_grid() function. Function get_comparison_table is unused. * refac: Remove redundant tests and refactorize test_indivudual_models (now test_models); now it runs the models using a for cycle instead of running each model one by one. Remove unnecessary folder test/. * Remove unused file R/test_vignettes.R * Remove unused data files. * Minor changes to vignettes. * Remove cowplot and pracma from dependencies and unnecessary test file test_plot_functions. * chore: change seroprev_model to seromodel. * chore: change seroprev_data to serodata. * chore: change model_object for seromodel_object. * Add option print_summary with deaful TRUE to run_seromodel (modelling module). * doc: update documentation for model_comparison and modelling modules. * doc: update documentation for visualization and modelling seroprevalence_data modules. * activate test-coverage github action for dev branch * run models inside the for loop in test_models instead of using lapply function * minor changes to documentation in all modules * Add back cowplot dependencie since its used for some plotting functions * change models names constant_foi_bi -> constant, continuous_foi_normal_bi -> tv_normal, continuous_foi_normal_log_bi -> tv_normal_log. tv stands for time-varying. * change models names constant_foi_bi -> constant, continuous_foi_normal_bi -> tv_normal, continuous_foi_normal_log_bi -> tv_normal_log. tv stands for time-varying. * refac: Divide test_models into three different tests (one for each current model). This is done in order to not use for loops in the coverage tests * Dev datasets (#40) * Remove year_init and year_end from the default dataset serodata * Remove year_init and year_end from the default dataset chagas2012 * Remove year_init and year_end from the dataset chik2015 * Remove year_init and year_end from the dataset veev2012 * doc: remove year_init and year_end from documentation * Dev plot foi (#41) * remove unused test datasets * add option to plot additional plot data to plot_foi and plot_seromodel methods * add test for the plot_foi method of the visualization module * update documentation for plot_foi and plot_seromodel. Add new simulated dataset serodata_simD and add test simulated data serodata_simD.R * add test test_plot_foi * change simulated foi data plot in plot_foi from scattered to line * add the simulated datasets simdata_constant, simdata_sw_dec and simdata_large_epi that will be used in the vignettes' article 'FoI models' * Dev vignettes: add contents to vignettes articles (#42) * version of the package set to 0.0.9 * doc: update README.Rmd * correct serofoi.Rproj * doc: add FoI models vignette * doc: modifications and corrections to Geting Started section of the vignettes * doc: vignettes publication test * doc: audd use_cases.Rmd vignette contents * doc: add updated README.md file * vignettes publication test * vignettes publication test * remove docs/ from .gitignore to test website publication * add doc/ files generated by pkgdown::build_site function * remove doc/ folder * vignettes publication test: add dev to push activation branches in pkgdown workflow and change the deployment branch to dev * Deploying to dev from @ 7c4f8f4 🚀 * website publication test: ignore docs folder. Remove dev from push trigger branches in pkgdown workflow and update the branch to gh-pages and the folder to ./ --------- Co-authored-by: megamezl <[email protected]> Co-authored-by: tracelac <[email protected]> Co-authored-by: zmcucunuba <[email protected]> Co-authored-by: GeraldineGomez <[email protected]> Co-authored-by: Miguel Enrique Gámez López <[email protected]> Co-authored-by: Jaime Pavlich-Mariscal <[email protected]> Co-authored-by: Hugo Gruson <[email protected]> Co-authored-by: JAIME ANDRÉS PAVLICH MARISCAL <[email protected]> Co-authored-by: Zulma Cucunubá <[email protected]>
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