Arrange the municipalities by number of cases #78
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Hi @GAcero02 , Many thanks for posting the improvement to the spatial distribution visualization bar. I'm going to create a branch to work on this enhancement. |
GeraldineGomez
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Feb 14, 2024
Added logic to sort ascending data by cases for improve and facilitate the visualisation in plot_mpio and plot_dpto functions. Refs: #78
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GeraldineGomez
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Feb 14, 2024
* feat: moved the colors variable before the conditional * feat: added logic to sort ascending data by cases Added logic to sort ascending data by cases for improve and facilitate the visualisation in plot_mpio and plot_dpto functions. Refs: #78
GeraldineGomez
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Feb 20, 2024
Added package reference of the reorder function Ref: #78
GeraldineGomez
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Feb 20, 2024
Added logic to sort ascending data by cases for improve and facilitate the visualisation in plot_dptos function. Refs: #78
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GeraldineGomez
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Feb 20, 2024
…ction (#99) * feat: moved the colors variable before the conditional * feat: added logic to sort ascending data by cases Added logic to sort ascending data by cases for improve and facilitate the visualisation in plot_mpio and plot_dpto functions. Refs: #78 * chore(skeleton): added package of reorder Added package reference of the reorder function Ref: #78 * feat(plot_dptos): added logic to sort cases Added logic to sort ascending data by cases for improve and facilitate the visualisation in plot_dptos function. Refs: #78
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GeraldineGomez
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Feb 20, 2024
…r fuction (#100) * 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]> * fix, chore and feat: plot functions, map visualisation, documentation and theme of report template (#68) * feat: adding package's logo in report template * chore (DESCRIPTION): remove data.table dependency and replacing httr to httr2 * feat (agrupar_mun): adding geo ocurrency data * fix (import_data): remove file logic of previous service * fix (get_path): replace httr implementation to httr2 and optimize the ref file search * update (obtener_ocurren_geo): adding code_event parameter * chore (vignette): updating the call of plot functions for ini_sin and fech_not * chore (README): updating the calling logic of inisintomas and fecha_notifica functions * chore (obtener_tip_ocurren_geo): adding nombre_event to documentation * feat: creation of initial package theme for ggplot visualisations * refactoring: remove plot_variable function, creating separate functions to each variable and adding fuente_data parameter - remove plot_variable function - creating separate functions to each variable - adding fuente_data parameter - adding index table to map visualisation * refactor: list_events and adding parameter validations in impor_event * chore: updating examples documentation * fix: remove eval parse invocations across cleaning functions * fix: removing eval parse invocations and references of geo ocurrence * chore: updating examples and adding new functions documentation * chore: updating examples with package's data * chore: updating examples with package's data * chore: updating examples with package's data * chore: updating examples documentation * chore: removing report template files * chore: adding color title in report template * chore: removing unnecessary import of report template * fix (plot_sex_semanaepi): replacing scales free to free_y * chore (README): updating file with dpto of Chocó and resizing images * chore (vignette): updating file with dpto of Chocó and resizing images * fix (report_skeleton): adding components of HTML visualisation * feat (plot_map): adding title and subtitle with geo ocurrence * fix (report_template): resizing images and set default dpto value * fix (report_template): resizing images, set default dpto value and removing unnecessary imports * chore: added internal keyword to scraping function * chore: added keyword internal to auxiliar functions, validations of inputs and updating examples and documentation * chore: added validations of inputs, rename functions and updating examples and documentation * chore: added validations of inputs and updating examples and documentation * chore: added validations of inputs, remove functions and updating examples and documentation * chore: updating examples and documentation with new definition of functions * chore[README]: updating documentation with new definition of functions and parameters * chore[vignette]: updating documentation with new definition of functions and parameters * chore[vignette]: updating documentation with new definition of functions and parameters * chore[examples]: updating documentation