Created
January 12, 2022 15:48
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Cruzar datos de positivos con vacunados (COVID-19, Peru - basado en datos abiertos del MINSA")
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library(tidyverse) | |
library(arrow) | |
# RDS de https://github.com/jmcastagnetto/covid-19-peru-limpiar-datos-minsa | |
positivos <- readRDS("tmp/positivos_covid_aumentado.rds") %>% | |
select(id_persona, fecha_resultado, metododx) %>% | |
distinct() %>% | |
mutate( | |
id_persona = as.integer(id_persona) | |
) | |
# Dataset intermedio de procesar los datos de vacunas | |
vacunados_ds <- open_dataset( | |
"tmp/arrow_augmented_data/" | |
) | |
vacunados_df <- tibble() | |
for (fn in vacunados_ds$files) { | |
cat(fn, "\n") | |
ofn <- str_replace(fn, "arrow_augmented_data", "vacunados_positivos") | |
df <- read_parquet(fn, col_select = c("id_persona", "fecha_vacunacion", "dosis", "flag_vacunacion_general")) %>% | |
filter(flag_vacunacion_general == TRUE) %>% | |
select(-flag_vacunacion_general) | |
if(nrow(df) > 0) { | |
tmp_df <- df %>% | |
left_join( | |
positivos, | |
by = "id_persona" | |
) | |
write_parquet( | |
tmp_df, | |
sink = ofn | |
) | |
} | |
cat("Done: ", ofn, "\n") | |
} | |
vac_pos <- open_dataset("tmp/vacunados_positivos/") | |
for (fn in vac_pos$files) { | |
epiyear <- str_extract(fn, "epi_year=\\d{4}") %>% | |
str_replace("=", "-") | |
epiweek <- str_extract(fn, "epi_week=\\d{1,2}") %>% | |
str_replace("=", "-") | |
ofn <- glue::glue("tmp/vacunados_positivos_{epiyear}_{epiweek}.csv") | |
tmp <- read_parquet(fn) | |
write_csv(tmp, ofn) | |
} | |
vac_pos_all <- vac_pos %>% | |
collect() | |
vac_pos_ids <- unique(vac_pos_all$id_persona) | |
novac_pos <- positivos %>% | |
filter(!id_persona %in% vac_pos_ids) | |
write_csv( | |
novac_pos, | |
"tmp/covid19_peru_positivos_no_vacunados.csv" | |
) |
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Código actualizado y datos en: https://github.com/jmcastagnetto/covid19-peru-positivos-vacunados-novacunados