Vaccination data for municipalities

[eguidotti]

Hi @wcota, thanks for this great repo!
I was wondering if there is a reason why the data for vaccines are not reported in the city files (?).
FYI, I have recently completed a repo with vaccination data for Brazilian municipios:
https://github.com/eguidotti/covid19br

[wcota]

Hi! I have been following a similar approach with Python to read the CSV files and process the vaccination data since July 2021, but only today I am publicly releasing the data (but it was used by collaborators and other research groups).
There are many problems in defining, for example, if we consider a municipality following the place of residence or application of the dose. The main problem is that the field "residence" comes from the internal SUS registration data, and many people (including me :) ) do not update it when moving to another city.
Tomorrow the first automatic update will happen and the data will be released. If you have time, you can compare it with yours. I have no idea when I will have time to document and explain what I do, but I hope to do it soon.

[wcota]

162d64a

[eguidotti]

Hi @wcota, that's great! I would be very thankful if you can take over the maintainance of this.
Below you can find some R code for a quick comparison. I sample checked a few IBGE codes.
The code computes the (cumulated number of) people with at least one vaccine dose from your repo and mine. There are indeed some differences, but more or less the trends look similar. Still, we need to compare people fully vaccinated and total number of doses. And for more IBGE of course. Hope this is a good starting point!

library(data.table)

read.gz <- function(url){
  file <- paste0(tempfile(), ".gz")
  download.file(url, file)
  fread(file)
}

u1 <- "https://github.com/wcota/covid19br/blob/master/vaccination/processed_AC.csv.gz?raw=true"
x1 <- read.gz(u1)

u2 <- "https://github.com/covid19datahub/covid19br/blob/main/data.csv.gz?raw=true"
x2 <- read.gz(u2)

ID.IBGE <- 1200336

a <- setkey(x1[x1$ibgeID==ID.IBGE], date)
a <- a[dose==1, .(PeopleVaccinated = sum(count)), by = date]
a$PeopleVaccinated <- cumsum(a$PeopleVaccinated)
plot(a$date, a$PeopleVaccinated, type = "l")

b <- x2[x2$IBGE==ID.IBGE]
lines(b$Date, b$PeopleVaccinated, col = 2)

[wcota]

Hi! I forgot to mention, but the municipality data are now available at https://github.com/wcota/covid19br-vac

[eguidotti]

Hi! Great work! I'm integrating your data and redirecting users from my repo to yours.

One question: I see that the column dose has a value of zero in correspondence of the vaccine "Johnson&Johnson". Am I correct to assume that:

• dose=0 corresponds to people fully vaccinated with one single shot?
• dose=1 is the first dose of a two-doses vaccination cicle?
• dose=2 is the second dose of a two-doses vaccination cicle?
• dose=3 is a booster dose?

Many thanks!

[wcota]

Yes, that's correct @eguidotti.

[eguidotti]

Data integrated! They should be available in the next 24h at https://covid19datahub.io
Thanks a lot!