with new definition of functions and parameters * fix (limpiar_fecha_event): duplicate sentence * fix (plot_map): removing duplicate parameter * fix: duplicate values and examples definitions * fix: spaces of functions * fix (skeleton): updated parameters of template * fix(skeleton): updating parameters in import function * feat, fix and chore: validations, variable names and linted and cleaned up the code (#72) * fix (skeleton): modified default output and removed lost reference * chore(plot_fecha_notifica): added input validations and updated documentation * fix(plot_map): added input validations, updated documentation and redefined map title * fix(plot_fecha_inisintomas): added input validations, updated documentation and value year to uni_marca * chore(plot_sex): added input validations, updated documentation * chore: create lintr config file from PR 67 * chore(.Rbuildignore): added .lintr config file from PR 67 * chore(DESCRIPTION): updated R depends, RoxygenNote and added Andres Moreno as contributor This changes from PR 66, PR 70 and .lintr check * chore(config): updated key additional_diseases to letter case of SIVIGILA * fix(skeleton): removed if complex from PR 67 and lintr check * fix and feat (cleaning_module): added validationsa and removing code based in lintr check This changes include: Added validations in almost all clean functions Added stringr::fixed where apply it Removed unnecessary TRUEs Removed variable initialization with c() Based PR 67 and lintr check * fix and feat (utils): Added validations, renamed variables, and removed code based on linting checks Changes in this commit: - Added validations to nearly all utility functions. - Applied stringr::fixed where necessary. - Removed unnecessary TRUE values. - Eliminated variable initialization with c(). - Replaced paste function with paste0. This addresses PR 67 and aligns with linting checks. * fix and feat (plotting_module): Added validations, renamed variables, functions and removed code based on linting checks Changes in this commit: - Added validations to all plotting functions. - Updated documentation and examples. - Renamed functions and variables related to municipalities and departments. - Removed unnecessary TRUE values. - Eliminated variable initialization with `c()`. - Replaced `paste` function with `paste0`. This commit addresses some items from PR 67 and aligns with linting checks. * fix and refactoring: validations, renamed variables and removed code based on linting checks Changes in this commit: - Refactoring validations of all functions. - Renamed variables related to municipalities and departments. - Eliminated variable initialization with `c()`. This commit addresses some items from PR 67 and aligns with linting checks. * fix and refactoring: validations and removed code based on linting checks Changes in this commit: - Refactoring validations of all functions. - Eliminated variable initialization with `c()`. - Replaced `paste` function with `paste0`. This commit addresses some items from PR 67 and aligns with linting checks. * fix(scraping): modified code base on linting checks Changes in this commit: - Eliminated variable initialization with `c()`. - Replaced `paste` function with `paste0`. - Applied stringr::fixed where necessary. This commit addresses items from PR 67 and aligns with linting checks. * chore(README): updated with linting changes, validations and functions * chore(vignette): Added 'nolint' comment for pak installation. This commit addresses items from PR 67 and aligns with linting checks. * fix(utils): added character validation and updated documentation * fix(limpiar_fecha_event): added character validation and updated documentation * fix(plot_map): remove repited departments and municipalities * chore(skeleton): include all parameters in function calls * chore(README): update parameters name and library setup * chore(README): update map visualisation * Fix map file size (#74) * Delete inst/extdata/depto_adm_shp directory fix: deleted old shapefiles * Create .delete fix: created new DANE shapes directory * fix: added new DANE shape files * fix: Update config.yml * fix: Update plotting.R to include new DANE shapes * fix: delete inst/extdata/depto_adm_shp_simp/.delete * updated plot map function --------- Co-authored-by: Andrés Moreno <[email protected]> Co-authored-by: Andrés Moreno <[email protected]> * Feat: removed and logic relate to dpto and mpio params (#75) * feat (plot_map): added logic when dpto and mpio values are absent * feat(geo_filtro/agrupar_dpto): added logic when dpto and mpio values are ausent * feat(utils): added logic when dpto and mpio values are ausent * fix(config): removed tilde in Cancer de Mama * chore(plotting): completed documentation of examples * feat(plot): added tendency option to plot_fecha_inisintomas and plot_fecha_notifica This commit includes: - Added tendency option to plot_fecha_inisintomas and plot_fecha_notifica - Updated documentation and examples with the new parameter "tipo" * feat(plot_mpios): updated input nomb_col with the return parameters of agrupar_mpio This