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update: import data, functions with multiple diseases and fix templat…
…e report (#47) * adding conditional for single color in plot by variable (#20) * dengue-example * adding single color for fill --------- Co-authored-by: zmcucunuba <[email protected]> * modify conditional of var_fill (#21) * dengue-example * adding single color for fill * modify conditional for var_fill --------- Co-authored-by: zmcucunuba <[email protected]> * modify dengue example and plot by variables (#23) * dengue-example * adding single color for fill * modify conditional for var_fill * modify conditional for var_fill * modify conditional for var_fill * modify dengue-example --------- Co-authored-by: zmcucunuba <[email protected]> * modify text size and color of plot by variable (#24) * dengue-example * adding single color for fill * modify conditional for var_fill * modify conditional for var_fill * modify conditional for var_fill * modify dengue-example * modify text size and color of plot by variable --------- Co-authored-by: zmcucunuba <[email protected]> * updating text size plot * automation porcentage of ages and total cases, correction of graphs (#25) * dengue-example * adding single color for fill * adecuación de la función plt by variable * modificaciones del ejemplo * últimos cambios a la función plot by variable * Texto del reporte automatizado * automating cases total and modify graphs * commit para hacer pull * Automatización, corrección de gráficas y numeraciónb * automation porcentage age cases and correction graphs * automation porcentage age cases and correction graphs * Automatización del porcentaje * add porcentage symbol --------- Co-authored-by: zmcucunuba <[email protected]> Co-authored-by: megamezl <[email protected]> * automation of total cases and correction of graphs (#26) * dengue-example * adding single color for fill * adecuación de la función plt by variable * modificaciones del ejemplo * últimos cambios a la función plot by variable * Texto del reporte automatizado * automating cases total and modify graphs * commit para hacer pull * Automatización, corrección de gráficas y numeraciónb * automation porcentage age cases and correction graphs * automation porcentage age cases and correction graphs * Automatización del porcentaje * add porcentage symbol --------- Co-authored-by: zmcucunuba <[email protected]> Co-authored-by: megamezl <[email protected]> * updating var_fill * restoring parameters function * updating single color plot by variable * update lifecycle RECON in README file * update lifecycle to maturing in README file * update and add functions of subnational report and package documentation (#32) * modify dengue-example (#22) * adding conditional for single color in plot by variable (#20) * dengue-example * adding single color for fill --------- Co-authored-by: zmcucunuba <[email protected]> * modify conditional of var_fill (#21) * dengue-example * adding single color for fill * modify conditional for var_fill --------- Co-authored-by: zmcucunuba <[email protected]> --------- Co-authored-by: zmcucunuba <[email protected]> * creating the package website * create initial sections of the basic report, cleaning and util functions, updating dengue example * creating function documentation on report_sections, clean_data and utils * fix param functions of get cases distributions by age and gender * adding plot titles and new gender and epiweek section * updatind documentation functions * fix plot function section by gender and epiweek * adding documentation new function of special population * adding new function of special population to basic report * adding spacial distribution section and utils * update documentation functions of spacial distribution section and utils * updating spacial distribution function * updating documentation functions of distribution spatial * updating spatial distribution function * standarization variables and creating clean general function * modify clean sivigila data function and create general functionto clean depto codes * create documentation of new clean functions * refactoring functions of onset and notification date sections * creating documentation function of notification data and onsent symp * modify general clean data function * modify clean sivigila data * creating components of gender and epiweek section * creating components of age and gender, special population section * creating components of age and gender, special population section * creating components of spacial distribution section * fixing variables components of special population and gender * fixing caption text sixe and breaks * removing message plot map * fixing caption text sixe and breaks * fixing caption text size * fixing caption text size and map * fixing title distribution age and week, and percentage cases by age * fixing percentage cases by age * creating skeleton template of basic report * updating template package * adding params to report basic skeleton * updating the documentation functions of the clean data module * fix: documentation of functions * clean: data, functions and files * clean: list disease and ReadMe file * remve: title map * remove day of label * renaming functions and variables * updating documentation functions * renaming function names and refactoring the vignettes content * renaming function names, refactoring the vignettes content and updating