Infodengue
Infodengue data¶
This endpoint gives access to data from the Infodengue project, which provide a number of epidemiological variables for all the Brazilian municipalities on a weekly time scale. The request parameters and data variables are described below.
For an example of API usage in Mosqlimate, please refer to API Demo. Python examples are found below.
Parameters Table¶
Input¶
| Parameter name | Required | Type | Description |
|---|---|---|---|
| *page | yes | int | Page to be displayed |
| *per_page | yes | int | How many items will be displayed per page (up to 100) |
| disease | yes | str | Dengue, Zika or Chik[ungunya] |
| start | yes | str (YYYY-mm-dd) | Start date (epidemiological week) |
| end | yes | str (YYYY-mm-dd) | End date (epidemiological week) |
| uf | no | str (UF) | Two letters brazilian's state abbreviation. E.g: SP |
| geocode | no | int | IBGE's municipality code |
Output (items)¶
| Parameter name | Type | Description |
|---|---|---|
| data_iniSE | str (YYYY-mm-dd) | Start date of epidemiological week |
| SE | int (YYYYWW) | Epidemiological week |
| casos_est | float | Estimated number of cases per week using the nowcasting model |
| casos_est_min | int | 95% credibility interval of the estimated number of cases |
| casos_est_max | int | 95% credibility interval of the estimated number of cases |
| casos | int | Number of notified cases per week (values are retrospectively updated every week) |
| municipio_geocodigo | int | IBGE's municipality code |
| p_rt1 | float | Probability (Rt > 1) |
| p_inc100k | float | Estimated incidence rate (cases per pop x 100.00 |
| Localidade_id | int | Sub-municipality division |
| nivel | int | Alert level (1 = green, 2 = yellow, 3 = orange, 4 = red) |
| id | int | Numeric index |
| versao_modelo | str | Model version |
| Rt | float | Point estimate of the reproductive number of cases |
| municipio_nome | str | Municipality's name |
| pop | float | Population (IBGE) |
| receptivo | int | Indicates climate receptivity, i.e., conditions for high vectorial capacity. 0 = unfavorable, 1 = favorable, 2 = favorable this week and last week, 3 = favorable for at least three weeks |
| transmissao | int | Evidence of sustained transmission: 0 = no evidence, 1 = possible, 2 = likely, 3 = highly likely |
| nivel_inc | int | Estimated incidence below pre-epidemic threshold, 1 = above pre-epidemic threshold but below epidemic threshold, 2 = above epidemic threshold |
| umidmax | float (%) | Average daily maximum humidity percentages along the week |
| umidmed | float (%) | Average daily humidity percentages along the week |
| umidmin | float (%) | Average daily minimum humidity percentages along the week |
| tempmax | float (°C) | Average daily maximum temperatures along the week |
| tempmed | float (°C) | Average daily temperatures along the week |
| tempmin | float (°C) | Average daily minimum temperatures along the week |
| casprov | int | Probable number of cases per week (cases - discarded cases) |
| casprov_est | float | TBD |
| casprov_est_min | int | credibility interval of the probable number of cases |
| casprov_est_max | int | credibility interval of the probable number of cases |
| casconf | int | Cases effectively confirmed with laboratory testing |
Details¶
page consists in the total amount of Items returned by the request divided by per_page. The pagination information is returned alongside with the returned request. E.g.:
'pagination': {
'items': 10, # Amout of Items being displayed
'total_items': 10, # Total amount of Items returned in the request
'page': 1, # *request parameter
'total_pages': 1, # Total amount of pages returned in the request
'per_page': 100 # *request parameter
},
Note: for fetching a big amount of pages, please consider using Async code
Usage examples¶
import requests
infodengue_api = "https://api.mosqlimate.org/api/datastore/infodengue/"
page = 1
pagination = f"?page={page}&per_page=100&"
filters = "disease=%s&start=%s&end=%s" % ("dengue", "2022-12-30", "2023-12-30")
resp = requests.get(infodengue_api + pagination + filters) # GET request
items = resp.json()["items"] # JSON data in dict format
resp.json()["pagination"] # Pagination*
library(httr)
library(jsonlite)
infodengue_api <- "https://api.mosqlimate.org/api/datastore/infodengue/"
page <- "1"
pagination <- paste0("?page=", page, "&per_page=100&")
filters <- paste0("disease=dengue&start=2022-12-30&end=2023-12-30")
url <- paste0(infodengue_api, pagination, filters)
resp <- GET(url)
content <- content(resp, "text")
json_content <- fromJSON(content)
items <- json_content$items
pagination_data <- json_content$pagination
*The response's pagination contains information about the amount of items returned
by the API call. These information can be used to navigate between the queried
data by changing the page parameter on the URL. See details
Example using the mosqlient package¶
The mosqlient is a Python package created to facilitate the use of API.
In the package, there is a function called get_infodengue that returns a pandas DataFrame with the data. This function accepts as filters the parameters start_date, end_date, diasese, geocode, and uf, with the same types defined in the parameters table above.
Below is a usable example of fetching data from the RJ state.