Dev feat: added risk population to incidence calculation #173

GeraldineGomez · 2024-05-16T16:45:33Z

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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, ...)
Feature: New functions have been created to import the risk population by event and incorporate it into various functions for calculating incidence.
- import_pob_incidencia
- import_pob_riesgo
- obtener_pob_incidencia
What is the current behavior? (You can also link to an open issue here)
The incidence calculation for all events or diseases was performed using population projections from DANE. This addresses issues:
What is the new behavior (if this is a feature change)?
The incidence calculation for sex, department, municipality, and Colombia utilizes the risk population of the event, sourced from the data shared by NIH, if it is available.
Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)
No, it does.

… data Ref: #172 & #146

…tion A new function has been created to import the risk population from the Health Ministry with its corresponding documentation, examples and validations. Ref: #172 & #146

Ref: #172 & #146

…w function name Ref: #172 & #146

… population A new function has been created to import the population that will be used in the incidence calculation. Depending on the value of the parameter poblacion, it imports either the at-risk population or the DANE population projections. It includes the corresponding documentation, examples and validations. Ref: #172 & #146

…nce pop and warnings A new function has been created to obtain the population that will be used in the incidence calculation. Depending on the value of the 'poblacion' parameter, it obtains either the at-risk population or the population projections from DANE. If there isn't any at-risk population available for the selected year, it obtains the population projections and displays different warnings to users based on the type of population obtained. It includes the corresponding documentation, examples, and validations. Ref: #172 & #146

…ta event A new function has been created to obtain the year value from the event or disease data with its corresponding documentation, examples, and validations. Ref: #172 & #146

A new parameter has been included in the function called poblacion to define the distribution of the data depending on the risk population or population projections. Ref: #172 & #146

Ref: #172 & #146

…idencia Ref: #172 & #146

Ref: #172 & #146

…ence Ref: #172 & #146

Ref: #172 & #146

Added invocation of the function obtener_year to obtain the event year and removed the validation. Ref: #172 & #146

…ncia Added invocation of the function obtener_pob_incidencia to obtain the incidence population and removed the validations related to data_incidencia. Ref: #172 & #146

Ref: #172 & #146

…gic for population and year Ref: #172 & #146

Ref: #172 & #146

Added invocation of the function obtener_year to obtain the event year and removed the corresponding validations. Ref: #172 & #146

…tion Ref: #172 & #146

… data_incidencia Ref: #172 & #146

Ref: #172 & #146

…aragraph of cases by sex A new function has been created to obtain the description paragraph for the distribution of cases by sex section in the template: Reporte Basico and along its corresponding documentation. Ref: #174

Ref: #172 & #146

… INS protocol Ref: #172 & #146

Ref: #172 & #146

Ref: #175

… more events Ref: #176

Ref: #176

…ies or more Ref: #176

Ref: #177

Ref: #172 & #146

…mula Ref: #172 & #146

Ref: #172 & #146

…ula for event incidence calculation Ref: #172 & #146

GeraldineGomez added 30 commits May 15, 2024 16:13

chore(import_pob_riesgo): added risk population paths to import their…

96b52cc

… data Ref: #172 & #146

feat(import_pob_riesgo): created a function to import the risk popula…

f0d93f6

…tion A new function has been created to import the risk population from the Health Ministry with its corresponding documentation, examples and validations. Ref: #172 & #146

chore: renamed function import_pob_proyecciones

baf803c

Ref: #172 & #146

fix(import_pob_proyecciones): added file exist validation

772a981

Ref: #172 & #146

chore(import_pob_proyecciones): updated docs and examples with the ne…

6f35606

…w function name Ref: #172 & #146

feat(obtener_year): created a function to obtain the year from the da…

9356ace

…ta event A new function has been created to obtain the year value from the event or disease data with its corresponding documentation, examples, and validations. Ref: #172 & #146

feat(calcular_incidencia): added poblacion parameter

216511e

A new parameter has been included in the function called poblacion to define the distribution of the data depending on the risk population or population projections. Ref: #172 & #146

chore: removed conditionals of the unidades geo

9255e9a

Ref: #172 & #146

chore: moved logic related to total_casos

e0a2edc

Ref: #172 & #146

feat: added invocation of obtener_pob_incidencia

9224b9e

Ref: #172 & #146

chore: removed validations of data_incidencia and year

eea00a3

Ref: #172 & #146

chore: updated documentation with the new logic for year and data_inc…

8383e95

…idencia Ref: #172 & #146

chore: replaced dontrun to donttest

13cf71f

Ref: #172 & #146

chore: removed accents and special characters

ebc2d33

Ref: #172 & #146

chore(import_pob_riesgo): removed accents and special characters

949f477

Ref: #172 & #146

chore(import_sep_data): replaced importa for obtiene

c25bee9

Ref: #172 & #146

chore(plotting): updated documentation with the new features of incid…

8eea757

…ence Ref: #172 & #146

chore(import_pob_riesgo): added label year to warning message

04c9dee

Ref: #172 & #146

chore(obtener_pob_incidencia): removed accent in población

20940a7

Ref: #172 & #146

feat(calcular_incidencia_geo): added invocation of obtener_year

f018e9b

Added invocation of the function obtener_year to obtain the event year and removed the validation. Ref: #172 & #146