documentation * updating documentation and titles plots * updating documentation list_available_diseases_years * fix: documentation functions, vignettes, ReadMe and Dengue Example * fixing general documentation * fix images ReadMe file * fix: ReadMe file and vignettess * remove some dependencies and functions deprecated * Adding tips to ReadMe and Vignettes * updating size images * updating size images ReadMe * adding space ReadMe file * updating align left images * Adding style images ReadMe and Vignettes * Adding style images ReadMe and Vignettes * Adding style images ReadMe and Vignettes * fix: style images ReadMe and Vignettes * fix: style images Vignettes * fix: echo ReadMe * fix: some variables and typo in ReadMe * fixing ReadMe and Vignettes, updating website * adding dependencie map and scale y for plot variable function * fix> scale y for plot variable function * improving group functions * updationg plot map function and dependencies * updationg plot map function and dependencies * updationg examples and documentation * updating examples and documentation * fix: function examples * remove files * fix examples and lintr of modules * fix message plot * divide map plot * adding new functions to municipalities and departments * adding new functions to municipalities and departments * adding new functions to municipalities and departments * adding new functions to municipalities and departments * modify plot and group municipalities and examples * modify plot and group municipalities and examples * modify plot and group municipalities and examples * export functions to departments and municipalities and examples * fix general syntax and rename functions of municipalities * fix called of function geo ocurrence * update template Reporte Basico * preview basic report * add function clean cols by exceptions * adding diseases like input choice on skeleton * modify forma exceptios cols disease in config file * adding analysis of notification department and municipality * update: functions on ReadMe file * update: version and README files --------- Co-authored-by: zmcucunuba <[email protected]> * fix: code style and indentation (#33) * creating the package website * create initial sections of the basic report, cleaning and util functions, updating dengue example * creating function documentation on report_sections, clean_data and utils * fix param functions of get cases distributions by age and gender * adding plot titles and new gender and epiweek section * updatind documentation functions * fix plot function section by gender and epiweek * adding documentation new function of special population * adding new function of special population to basic report * adding spacial distribution section and utils * update documentation functions of spacial distribution section and utils * updating spacial distribution function * updating documentation functions of distribution spatial * updating spatial distribution function * standarization variables and creating clean general function * modify clean sivigila data function and create general functionto clean depto codes * create documentation of new clean functions * refactoring functions of onset and notification date sections * creating documentation function of notification data and onsent symp * modify general clean data function * modify clean sivigila data * creating components of gender and epiweek section * creating components of age and gender, special population section * creating components of age and gender, special population section * creating components of spacial distribution section * fixing variables components of special population and gender * fixing caption text sixe and breaks * removing message plot map * fixing caption text sixe and breaks * fixing caption text size * fixing caption text size and map * fixing title distribution age and week, and percentage cases by age * fixing percentage cases by age * creating skeleton template of basic report * updating template package * adding params to report basic skeleton * updating the documentation functions of the clean data module * fix: documentation of functions * clean: data, functions and files * clean: list disease and ReadMe file * remve: title map * remove day of label * renaming functions and variables * updating documentation functions * renaming function names and refactoring the vignettes content * renaming function names, refactoring the vignettes content and updating documentation * updating documentation and titles plots * updating documentation list_available_diseases_years * fix: documentation functions, vignettes, ReadMe and Dengue Example * fixing general documentation * fix images ReadMe file * fix: ReadMe file and vignettess * remove some dependencies and functions deprecated * Adding tips to ReadMe and Vignettes * updating size images * updating size images ReadMe * adding space ReadMe file * updating align left images * Adding style images ReadMe and Vignettes * Adding style images ReadMe and Vignettes * Adding style images ReadMe and Vignettes * fix: style images ReadMe and Vignettes * fix: style images Vignettes * fix: echo ReadMe * fix: some variables and typo in ReadMe * fixing ReadMe and Vignettes, updating website * adding dependencie map and scale y for plot variable function * fix> scale y for plot variable function * improving group functions * updationg plot map function and dependencies * updationg plot map