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Dev feat: added incidence calculation and fix some typos, visualisations and labels #138

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merged 103 commits into from
Apr 24, 2024

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  • Please check if the PR fulfills these requirements
  • I have read the CONTRIBUTING guidelines
  • A new item has been added to NEWS.md
  • Tests for the changes have been added (for bug fixes / features)
  • Docs have been added / updated (for bug fixes / features)
  • Checks have been run locally and pass
  • What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)
  • Feat: incidence calculation by Colombia, department, municipality and sex has been created. Includes functions to plot the results as a bar graph and a tables. A new section in the report template has been created called Incidencia and two subsections Incidencia por sexo and Incidencia según distribución geográfica.
  • Fix: some typo, labels, plots and mapping keys of the config file were included as well. The plots regarding to cases by multiple years, cases types, geographic area and ethnicity groups present the bars in stack. The month with most cases is presented with the name.
  • What is the current behavior? (You can also link to an open issue here)
    The package does not include the incidence calculation in PR Calculate incidence by event #108 and some errors or improvements related to plots or typos in the report template in PR Dev fix: order variables, documentation of group and visualisation module and deleted column cod_eve #134.

  • What is the new behavior (if this is a feature change)?
    In the import module a new function has been created to import the population projections of DANE called impor_data_incidencia. In the group module three functions have been created to calculate the incidence called:
    calcular_incidencia, calcular_incidencia_geo, calcular_incidencia_sex. In the plot module two functions have been created to plot in tables the incidence and a new parameter has been added in functions plot_map and plot_sex called col_distribucion to plot the incidence in map format and bars. A new section in the report template has been created for the incidence called Incidencia and two subsections called Incidencia por sexo and Incidencia según distribución geográfica.

In the group and plot module have been fixed the visualisation, tags, moths, and typos issues.

  • Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)
    No, it does.

…ation projections

A new function has been created to import the data incidence or the population projections from DANE and its corresponding documentation.

Ref: #108
…rojections

A new function has been created to clean the data incidence or the population projections from DANE and its corresponding documentation.

Ref: #108
… or mpio

A new function has been created to calculate the incidence by Colombia, department or municipality and its corresponding documentation.

Ref: #108
…ts and municipalities

A new function has been created to calculate the incidence for all departments of Colombia,  or all municipalities of a department and its corresponding documentation.

Ref: #108
…eir values

A new internal function has been created called obtener_dpto_mpio and its corresponding documentation to refactoring the department and municipality validation and gets their values.

Ref: #108
…event

A new function has been created called obtener_cond_inciden_event and its corresponding documentation to simplify getting the conditions to calculate the incidence by event.

Ref: #108
A new function has been created to calculate the incidence by sexes, department and municipality with its corresponding validations and documentation.

Ref: #108
…and apply str_to_title to nombre_evento column

Ref: #108
@GeraldineGomez GeraldineGomez merged commit 7cce2fa into main Apr 24, 2024
7 of 8 checks passed
@GeraldineGomez GeraldineGomez deleted the dev branch April 24, 2024 21:42
@GeraldineGomez GeraldineGomez restored the dev branch April 24, 2024 21:42
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