feat(calcular_incidencia_geo): added invocation of obtener_pob_incide…

14322f4

…ncia Added invocation of the function obtener_pob_incidencia to obtain the incidence population and removed the validations related to data_incidencia. Ref: #172 & #146

fix(calcular_incidencia_geo): iterate by row for dptos in data_agrupada

f0a7522

Ref: #172 & #146

fix(calcular_incidencia_geo): iterate by row for mpios in data_agrupada

94f8f87

Ref: #172 & #146

chore(calcular_incidencia_geo): updated documentation with the new lo…

5c82e37

…gic for population and year Ref: #172 & #146

chore(calcular_incidencia_geo): replaced dontrun with donttest

e3e37fc

Ref: #172 & #146

feat(calcular_incidencia_sex): added invocation of obtener_year

9a0ea08

Added invocation of the function obtener_year to obtain the event year and removed the corresponding validations. Ref: #172 & #146

feat(calcular_incidencia_sex): added logic to import incidence popula…

300704d

…tion Ref: #172 & #146

feat(calcular_incidencia_sex): added MINS warning and validations for…

c21a079

… data_incidencia Ref: #172 & #146

fix(obtener_cond_inciden_event): included additional columns

fbcb30f

Ref: #172 & #146

GeraldineGomez linked an issue May 17, 2024 that may be closed by this pull request

Fix paragraph on the distribution of cases by sex - including special cases or events #174

Closed

GeraldineGomez added 10 commits May 17, 2024 15:21

fix: added logic to special events - Malaria

45a5755

Ref: #172 & #146

fix: added key special_events - Malaria

716f31e

Ref: #172 & #146

fix: logic to obtain incidence formula (population) by event based on…

d5a3e54

… INS protocol Ref: #172 & #146

chore: updated default value of population parameter to NULL

6d036cb

Ref: #172 & #146

fix: replaced toupper with tolower for the year label

a823487

Ref: #172 & #146

fix: removed event name in the warning message

2ea0c41

Ref: #172 & #146

fix(skeleton): size of text block for long names

f5b720a

Ref: #175

fix: separate the year from the event name

5b1fbe1

Ref: #175

fix: modified the heigh of the cases plot by year when there are 3 or…

4f1a2df

… more events Ref: #176

GeraldineGomez linked an issue May 17, 2024 that may be closed by this pull request

Modified heigh of plots #176

Closed

GeraldineGomez added 5 commits May 17, 2024 15:51

fix: modified the heigh of the plot cases by onset symptom

4f50421

Ref: #176

fix: modified the heigh of the spatial plot when exist 15 municipalit…

2500898

…ies or more Ref: #176

fix(skeleton): hide epi sex and age sex distribution

8e06f72

Ref: #177

fix: lintr for word materna

d9c59ab

Ref: #177

feat: added conditions for the numerator and denominator

1bbe671

Ref: #172 & #146

GeraldineGomez linked an issue May 17, 2024 that may be closed by this pull request

Hide epi/age sex distribution for the event Mortalidad Materna #177

Closed

GeraldineGomez added 6 commits May 17, 2024 22:37

fix: added default logic when the ins protocol is not clear

df499e1

Ref: #172 & #146

fix: added n_distinct for dpto and mpio logic

67d502f

Ref: #172 & #146

fix: removed logic of empty incidence conditions

1b66317

Ref: #172 & #146

chore: replaced XLSX file with RDA file for the event's incidence for…

b740543

…mula Ref: #172 & #146

chore: updated incidence_events key to reference rda file

7bee8fa

Ref: #172 & #146

chore: replaced logic with XLSX file with RDA file to obtain the form…

423c8b2

…ula for event incidence calculation Ref: #172 & #146

GeraldineGomez linked an issue May 18, 2024 that may be closed by this pull request

Fix long titles on the cover of the report #175

Closed

GeraldineGomez merged commit dbc529e into main May 18, 2024
8 checks passed

GeraldineGomez deleted the feat-pop-risk-incidence-172 branch May 18, 2024 20:44

GeraldineGomez mentioned this pull request May 18, 2024

Comentarios SIVIREP #146

Closed

GeraldineGomez restored the feat-pop-risk-incidence-172 branch May 29, 2024 16:20

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Dev feat: added risk population to incidence calculation #173

Dev feat: added risk population to incidence calculation #173

GeraldineGomez commented May 16, 2024 •

edited

Dev feat: added risk population to incidence calculation #173

Dev feat: added risk population to incidence calculation #173

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GeraldineGomez commented May 16, 2024 • edited

GeraldineGomez commented May 16, 2024 •

edited