In jmones/covid19-data-explorations: COVID-19 data explorations

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

THIS IS WORK IN PROGRESS

knitr::opts_chunk$set(echo = TRUE, message = FALSE)

Exploration to replicate an italian paper on pollution to human transmission of COVID-19

Original paper

Diffusion of COVID-19 Outbreaks: The Interaction between Air Pollution-to-Human and Human-to-Human Transmission Dynamics in Hinterland Regions with Cold Weather and Low Average Wind Speed https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3567841

Required datasets

| Dataset | Description | Source | |---------|--------|------| | covid_tests_catalonia | Number of infected per city | Tests of COVID-19 in Catalonia, Government of Catalonia | | | Meteorological indicators: average, moisture, wind, days of rain and fog | | | | density | |

Analysis

library(drake)
library(ggeffects)
library(stargazer)
library(tidyverse)

load(paste0("../", file_in("data/covid_tests_catalonia.rda")))

covid_tests_catalonia <- covid_tests_catalonia %>% 
  filter(!is.na(MunicipiCodi)) %>% 
  mutate(MunicipiDescripcio = as_factor(MunicipiDescripcio),
         ComarcaDescripcio = as_factor(ComarcaDescripcio)) %>% 
  mutate(MunicipiDescripcio = relevel(MunicipiDescripcio, ref="Barcelona"),
         ComarcaDescripcio = relevel(ComarcaDescripcio, ref="Barcelonès"))

mod1 <- lm(ResultatCovidCodi~SexeDescripcio, data=covid_tests_catalonia)
mod2 <- update(mod1,.~. + ComarcaDescripcio)

stargazer(mod1,mod2,
          type="html",
          no.space = TRUE,
          header=FALSE)

p <- ggpredict(mod2,terms = "SexeDescripcio") %>% as_tibble()

ggplot(p, aes(x,predicted)) +
  geom_point() +
  geom_errorbar(aes(ymin=conf.low, ymax=conf.high),
                width=0.05) +
  theme_minimal() +
  labs(x="",
       y="Probabilitat de positiu de COVID19") #+
#  ylim(0.41,0.49)

p <- ggpredict(mod2,terms = "ComarcaDescripcio") %>% as_tibble()

ggplot(p, aes(predicted,reorder(x,desc(predicted)))) +
  geom_point() +
  geom_errorbarh(aes(xmin=conf.low, xmax=conf.high),
                height=0.05) +
  theme_minimal() +
  labs(y="",
       x="Probabilitat de positiu de COVID19") +
  theme(axis.text.y = element_text(hjust=0,size=8))

jmones/covid19-data-explorations documentation built on April 24, 2020, 9:45 p.m.