Add test suite #93

creating base line of package

…nto dev-feature-strmodel

…rofoi into dev-feature-strmodel-miguel

…ture

* arreglo carpetas R/stanmodels * Funciones finales pendientes a modificación * Delete Funciones eliminadas.docx * Delete Explicación del código del paquete SEROFOI.docx * Documentación en inglés y español * Documentación lista * modify package structure * modify package structure * modify names and folder test * Creation of general modules and revision of functions * refactoring visualization functions and define some general pck structure * update readme file * update readme file * general settings * modify dependecies, document and name functions Co-authored-by: Zulma M. Cucunubá <[email protected]> Co-authored-by: megamezl <[email protected]> Co-authored-by: megamezl <[email protected]>

…ction separation by model.

…turns an object with the result from running the specified model. The model is specified through the variable model_name. Right now there are 3 supported models: constant_foi_Bi, continuous_foi_normal_Bi and continuous_foi_normal_log. The three of them are tested in tests/test_individual_models.R. Additionally, the names from several parameters were changed for them to be more intuitive and consistent.

…The functions plot_seroprev, plot_foi and plot_rhats return the sero prevalence, the force of infection and the rhats-convergence plots respectively, receiving as a parameter an object with the model that must include the model data (model_object). The function plot_model calls these functions and arrange the plots in a gridExtra vertical arrangge for visualization of the results. Some names of parameters and objects were change for onsistency reasons.

…el_object now includes model_data, this last is not required as an argument anymore. 2) We created the save_or_read_model function in order for run_model to determine whether the respective .RDS file exists. If it doesn't, the model object is created through rstan::stan_model and saved as an .RDS file. Otherwise, it reads the corresponding .RDS file. save_or_read_model takes the path of the rds and the stan model file from the configuration file now. 3) Some parameters and objects names were changed for consistency. The script R/model_comparison.R was updated accordingly (mainly syntax changes). The use of the modeling module is shown in tests/test_individual_models.R.

….R. Remove old tests folders and test scripts.

update dependecies, documentation and name functions

…stanmodels.

* 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). Co-authored-by: megamezl <[email protected]>

* 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 Co-authored-by: megamezl <[email protected]>

* 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. --------- 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]>

* 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. --------- 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]>

…grid

* 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 --------- 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]>

* 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 --------- 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]>

* 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]>

Cucunubá2017 -> cucunubá2017, Carrera2020 -> carrera2020

* Remove files generated by pkgdown * Restore original pkgdown workflow

…repository

doc: update vignettes urls in the README as well as the installation repository

* Set up google analytics on documentation website * Add epiversetheme in DESCRIPTION

… information (ntorresd). (#58)

… … (#75) * small tweaks to dcoumentation titles so that we idenfiy them well as articles in r-univers * small tweaks to dcoumentation titles so that we idenfiy them well as articles in r-univers

* update: lifecycle stage README.md * update: lifecycle stage README.Rmd

* 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' * added scripts to test exceptions of visualisation module functions * 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 ./ * doc: minor corrections to vignettes/references.bib * remove skip_on_ci() from all tests * Remove files generated by pkgdown (#45) * Remove files generated by pkgdown * Restore original pkgdown workflow * Issue 47: fix inflexible age group structure definition for visualization (#49) * remove link.svg file * chore: update .gitignore file * fix predicted_prev age definition in function get_prev_expanded (modelling module). Add test for error reproduction. * Issue 47: fix inflexible age group structure definition for visualization (#49) * remove link.svg file * chore: update .gitignore file * fix predicted_prev age definition in function get_prev_expanded (modelling module). Add test for error reproduction. * Update _pkgdown.yml * Dev (#44) * 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]> * Remove files generated by pkgdown (#45) * Remove files generated by pkgdown * Restore original pkgdown workflow * creating scripts for module tests * refac: unify individual models tests into a single test for the modelling module. Remove unnecessary files * add option bin_data to prepare_serodata (modelling) and plot_seroprev_fitted (visualization). * test for the modelling module now compares the results with a standardize dataframe of the expanded prevalence which contains significant information about the seroprevalence fitting * add models_serialization.R to tests/testthat. This script saves the model objects information into json format to avoid re-running and standardize models accross platforms for tests purposes. * refactorize test for the visualization model reading the models from the corresponding json files. * Added missing deps * Added missing newline at the end * Added missing data * misc fixes * moved RDS files outside data/ dir to comply with r-cmd-check * Removed r-cmd-check warnings * Removed save_or_load_model, since rstantools does that job now * migrated to rstantools * added dev to trigger action * fix: update config R-CMD-check.yaml adding devel and oldrel-1 libraries for ubuntu release * Revert "fix: update config R-CMD-check.yaml adding devel and oldrel-1 libraries for ubuntu release" This reverts commit ed861cc. * fix: update config R-CMD-check.yaml removing release libraries for ubuntu release * add missing config files * remove obsolete src dir * add missing dependency lines * update config R-CMD-check.yaml adding macos, windows and ubuntu-latests devel/release and oldrel-1 * remove stray line * fix: small change to stanmodels.R (normal_log_model) * doc: minor correction to documentation. This addresses an R-CMD-check warning for ubuntu-latests (oldrel-1) * doc: minor correction to documentation. This addresses an R-CMD-check warning for ubuntu-latests (oldrel-1) - 2nd try --------- 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]> Co-authored-by: Miguel Enrique Gamez Lopez <[email protected]> Co-authored-by: Sebastian Funk <[email protected]>

This commit changes the removed preloaded dataset `serodata` for the identical `chagas2012`.