function and dependencies * updationg examples and documentation * updating examples and documentation * fix: function examples * remove files * fix examples and lintr of modules * fix message plot * divide map plot * adding new functions to municipalities and departments * adding new functions to municipalities and departments * adding new functions to municipalities and departments * adding new functions to municipalities and departments * modify plot and group municipalities and examples * modify plot and group municipalities and examples * modify plot and group municipalities and examples * export functions to departments and municipalities and examples * fix general syntax and rename functions of municipalities * fix called of function geo ocurrence * update template Reporte Basico * preview basic report * add function clean cols by exceptions * adding diseases like input choice on skeleton * modify forma exceptios cols disease in config file * adding analysis of notification department and municipality * update: functions on ReadMe file * update: version and README files * fix: typo, identation of code * update functions and documentation of subnational report (#34) * creating the package website * create initial sections of the basic report, cleaning and util functions, updating dengue example * creating function documentation on report_sections, clean_data and utils * fix param functions of get cases distributions by age and gender * adding plot titles and new gender and epiweek section * updatind documentation functions * fix plot function section by gender and epiweek * adding documentation new function of special population * adding new function of special population to basic report * adding spacial distribution section and utils * update documentation functions of spacial distribution section and utils * updating spacial distribution function * updating documentation functions of distribution spatial * updating spatial distribution function * standarization variables and creating clean general function * modify clean sivigila data function and create general functionto clean depto codes * create documentation of new clean functions * refactoring functions of onset and notification date sections * creating documentation function of notification data and onsent symp * modify general clean data function * modify clean sivigila data * creating components of gender and epiweek section * creating components of age and gender, special population section * creating components of age and gender, special population section * creating components of spacial distribution section * fixing variables components of special population and gender * fixing caption text sixe and breaks * removing message plot map * fixing caption text sixe and breaks * fixing caption text size * fixing caption text size and map * fixing title distribution age and week, and percentage cases by age * fixing percentage cases by age * creating skeleton template of basic report * updating template package * adding params to report basic skeleton * updating the documentation functions of the clean data module * fix: documentation of functions * clean: data, functions and files * clean: list disease and ReadMe file * remve: title map * remove day of label * renaming functions and variables * updating documentation functions * renaming function names and refactoring the vignettes content * renaming function names, refactoring the vignettes content and updating documentation * updating documentation and titles plots * updating documentation list_available_diseases_years * fix: documentation functions, vignettes, ReadMe and Dengue Example * fixing general documentation * fix images ReadMe file * fix: ReadMe file and vignettess * remove some dependencies and functions deprecated * Adding tips to ReadMe and Vignettes * updating size images * updating size images ReadMe * adding space ReadMe file * updating align left images * Adding style images ReadMe and Vignettes * Adding style images ReadMe and Vignettes * Adding style images ReadMe and Vignettes * fix: style images ReadMe and Vignettes * fix: style images Vignettes * fix: echo ReadMe * fix: some variables and typo in ReadMe * fixing ReadMe and Vignettes, updating website * adding dependencie map and scale y for plot variable function * fix> scale y for plot variable function * improving group functions * updationg plot map function and dependencies * updationg plot map function and dependencies * updationg examples and documentation * updating examples and documentation * fix: function examples * remove files * fix examples and lintr of modules * fix message plot * divide map plot * adding new functions to municipalities and departments * adding new functions to municipalities and departments * adding new functions to municipalities and departments * adding new functions to municipalities and departments * modify plot and group municipalities and examples * modify plot and group municipalities and examples * modify plot and group municipalities and examples * export functions to departments and municipalities and examples * fix general syntax and rename functions of municipalities * fix called of function geo ocurrence * update template Reporte Basico * preview basic report * add function clean cols by exceptions * adding diseases like input choice on skeleton * modify forma exceptios cols disease in config file * adding analysis