commit includes: - Updated input nomb_col with the return parameters of agrupar_mpio - Updated function's documentation and examples * chore(plotting_module): updated documentation and examples * fix(plot_mpio): moved parameter nom_col validation * feat(divipola_data): created data set with codes and geo info of DIVIPOLA This commit includes: - Creation of RData files and xlsx - Creation of R file description of dataset * fix(lintr): lenght of example descriptions * feat(import_geo_cods): added option to load DIVOPOLA data directly from a file * fix(plot_mpio): reference correct data frame to define the nomb_col * feat(plot_map): removed message of st_read and fixed name column of polygon * fix(agrupar_mpio): column name reference to geo ocurrence when dpto is empty or not filter * check(geo_filter): validated behavior with mpio * check(modificar_cod_mun): validated composition of code * check(utils): validated modify cod mpio * fix(modficar_cod_mun ): cod_dpto variances * feat(plot_map): added Colombia map option and logic * chore: updated documentation and skeleton * feat(estandarizar_geo_cod): added complete DIVIPOLA standart into mpios * feat(geo_filtro): removed modificar_cod_mun * feat(plot_map): removed function called of modificar_cod_mun * chore(plot_map): passed first dpto validation * feat(plot_map): updating conditional to polygon_seleccionado$MPIO_CCDGO == data_dept$codigo_municipio * feat(estandarizar_texto): creating function and adding in obtener_info_depts * chore(modificar_cod_mun): removed function of documentation * chore(plot_map): added correct parameter in geo_filtro * chore(estandarizar_texto): updated input of example * chore(config): fix feo column names * chore(config): added key related diseases * chore(config): removed accent of departments * chore(skeleton): removed accent of deparments * feat(standardize_geo_cods): added validation when format is complete for dept or mun * lintr(plot_map): fixed items of lintr scanner * chore(README): removed accent of department * chore(README): removed accent of example department * removed estandarizar_texto function * chore(plot_map): defined font family * feat(list_events): added zika disease * fix: removed temp validations * fix: added lenght validation in pos related to dpto and mpio * fix: position title * fix: modify legend position of plots * Dev feat: updated validation response from SIVIGILA API (#80) * feat (plot_map): added logic when dpto and mpio values are absent * feat(geo_filtro/agrupar_dpto): added logic when dpto and mpio values are ausent * feat(utils): added logic when dpto and mpio values are ausent * fix(config): removed tilde in Cancer de Mama * chore(plotting): completed documentation of examples * feat(plot): added tendency option to plot_fecha_inisintomas and plot_fecha_notifica This commit includes: - Added tendency option to plot_fecha_inisintomas and plot_fecha_notifica - Updated documentation and examples with the new parameter "tipo" * feat(plot_mpios): updated input nomb_col with the return parameters of agrupar_mpio This commit includes: - Updated input nomb_col with the return parameters of agrupar_mpio - Updated function's documentation and examples * chore(plotting_module): updated documentation and examples * fix(plot_mpio): moved parameter nom_col validation * feat(divipola_data): created data set with codes and geo info of DIVIPOLA This commit includes: - Creation of RData files and xlsx - Creation of R file description of dataset * fix(lintr): lenght of example descriptions * feat(import_geo_cods): added option to load DIVOPOLA data directly from a file * fix(plot_mpio): reference correct data frame to define the nomb_col * feat(plot_map): removed message of st_read and fixed name column of polygon * fix(agrupar_mpio): column name reference to geo ocurrence when dpto is empty or not filter * check(geo_filter): validated behavior with mpio * check(modificar_cod_mun): validated composition of code * check(utils): validated modify cod mpio * fix(modficar_cod_mun ): cod_dpto variances * feat(plot_map): added Colombia map option and logic * chore: updated documentation and skeleton * feat(estandarizar_geo_cod): added complete DIVIPOLA standart into mpios * feat(geo_filtro): removed modificar_cod_mun * feat(plot_map): removed function called of modificar_cod_mun * chore(plot_map): passed first dpto validation * feat(plot_map): updating conditional to polygon_seleccionado$MPIO_CCDGO == data_dept$codigo_municipio * feat(estandarizar_texto): creating function and adding in obtener_info_depts * chore(modificar_cod_mun): removed function of documentation * chore(plot_map): added correct parameter in geo_filtro * chore(estandarizar_texto): updated input of example * chore(config): fix feo column names * chore(config): added key related diseases * chore(config): removed accent of departments * chore(skeleton): removed accent of deparments * feat(standardize_geo_cods): added validation when format is complete for dept or mun * lintr(plot_map): fixed items of lintr scanner * chore(README): removed accent of department * chore(README): removed accent of example department * removed estandarizar_texto function * chore(plot_map): defined font family * feat(list_events): added zika disease * fix: removed temp validations * fix: added lenght validation in pos related to dpto and mpio * fix: position title * fix: modify legend position of plots * feat: updated validation response from SIVIGILA API * feat(skeleton): added suggestion section in report (#83) Created suggestion section in the report template: Reporte Basico, as a result of usability testing and learning approach of the package Refs: #82 * feat(skeleton): added toggle options for report sections (#89) * feat(skeleton): added toggle for temporal distribution section Created toggle for temporal distribution section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): added toggle for sex and epiweek distribution section Created toggle for sex and epiweek section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): modified the paragraph text of temporal distribution with paste0 Modified the paragraph text of temporal distribution with paste0 for toggle option and fixed the month with the most cases. Refs: #85 * feat(skeleton): added toggle for age distribution section Created toggle for age section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): added toggle for age and sex distribution section Created toggle for age and sex section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): added toggle for municipality distribution section Created toggle for municipality section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): added toggle for spatial distribution section Created toggle for spatial section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): added toggle for suggestions section Created toggle for suggestions section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * fix(impor_data_event): adding extra validation for dengue 2016 (#91) * fix(impor_data_event): adding extra validation for dengue 2016 Created extra validation for cod_eve column in the data that provides SIVIGILA source because, it appears duplicated in Dengue 2016 Refs: #90 * fix(impor_data_event): refactoring validation for dengue 2016 Refactoring extra validation for cod_eve column in the data that provides SIVIGILA source. It appears duplicated in Dengue 2016 Refs: #90 * feat(skeleton): removed toggle option for suggestion section (#93) * feat(skeleton): added toggle for temporal distribution section Created toggle for temporal distribution section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): added toggle for sex and epiweek distribution section Created toggle for sex and epiweek section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): modified the paragraph text of temporal distribution with paste0 Modified the paragraph text of temporal distribution with paste0 for toggle option and fixed the month with the most cases. Refs: #85 * feat(skeleton): added toggle for age distribution section Created toggle for age section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): added toggle for age and sex distribution section Created toggle for age and sex section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): added toggle for municipality distribution section Created toggle for municipality section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): added toggle for spatial distribution section Created toggle for spatial section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): added toggle for suggestions section Created toggle for suggestions section in the report template: Reporte Basico. Includes the section title, text, calculations and plots. Refs: #85 * feat(skeleton): removed toggle for suggestion section Removed toggle for suggestions section in the report template: Reporte Basico. Refs: #85 * feat: added logic to sort ascending data by cases (#96) * feat: moved the colors variable before the conditional * feat: added logic to sort ascending data by cases Added logic to sort ascending data by cases for improve and facilitate the visualisation in plot_mpio and plot_dpto functions. Refs: #78 * feat: added logic to sort cases and package reference of the order fuction (#99) * feat: moved the colors variable before the conditional * feat: added logic to sort ascending data by cases Added logic to sort ascending data by cases for improve and facilitate the visualisation in plot_mpio and plot_dpto functions. Refs: #78 * chore(skeleton): added package of reorder Added package reference of the reorder function Ref: #78 * feat(plot_dptos): added logic to sort cases Added logic to sort ascending data by cases for improve and facilitate the visualisation in plot_dptos function. Refs: #78 --------- 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]> Co-authored-by: Andrés Moreno <[email protected]> Co-authored-by: Andrés Moreno <[email protected]>
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It is recommended to organize municipalities by number of cases to improve understanding and decision making.
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