The global setup for this Rmarkdown document is:
knitr::opts_chunk$set(
echo = TRUE,
message = FALSE,
warning = FALSE,
results = "hide",
error = FALSE,
comment = ''
)
This document exists in the repository at https://github.com/codatmo/Data/ as index.Rmd
and rendered in html as https://github.com/codatmo/Data/index.html.
Additional data and descriptions are at https://github.com/codatmo/Data/blob/main/README.md which also contains a link to this file.
This model is part of the CoDatMo (Co)vid (Dat)a (Mo)deling site (https://codatmo.github.io/) which is intended to replicate and make available important COVID models written in Bayesian modeling languages like Stan or PyMC3.
This page explain various data sets in the repo and show how to load them in R data frames.
library(tidyr)
# be sure to set working directory correctly
deaths <- read.csv("NHS_Regions_Datasets/nhs_regions_deaths.csv",
header=FALSE)
deaths_t <- t(deaths)
region_names <- deaths_t[1,2:8]
deaths.df <- data.frame(deaths_t[c(-1,-2),])
colnames(deaths.df) <- c('week', region_names)
deaths_long.df <- gather(deaths.df,'area','deaths',2:8)
deaths_long.df$death_count <- as.numeric(deaths_long.df$deaths)
deaths_long.df$date <- as.Date(deaths_long.df$week)
Deaths are collected weekly.
library(ggplot2)
ggplot(deaths_long.df) +
aes(x=date, y=death_count, group=area, color=area) +
geom_line() -> p1
p1
library(tidyr)
calls_111 <- read.csv("NHS_Regions_Datasets/nhs_regions_111_calls.csv",
header=FALSE, row.names=NULL)
calls_111_t <- t(calls_111)
calls_111.df <- data.frame(calls_111_t)
colnames(calls_111.df) <- c('date',calls_111_t[1,2:8])
calls_111.df <- calls_111.df[c(-1,-2),] #get rid of names and source
calls_111_long.df <- gather(calls_111.df, 'loc', 'call_count', 2:8)
calls_111_long.df$calls <- as.numeric(calls_111_long.df$call_count)
head(calls_111_long.df)
library(ggplot2)
library(gridExtra)
ggplot(calls_111_long.df) +
aes(x=date, y=calls, group=loc, color=loc) +
geom_line() -> p2
p2
saveRDS(calls_111.df, "NHS_Regions_Datasets/nhs_regions_111_calls.Rds")
saveRDS(deaths.df, "NHS_Regions_Datasets/nhs_regions_deaths.Rds")
Serializing data for use by other projects. Known uses: