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Analyzing demographic data with epiCo

epiCo’s demographic module is a tool for demographic descriptive analysis and risk assessment of epidemiological events in Colombia. Based on linelist data provided by the Colombian National Surveillance System (SIVIGILA) and demographic data from the Colombian National Administrative Department of Statistics (DANE).

The module allows you to:

In the following vignette, you will learn how to:

  1. Navigate the Codification of the Political Administrative Division of Colombia (DIVIPOLA).
  2. Consult, visualize, and interpret Colombian population pyramids at different administrative levels.
  3. Interpret the demographic variables reported by the SIVIGILA (as ethnicities, special population groups, and occupational labels).
  4. Understand the typical SIVIGILA epidemiological data.
  5. Estimate weekly and monthly incidence rates for a municipality, department, or country.
  6. Integrate the age distributions of cases with population pyramids to obtain an age-risk assessment for a disease.

2. Population pyramids

epiCo provides a built-in dataset with the population projections of Colombia at the national, departmental, and municipality levels (provided by the DANE). These datasets contains the population projections from 2012 to 2024 for ages from 0 to 100 years. However, for the municipal projections it has the ages from 0 to over 85 years old.

Users can perform queries on this data by using the population_pyramid function, providing the DIVIPOLA code of the territory of interest and the year to consult.

ibague_code <- "73001" # DIVIPOLA code for the city of Ibagu<U+00E9>
year <- 2016 # Year to consult
ibague_pyramid_2016 <- population_pyramid(ibague_code, year) # Population
# pyramid (dataframe) for the city of Ibagu<U+00E9> in the year 2019
# dissagregated by sex
knitr::kable(ibague_pyramid_2016[1:5, ])
age population sex
0 15839 F
5 17539 F
10 20171 F
15 23059 F
20 22659 F

Definitions of age ranges and plotting are also provided for both: total number of individuals, or proportion of individuals

ibague_code <- "73001" # DIVIPOLA code for the city of Ibagu<U+00E9>
year <- 2019 # Year to consult
age_range <- 5 # Age range or window
ibague_pyramid_2019 <- population_pyramid(ibague_code, year,
  range = age_range,
  sex = TRUE, total = TRUE,
  plot = TRUE, language = "EN"
)

3. Demographic variables

Events of epidemiological relevance are reported to the SIVIGILA using an official notification form (see link).

epiCo provides a function to consult the dictionaries for the ethnicity categories, special population groups, and occupation codifications used by the SIVIGILA. As shown in the following example:

demog_data <- data.frame(
  id = c(0001, 002, 003, 004, 005, 006, 007, 008),
  ethnicity_label = c(3, 4, 2, 3, 3, 3, 2, 3),
  occupation_label = c(6111, 3221, 5113, 5133, 6111, 23, 25, 99),
  sex = c("F", "M", "F", "F", "M", "M", "F", "M"),
  stringsAsFactors = FALSE
)


ethnicities <- describe_ethnicity(demog_data$ethnicity_label, language = "EN")
knitr::kable(ethnicities)
code description
2 They are communities that have their own ethnic and cultural identity; They are characterized by a nomadic tradition, and have their own language, which is Romanesque
3 Population located in the Archipelago of San Andres, Providencia and Santa Catalina, with Afro-Anglo-Antillean cultural roots, whose members have clearly differentiated sociocultural and linguistic traits from the rest of the Afro-Colombian population
4 Population located in the municipality of San Basilio de Palenque, department of Bolivar, where palenquero is spoken, a Creole language

occupations <- describe_occupation(
  isco_codes = demog_data$occupation_label,
  sex = demog_data$sex,
  plot = "treemap"
)
#> 2 codes are invalid.

knitr::kable(occupations$data)
major major_label sub_major sub_major_label minor minor_label unit unit_label sex count
5 Service Workers and Shop and Market Sales Workers 51 Personal and Protective Services Workers 511 Travel Attendants and Related Workers 5113 Travel guides F 1
5 Service Workers and Shop and Market Sales Workers 51 Personal and Protective Services Workers 513 Personal Care and Related Workers 5133 Home-based personal care workers F 1
6 Skilled Agricultural and Fishery Workers 61 Market-Oriented Skilled Agricultural and Fishery Workers 611 Market Gardeners and Crop Growers 6111 Field crop and vegetable growers F 1
2 Professionals 23 Teaching Professionals NA NA NA NA M 1
3 Technicians and Associate Professionals 32 Life Science and Health Associate Professionals 322 Modern Health Associate Professionals (Except Nursing) 3221 Medical assistants M 1
6 Skilled Agricultural and Fishery Workers 61 Market-Oriented Skilled Agricultural and Fishery Workers 611 Market Gardeners and Crop Growers 6111 Field crop and vegetable growers M 1
NA NA NA NA NA NA NA NA NA 2

4. Epidemiological data

epiCo is a tool that produces analyses based on epidemiological data extracted from SIVIGILA or provided by the user. epi_data is a built-in file that shows an example of the structure used by the package, which is the same as the one reported by SIVIGILA. This file contains the cases of all the municipalities in Tolima for the years 2015-2021.

The following analyses use the dengue cases reported in Tolima in 2019.

data("epi_data")

data_tolima <- epi_data[lubridate::year(epi_data$fec_not) == 2019, ]
knitr::kable(data_tolima[1:5, 4:12])
cod_mun_o cod_pais_r cod_dpto_r cod_mun_r cod_dpto_n cod_mun_n edad sexo per_etn
73001 170 73 73001 25 25307 11 F 6
73268 170 73 73268 73 73268 18 F 6
73200 170 73 73200 11 11001 13 M 6
73671 170 73 73671 73 73671 16 M 6
73671 170 73 73671 73 73671 15 M 6

5. Estimation of incidence rates

The incidence rate feature of epiCo requires the incidence package to produce a modified incidence object. Instead of a count vector (or matrix), it transforms the object to provide a rate element accounting for the number of cases in the time period divided by the total number of inhabitants in the specific region and year.

epiCo uses the DANE population projections as denominators; therefore, it is necessary to provide the administration level at which incidences are calculated.

incidence_object <- incidence(
  dates = data_tolima$fec_not,
  groups = data_tolima$cod_mun_o,
  interval = "1 epiweek"
)
incidence_rate_object <- incidence_rate(incidence_object, level = 2)
knitr::kable(incidence_rate_object$counts[1:5, 1:12])
73001 73024 73026 73030 73043 73055 73067 73124 73148 73152 73168 73200
12 1 1 0 0 0 1 0 0 0 1 1
12 0 1 1 0 1 0 0 1 0 16 0
17 1 1 0 0 1 2 0 0 0 4 0
15 0 1 0 0 3 0 0 2 0 10 0
23 0 1 0 0 1 0 0 0 0 15 0

If groups in the incidence object are not within the DIVIPOLA coding for municipalities (level 2) or departments (level 1), or a national estimation is intended (level 0), the function will not be able to estimate an incidence rate.

6. Estimation of risk by age group

Normalization of data is a key aspect of epidemiology. epiCo allows for the age distribution of cases and normalizes the epidemiological data with the age structure of a population. This normalization allows us to estimate the age risk of a disease according to the age structure of the general population in a municipality, department, or country in a certain year.

data_ibague <- data_tolima[data_tolima$cod_mun_o == 73001, ]

age_risk_data <- age_risk(
  age = as.integer(data_ibague$edad),
  population_pyramid = ibague_pyramid_2019$data,
  sex = data_ibague$sexo, plot = TRUE, language = "EN"
)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.