8 demographics vignette #32
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…-trace/epiCo into 8-demographics-vignette
* 24 fix incidence historic length handling (#28) * #24 verify incidence and observations * #24 Verify length of the incidence historic * #24 adding warnings and final tests * Fix warnings * Fix unused variable * 26 modify moran index function (#29) * #26 modified function and test * Revert "#26 modified function and test" This reverts commit 52f24b0. * #26 modified function and test * Update lint * Fix lint * Update demographics.R * Age ranges feature Include the feature to customize the age ranges for the population pyramids and specific age rates * Update * Create detect_outbreaks_ewma.Rd --------- Co-authored-by: Juan Montenegro Torres <60274234+Juanmontenegro99@users.noreply.github.com>
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* Create test-endemic_channel * Tests endemic channel (#25) * #23 create endemic channel test * #23 update endemic channel assertions * Update documentation * Update lint * Uptade lint * Update lint * Update README.md (#27) * 24 fix incidence historic length handling (#28) * #24 verify incidence and observations * #24 Verify length of the incidence historic * #24 adding warnings and final tests * Fix warnings * Fix unused variable * 26 modify moran index function (#29) * #26 modified function and test * Revert "#26 modified function and test" This reverts commit 52f24b0. * #26 modified function and test * Update lint * Fix lint * 8 demographics vignette (#32) * Vignette creation * Update demographics-vignette.Rmd * Update demographics-vignette.Rmd * Actualizar demographics-vignette.Rmd * Actualizar demographics-vignette.Rmd * Update demographics-vignette.Rmd * Update demographics-vignette.Rmd * Update demographics-vignette.Rmd * Update of vignette format * 30 population pyramids age ranges (#31) * 24 fix incidence historic length handling (#28) * #24 verify incidence and observations * #24 Verify length of the incidence historic * #24 adding warnings and final tests * Fix warnings * Fix unused variable * 26 modify moran index function (#29) * #26 modified function and test * Revert "#26 modified function and test" This reverts commit 52f24b0. * #26 modified function and test * Update lint * Fix lint * Update demographics.R * Age ranges feature Include the feature to customize the age ranges for the population pyramids and specific age rates * Update * Create detect_outbreaks_ewma.Rd --------- Co-authored-by: Juan Montenegro Torres <60274234+Juanmontenegro99@users.noreply.github.com> * Update demographic_vignette.Rmd * Update demographic_vignette.Rmd --------- Co-authored-by: Juan Montenegro Torres <60274234+Juanmontenegro99@users.noreply.github.com> * Create endemic_channel.Rmd * Create endemic_channel_figure.png Figure for the endemic channel vignette * Update logo New epiCo logo * Update README * Update endemic_channel.Rmd * Style updates * Restore dependency on R 3.2.0 because of anyNA() * Spatiotemporal vignette (#37) * Create spatiotemporal_vignette.Rmd * Fix vignettes * Fix lint errors * Fix styler * Temporal fix lint * upload data * Update tests and fix age range parameter (#35) * Update tests and fix age range parameter * Create project and fix concatenation_linter * Update vignettes with the new data * #40 * fix warnings lint * Fix lint warnings * fix warnings * Delete unnecessary files * Fix lint warnings * Delete commented code --------- Co-authored-by: Juan Montenegro Torres <60274234+Juanmontenegro99@users.noreply.github.com> * 41 fix path bug (#42) Relocate data and fix #41. * update moran's example * Fix bug in morans_index map Now morans_index function returns a list with the data and the leaflet map that can be displayed later * Bug age risk (#44) * Add error handling age_risk Function now checks that if `gender` info is provided it has the same number of elements as `age` * Fix age_risk bug The plot argument in the helping function `graphics::hist` has to be FALSE to avoid attempts of displaying data * Fix age_risk bug The function now can handle the case when users have a populatio_pyramid dissagreggated by gender but still want to estimate an age_risk distribution where genders are aggregated * Style fix * Delete unnecessary files * Update test-demographics.R (#47) * Handle warnings * Documentation and style changes * style and documentation changes * fix lint warnings --------- Co-authored-by: juan-umana <jd.umana10@uniandes.edu.co> Co-authored-by: Juan D. Umaña <juan.umanacaro@gmail.com> Co-authored-by: Juanmontenegro99 <jf.montenegro@uniandes.edu.co> Co-authored-by: Hugo Gruson <Bisaloo@users.noreply.github.com> Co-authored-by: Julian Otero <56242573+jd-otero@users.noreply.github.com>
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First version of demographics vignette as listed in #8