of notification department and municipality * update: functions on ReadMe file * update: version and README files * fix: typo, identation of code * update: functions and documentation of subnational report * fix: import and plot functions (#38) * creating the package website * create initial sections of the basic report, cleaning and util functions, updating dengue example * creating function documentation on report_sections, clean_data and utils * fix param functions of get cases distributions by age and gender * adding plot titles and new gender and epiweek section * updatind documentation functions * fix plot function section by gender and epiweek * adding documentation new function of special population * adding new function of special population to basic report * adding spacial distribution section and utils * update documentation functions of spacial distribution section and utils * updating spacial distribution function * updating documentation functions of distribution spatial * updating spatial distribution function * standarization variables and creating clean general function * modify clean sivigila data function and create general functionto clean depto codes * create documentation of new clean functions * refactoring functions of onset and notification date sections * creating documentation function of notification data and onsent symp * modify general clean data function * modify clean sivigila data * creating components of gender and epiweek section * creating components of age and gender, special population section * creating components of age and gender, special population section * creating components of spacial distribution section * fixing variables components of special population and gender * fixing caption text sixe and breaks * removing message plot map * fixing caption text sixe and breaks * fixing caption text size * fixing caption text size and map * fixing title distribution age and week, and percentage cases by age * fixing percentage cases by age * creating skeleton template of basic report * updating template package * adding params to report basic skeleton * updating the documentation functions of the clean data module * fix: documentation of functions * clean: data, functions and files * clean: list disease and ReadMe file * remve: title map * remove day of label * renaming functions and variables * updating documentation functions * renaming function names and refactoring the vignettes content * renaming function names, refactoring the vignettes content and updating documentation * updating documentation and titles plots * updating documentation list_available_diseases_years * fix: documentation functions, vignettes, ReadMe and Dengue Example * fixing general documentation * fix images ReadMe file * fix: ReadMe file and vignettess * remove some dependencies and functions deprecated * Adding tips to ReadMe and Vignettes * updating size images * updating size images ReadMe * adding space ReadMe file * updating align left images * Adding style images ReadMe and Vignettes * Adding style images ReadMe and Vignettes * Adding style images ReadMe and Vignettes * fix: style images ReadMe and Vignettes * fix: style images Vignettes * fix: echo ReadMe * fix: some variables and typo in ReadMe * fixing ReadMe and Vignettes, updating website * adding dependencie map and scale y for plot variable function * fix> scale y for plot variable function * improving group functions * updationg plot map function and dependencies * updationg plot map function and dependencies * updationg examples and documentation * updating examples and documentation * fix: function examples * remove files * fix examples and lintr of modules * fix message plot * divide map plot * adding new functions to municipalities and departments * adding new functions to municipalities and departments * adding new functions to municipalities and departments * adding new functions to municipalities and departments * modify plot and group municipalities and examples * modify plot and group municipalities and examples * modify plot and group municipalities and examples * export functions to departments and municipalities and examples * fix general syntax and rename functions of municipalities * fix called of function geo ocurrence * update template Reporte Basico * preview basic report * add function clean cols by exceptions * adding diseases like input choice on skeleton * modify forma exceptios cols disease in config file * adding analysis of notification department and municipality * update: functions on ReadMe file * update: version and README files * fix: typo, identation of code * update: functions and documentation of subnational report * generate NAMESPACE * fix: documentation and definition of import functions * fix: documentation and definition of plot functions * update: clean functions and vignette * Set up pkgdown website (#37) * Copy pkgdown workflow from pkgtemplate * Remove docs/ folder * Remove Meta/ folder * translation to Spanish of functions, documentation and vignettes (#39) * translation and updated functions and documentation of import data module * translation and updated functions and documentation of cleaning data module * translation and updated functions and documentation of group data module * translation and updated functions and documentation of filter data module * translation and updated functions and documentation of plotting module * translation and updated functions and documentation of utils module * translation and updating of filtering and parsing functions and their documentation * translation and updating of Reporte Basico template * translation and updating README files * translation and updating sections of Reporte Basico template * updating parameters and exceptions of disease * translation and updating sections of package vignette * updating README file with all sections and translated functions * updating of the import module functions documentation in Spanish * Updating the documentation of the cleaning module functions in Spanish * Updating the documentation of the checking module functions in Spanish * Updating the documentation of the plotting module functions in Spanish * Updating the documentation of the utils module functions in Spanish * Updating the documentation of the general functions in Spanish * Updating get started section and user descriptions of the package in README files and vignette * deleting some extra files of the Reporte Basico template * updating users definition and import package README file * change parameters of skeleton template * updating documentation with the new package logo (#40) * fix descriptions of report template sections and adding multiple group diseases (#42) * fix: disease o event title on skeleton Reporte Basico * fix: description of temporal distribution, sex and conclusion sections * adding multiple diseases import, plot and group * adding multiple diseases to agrupar_cols_casos (#43) * fix: disease o event title on skeleton Reporte Basico * fix: description of temporal distribution, sex and conclusion sections * adding multiple diseases import, plot and group * adding nombre_evento to agrupar_cols_casos * adding validation to mortalidad event (#45) * fix: disease o event title on skeleton Reporte Basico * fix: description of temporal distribution, sex and conclusion sections * adding multiple diseases import, plot and group * adding nombre_evento to agrupar_cols_casos * fix: temporal section month with most cases and validation of malaria import * adding validation to mortalidad event * Fix report template (#46) * fix: disease o event title on skeleton Reporte Basico * fix: description of temporal distribution, sex and conclusion sections * adding multiple diseases import, plot and group * adding nombre_evento to agrupar_cols_casos * fix: temporal section month with most cases and validation of malaria import * adding validation to mortalidad event * adding condition of validation mortality * updating plotting for multiples diseases (#48) * fix: disease o event title on skeleton Reporte Basico * fix: description of temporal distribution, sex and conclusion sections * adding multiple diseases import, plot and group * adding nombre_evento to agrupar_cols_casos * fix: temporal section month with most cases and validation of malaria import * adding validation to mortalidad event * adding condition of validation mortality * updating plot multiple disease and vignettes * updating visualisation function for multiple diseases (#49) * fix: disease o event title on skeleton Reporte Basico * fix: description of temporal distribution, sex and conclusion sections * adding multiple diseases import, plot and group * adding nombre_evento to agrupar_cols_casos * fix: temporal section month with most cases and validation of malaria import * adding validation to mortalidad event * adding condition of validation mortality * updating plot multiple disease and vignettes * remove whitespace * updating generic plotting function for multiple disease visualisation * fix: whitespace on report basic template (#50) * fix: disease o event title on skeleton Reporte Basico * fix: description of temporal distribution, sex and conclusion sections * adding multiple diseases import, plot and group * adding nombre_evento to agrupar_cols_casos * fix: temporal section month with most cases and validation of malaria import * adding validation to mortalidad event * adding condition of validation mortality * updating plot multiple disease and vignettes * remove whitespace * updating generic plotting function for multiple disease visualisation * fixing whitespaces * fix condition of morbility (#51) * fix: disease o event title on skeleton Reporte Basico * fix: description of temporal distribution, sex and conclusion sections * adding multiple diseases import, plot and group * adding nombre_evento to agrupar_cols_casos * fix: temporal section month with most cases and validation of malaria import * adding validation to mortalidad event * adding condition of validation mortality * updating plot multiple disease and vignettes * remove whitespace * updating generic plotting function for multiple disease visualisation * fixing whitespaces * fix conditional of morbility on skeleton * updating conditional of morbility on skeleton * fix process and implicated functions to import event data (#56) * fix (get_path_data_disease): updating response and building of the path ref * fix (import_data_event): the event name is convert to a title string * fix (import_sep_data): adding logic for new files of SIVIGILA --------- Co-authored-by: GeraldineGomez <[email protected]> * fix (import_data): updating functions related to import and clean process (#57) * fix (get_path_data_disease): updating response and building of the path ref * fix (import_data_event): the event name is