…ule. This change is meant to simplify `fit_seromodel()`. This commit also changes the name of the stanfit object in the output of `fit_seromodel()` from `fit` to `seromodel_fit`.

… .RDS and updates test_visualization accordingly

* remove serodata .Rdata and .Rd files * remove R/serodata.R * doc: update functions documentation replacing for in examples * doc: update serofoi logo * doc: update README and vignettes This commit changes the removed preloaded dataset `serodata` for the identical `chagas2012`. * fix: minor correction to test_modelling

Simplify fit_seromodel() output and related refactorizations

…#59) * fix: add exception to function plot_foi() to plot a FOI trend with different length along with the data for the case when their sizes don't coincide * clean test_visualisation * feature: add three functions to simulate datasets. get_sim_counts() generates a list with simulated counts by age following a binomial distribution. generate_sim_data() uses the counts generated by get_sim_counts() to create a dataframe with the necessary structure to use other functions of the package. group_sim_data() serves to group the previously generated dataset by age group; right now it groups the data by periods of 5 years. * add test_simulate_data to test the data simulation functions in the seroprevalence_data module

…gests

Commits on Aug 8, 2022

Initial commit

tracelac authored Aug 8, 2022

Configuration menu

View commit details

Copy full SHA for fee9be3

Browse repository at this point

Copy the full SHA

fee9be3 View commit details

Browse the repository at this point in the history

Commits on Aug 9, 2022

Adding package skeleton

GeraldineGomez committed Aug 9, 2022

Configuration menu

View commit details

Copy full SHA for d157dce

Browse repository at this point

Copy the full SHA

d157dce View commit details

Browse the repository at this point in the history

Commits on Sep 20, 2022

Update README.md

zmcucunuba authored Sep 20, 2022

Configuration menu

View commit details

Copy full SHA for de08085

Browse repository at this point

Copy the full SHA

de08085 View commit details

Browse the repository at this point in the history

Commits on Nov 3, 2022

modify names and folder test

GeraldineGomez committed Nov 3, 2022

Configuration menu

View commit details

Copy full SHA for a74b3d3

Browse repository at this point

Copy the full SHA

a74b3d3 View commit details

Browse the repository at this point in the history

Commits on Nov 11, 2022

general settings

GeraldineGomez committed Nov 11, 2022

Configuration menu

View commit details

Copy full SHA for 6f6d804

Browse repository at this point

Copy the full SHA

6f6d804 View commit details

Browse the repository at this point in the history

Commits on Jan 9, 2023

renaming variables, inputs and outputs

megamezl committed Jan 9, 2023

Configuration menu

View commit details

Copy full SHA for df169bd

Browse repository at this point

Copy the full SHA

df169bd View commit details

Browse the repository at this point in the history

Commits on Jan 12, 2023

funciones que deben estar listas

megamezl committed Jan 12, 2023

Configuration menu

View commit details

Copy full SHA for bcf5402

Browse repository at this point

Copy the full SHA

bcf5402 View commit details

Browse the repository at this point in the history

Commits on May 2, 2023

Rename serofoi logo and use svg file (#51 )

Bisaloo authored May 2, 2023

Configuration menu

View commit details

Copy full SHA for 3cdfbfe

Browse repository at this point

Copy the full SHA

3cdfbfe View commit details

Browse the repository at this point in the history

Commits on Jun 20, 2023

Added commas to description file (#68 )

ben18785 authored Jun 20, 2023

Configuration menu

View commit details

Copy full SHA for f5a7595

Browse repository at this point

Copy the full SHA

f5a7595 View commit details

Browse the repository at this point in the history

Commits on Sep 7, 2023

Fixes #115 (#116 )

jpavlich authored Sep 7, 2023

Configuration menu

View commit details

Copy full SHA for 308c0bd

Browse repository at this point

Copy the full SHA

308c0bd View commit details

Browse the repository at this point in the history

Add test suite #93

Add test suite #93

Commits on Aug 8, 2022

Commits on Aug 9, 2022

Commits on Sep 12, 2022

Commits on Sep 15, 2022

Commits on Sep 20, 2022

Commits on Sep 21, 2022

Commits on Oct 21, 2022

Commits on Oct 30, 2022

Commits on Oct 31, 2022

Commits on Nov 3, 2022

Commits on Nov 9, 2022

Commits on Nov 10, 2022

Commits on Nov 11, 2022

Commits on Nov 21, 2022

Commits on Dec 21, 2022

Commits on Jan 7, 2023

Commits on Jan 9, 2023

Commits on Jan 11, 2023

Commits on Jan 12, 2023

Commits on Jan 14, 2023

Commits on Jan 19, 2023

Commits on Jan 20, 2023

Commits on Jan 24, 2023

Commits on Jan 25, 2023

Commits on Mar 22, 2023

Commits on Mar 28, 2023

Commits on Mar 29, 2023

Commits on Apr 4, 2023

Commits on Apr 5, 2023

Commits on Apr 6, 2023

Commits on Apr 13, 2023

Commits on May 2, 2023

Commits on May 24, 2023

Commits on Jun 7, 2023

Commits on Jun 20, 2023

Commits on Jun 21, 2023

Commits on Jun 29, 2023

Commits on Aug 14, 2023

Commits on Aug 15, 2023

Commits on Aug 22, 2023

Commits on Aug 23, 2023

Commits on Aug 24, 2023

Commits on Sep 7, 2023

Commits on Sep 11, 2023