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April 26, 2021 16:35
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math370-final
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--- | |
title: "370 Work" | |
author: "Ryan Grossman" | |
date: "4/20/2021" | |
output: html_document | |
--- | |
```{r setup, include=FALSE} | |
knitr::opts_chunk$set(echo = TRUE) | |
``` | |
```{r} | |
library(tidyverse) | |
library(covidcast) | |
setwd("~/Documents/public health 460/data") | |
us_locations <- read_csv("us_locations.csv") | |
covid_cases <- covidcast_signal(data_source = "jhu-csse", | |
signal = "confirmed_incidence_num", | |
start_day = "2021-01-01", end_day = "2021-04-19", | |
geo_values = ) | |
vaccine_acceptance <- suppressMessages( | |
covidcast_signal(data_source = "fb-survey", signal = "smoothed_covid_vaccinated_or_accept", | |
start_day = "2021-03-22", end_day = "2021-04-19", | |
geo_type = "county") | |
) | |
mask_wearing <- suppressMessages( | |
covidcast_signal(data_source = "fb-survey", signal = "smoothed_wearing_mask_7d", | |
start_day = "2021-01-01", end_day = "2021-04-19", | |
geo_type = "county") | |
) | |
travel <- suppressMessages( | |
covidcast_signal(data_source = "safegraph", signal = "full_time_work_prop_7dav", | |
start_day = "2021-01-01", end_day = "2021-04-19", | |
geo_type = "county") | |
) | |
symptom_search <- suppressMessages( | |
covidcast_signal(data_source = "google-symptoms", signal = "sum_anosmia_ageusia_smoothed_search", | |
start_day = "2021-01-01", end_day = "2021-04-19", | |
geo_type = "county") | |
) | |
doctor_visits <- suppressMessages( | |
covidcast_signal(data_source = "doctor-visits", signal = "smoothed_adj_cli", | |
start_day = "2021-01-01", end_day = "2021-04-19", | |
geo_type = "county") | |
) | |
covid_like_symptoms <- suppressMessages( | |
covidcast_signal(data_source = "fb-survey", signal = "smoothed_cli", | |
start_day = "2021-01-01", end_day = "2021-04-19", | |
geo_type = "county") | |
) | |
``` | |
```{r} | |
num_covid_cases <- covid_cases %>% | |
group_by(geo_value) %>% | |
summarize(num_covid_cases = sum(value)) | |
num_covid_cases | |
avg_vaccine <- vaccine_acceptance %>% | |
group_by(geo_value) %>% | |
summarize(avg_vaccine = mean(value)) | |
avg_vaccine | |
avg_mask <- mask_wearing %>% | |
group_by(geo_value) %>% | |
summarize(avg_mask = mean(value)) | |
avg_mask | |
avg_travel <- travel %>% | |
group_by(geo_value) %>% | |
summarize(avg_travel = mean(value)) | |
avg_travel | |
avg_symptomsearch <- symptom_search %>% | |
group_by(geo_value) %>% | |
summarize(avg_symptomsearch = mean(value)) | |
avg_symptomsearch | |
avg_docvisits <- doctor_visits %>% | |
group_by(geo_value) %>% | |
summarize(avg_docvisits = mean(value)) | |
avg_docvisits | |
avg_covidlikesymptoms <- covid_like_symptoms %>% | |
group_by(geo_value) %>% | |
summarize(avg_covidlikesymptoms = mean(value)) | |
avg_covidlikesymptoms | |
``` | |
```{r} | |
data <- left_join(x = num_covid_cases, y = avg_vaccine) | |
data <- left_join(x = data, y = avg_mask) | |
data <- left_join(x = data, y = us_locations) | |
data <- left_join(x = data, y = avg_travel) | |
data <- left_join(x = data, y = avg_symptomsearch) | |
data <- left_join(x = data, y = avg_docvisits) | |
data <- left_join(x = data, y = avg_covidlikesymptoms) | |
data <- mutate(data, fraction_infected = (num_covid_cases)/(population)) | |
data <- filter(data, !is.na(avg_vaccine)) | |
data <- filter(data, !is.na(avg_mask)) | |
data <- filter(data, !is.na(avg_travel)) | |
data <- filter(data, !is.na(avg_symptomsearch)) | |
data <- filter(data, !is.na(avg_docvisits)) | |
data <- filter(data, !is.na(avg_covidlikesymptoms)) | |
``` | |
```{r} | |
mod1 <- lm(fraction_infected ~avg_vaccine, data = data) | |
mod2 <- lm(fraction_infected ~avg_mask, data = data) | |
summary(mod1) | |
summary(mod2) | |
``` | |
```{r} | |
ggplot(data, aes(avg_vaccine, fraction_infected)) + geom_point() + geom_smooth(method = 'lm') | |
``` | |
```{r} | |
e.mod1 <- mod1$residuals | |
e.mod2 <- mod2$residuals | |
#ggplot(data, aes(avg_vaccine, e.mod1)) + geom_point(alpha = 0.4) | |
ggplot(data, aes(avg_mask, e.mod2)) + geom_point(alpha = 0.4) | |
model <- lm(fraction_infected ~ avg_vaccine + avg_travel + avg_symptomsearch + avg_mask + avg_docvisits + avg_covidlikesymptoms, data = data) | |
#mse(model, data) | |
library(olsrr) | |
summary(model) | |
ols_step_forward_p(model) | |
``` | |
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Credit and author: Ryan Grossman