convert to a title string * fix (import_sep_data): adding logic for new files of SIVIGILA * fix (convert_edad): updating convertion edad and uni_med fields and format dates * fix (import_data): addinfg microdata request from bin files * fix (DESCRIPTION): adding readxl dependencie --------- Co-authored-by: GeraldineGomez <[email protected]> * fix (import_data): updating functions related to sex semana epi component (#58) * fix (get_path_data_disease): updating response and building of the path ref * fix (import_data_event): the event name is convert to a title string * fix (import_sep_data): adding logic for new files of SIVIGILA * fix (convert_edad): updating convertion edad and uni_med fields and format dates * fix (import_data): addinfg microdata request from bin files * fix (DESCRIPTION): adding readxl dependencie * fix (agrupar_sex_semanaepi): remove columns related to geo components * fix (plot_sex_semanaepi): remove experimental scale --------- Co-authored-by: GeraldineGomez <[email protected]> * fix (import_data): remove sca problems (#59) * fix (get_path_data_disease): updating response and building of the path ref * fix (import_data_event): the event name is convert to a title string * fix (import_sep_data): adding logic for new files of SIVIGILA * fix (convert_edad): updating convertion edad and uni_med fields and format dates * fix (import_data): addinfg microdata request from bin files * fix (DESCRIPTION): adding readxl dependencie * fix (agrupar_sex_semanaepi): remove columns related to geo components * fix (plot_sex_semanaepi): remove experimental scale * fix (import_data): remove whitespace and reduce a line --------- Co-authored-by: GeraldineGomez <[email protected]> * fix (import_data): remove whitespace (#60) * fix (get_path_data_disease): updating response and building of the path ref * fix (import_data_event): the event name is convert to a title string * fix (import_sep_data): adding logic for new files of SIVIGILA * fix (convert_edad): updating convertion edad and uni_med fields and format dates * fix (import_data): addinfg microdata request from bin files * fix (DESCRIPTION): adding readxl dependencie * fix (agrupar_sex_semanaepi): remove columns related to geo components * fix (plot_sex_semanaepi): remove experimental scale * fix (import_data): remove whitespace and reduce a line * fix (import_data): remove whispace --------- Co-authored-by: GeraldineGomez <[email protected]> * fix and docs: updating, clean and name chunks of vignettes and README, adding contributors to DESCRIPTION file (#61) * chore (DESCRIPTION): updating package's contributors * docs (vignette-sivirep): updating, clean and name chunks * docs (README): updating, clean and name chunks * fix (DESCRIPTION): add and remove commas * fix (DESCRIPTION): author and manteiner * fix (checking_data): updating examples with the full clean function and refactoring access to column * fix (format_fecha): adding correct date format in example * fix (import_sep_data): remove URL of the example * fix (plot_fecha_inisintomas and plot_edad): adding in examples the full clean function * fix (obtener_meses_mas_casos): adding to examples the full clean function * chore: updating examples and functions documentation * remove: old figures of unamed chunks --------- Co-authored-by: GeraldineGomez <[email protected]> * test and chore: adding example test data and updating the documentation of functions (#63) * feat (data): creating data example * chore: remove skeleton folder * chore (examples): updating examples with dengue2020 data and the full clean function * fix (dengue2020): adding terminal newline --------- Co-authored-by: GeraldineGomez <[email protected]> * fix: data, examples and nombre_evento parameter of report template (#64) * fix (examples): adding parameter year to full clean function and updating documentation * fix (examples): adding parameter year to full clean function and updating documentation * fix (examples): adding parameter year to full clean function and updating documentation * fix (examples): adding parameter year to full clean function and updating documentation * fix (dengue2020): compress data * fix (params): change value of nombre_evento to Dengue * remove: whitespace in example --------- Co-authored-by: GeraldineGomez <[email protected]> * fix: data example, import data function and documentation (#65) * fix (examples): adding parameter year to full clean function and updating documentation * fix (examples): adding parameter year to full clean function and updating documentation * fix (examples): adding parameter year to full clean function and updating documentation * fix (examples): adding parameter year to full clean function and updating documentation * fix (dengue2020): compress data * fix (params): change value of nombre_evento to Dengue * remove: whitespace in example * fix (DESCRIPTION): adding R dependency * fix (dengue2022): generate the data with version 2 * fix (import_data): adding cache parameter * fix (plot_map_dpto): remove unused shp files and example * remove: unused shape files * chore: updating documentation of functions --------- Co-authored-by: GeraldineGomez <[email protected]> --------- Co-authored-by: zmcucunuba <[email protected]> Co-authored-by: megamezl <[email protected]> Co-authored-by: Hugo Gruson <[email protected]> Co-authored-by: GeraldineGomez <[email protected]>
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