Sam Abbott seabbs

## explore-covid-19-data-truncation
# Note: estimate_truncation is experimental so use this for exploratory purposes
# only and/or with a high level of interpretation
# Packages ----------------------------------------------------------------
# install packages
# install.packages(c("data.table", "purrr", "remotes", "EpiNow2"))
library(data.table)
library(purrr)
library(covidregionaldata)
library(EpiNow2)

## covid19-utla-rt-from-admissions.R
# Packages ----------------------------------------------------------------
library(covid19.nhs.data)
library(vroom)
library(dplyr)
library(tidyr)
library(lubridate)
library(gganimate)
#devtools::install_github("thomasp85/transformr")
library(transformr)
library(gifski)

## covidregionaldata-0.9.1-overview.R
library(covidregionaldata)

# set up a data cache
start_using_memoise()
#> Using a cache at: /tmp/RtmphiSeWY

# check for supported countries
get_available_datasets()
#> # A tibble: 18 x 8
#>    origin   class level_1_region level_2_region level_3_region type  data_urls

## process-rt.R
# Packages ----------------------------------------------------------------
require(data.table, quietly = TRUE)
require(EpiNow2, quietly = TRUE)
require(purrr)
require(ggplot2)

# Target date -------------------------------------------------------------
creation_date <- Sys.Date()
extraction_date <- creation_date

## covid19-ltla-admissions.R
# Packages ----------------------------------------------------------------
library(covid19.nhs.data)
library(dplyr)
library(tidyr)
library(lubridate)
library(gganimate)
#devtools::install_github("thomasp85/transformr")
library(transformr)
library(gifski)
library(ggplot2)

## covid19-utla-admissions.R
# Packages ----------------------------------------------------------------
library(covid19.nhs.data)
library(dplyr)
library(tidyr)
library(lubridate)
library(gganimate)
#devtools::install_github("thomasp85/transformr")
library(transformr)
library(gifski)
library(ggplot2)

## update-site.sh
 #!bin/bash

 cd /home/azureuser/
 git clone git@github.com:epiforecasts/covid-rt-estimates.git
 cd covid-rt-estimates
 sudo bash bin/update-docker.sh "build"
 sudo bash bin/update-via-docker.sh

FILE=last-update/update-complete
while [ ! -f "$FILE" ]; do

## update-estimate-git.sh
#!bin/bash
cd /home/azureuser/covid-rt-estimates
git add --all
git commit -m "update estimates"
git push

## change_with_rw_padding
library(EpiNow2)
library(data.table)

# Get example case counts
reported_cases <- EpiNow2::example_confirmed[1:60]

# Add a dummy breakpoint (used only when optionally estimating breakpoints)
reported_cases <- reported_cases[, breakpoint := data.table::fifelse((date >= as.Date("2020-03-16") & date <= as.Date("2020-03-29")) |  date >= as.Date("2020-04-11"),
                                                                     1, 0)]
# Set up example generation time

## update-rt-estimates.sh
#!/bin/bash

# Get rid of the older update script
rm update-via-ssh.sh

# Get the new update script
curl --fail https://raw.githubusercontent.com/epiforecasts/covid-rt-estimates/master/bin/update-via-ssh.sh > update-via-ssh.sh

# Run the update script
bash update-via-ssh.sh ~/.ssh/id_rsa azureuser@$1 github-username-here github-pat-here
	# Note: estimate_truncation is experimental so use this for exploratory purposes
	# only and/or with a high level of interpretation
	# Packages ----------------------------------------------------------------
	# install packages
	# install.packages(c("data.table", "purrr", "remotes", "EpiNow2"))
	library(data.table)
	library(purrr)
	library(covidregionaldata)
	library(EpiNow2)
	# Packages ----------------------------------------------------------------
	library(covid19.nhs.data)
	library(vroom)
	library(dplyr)
	library(tidyr)
	library(lubridate)
	library(gganimate)
	#devtools::install_github("thomasp85/transformr")
	library(transformr)
	library(gifski)
	library(covidregionaldata)

	# set up a data cache
	start_using_memoise()
	#> Using a cache at: /tmp/RtmphiSeWY

	# check for supported countries
	get_available_datasets()
	#> # A tibble: 18 x 8
	#> origin class level_1_region level_2_region level_3_region type data_urls
	# Packages ----------------------------------------------------------------
	require(data.table, quietly = TRUE)
	require(EpiNow2, quietly = TRUE)
	require(purrr)
	require(ggplot2)

	# Target date -------------------------------------------------------------
	creation_date <- Sys.Date()
	extraction_date <- creation_date
	#!bin/bash

	cd /home/azureuser/
	git clone git@github.com:epiforecasts/covid-rt-estimates.git
	cd covid-rt-estimates
	sudo bash bin/update-docker.sh "build"
	sudo bash bin/update-via-docker.sh

	FILE=last-update/update-complete
	while [ ! -f "$FILE" ]; do
	#!bin/bash
	cd /home/azureuser/covid-rt-estimates
	git add --all
	git commit -m "update estimates"
	git push
	library(EpiNow2)
	library(data.table)

	# Get example case counts
	reported_cases <- EpiNow2::example_confirmed[1:60]

	# Add a dummy breakpoint (used only when optionally estimating breakpoints)
	reported_cases <- reported_cases[, breakpoint := data.table::fifelse((date >= as.Date("2020-03-16") & date <= as.Date("2020-03-29")) \| date >= as.Date("2020-04-11"),
	1, 0)]
	# Set up example generation time
	#!/bin/bash

	# Get rid of the older update script
	rm update-via-ssh.sh

	# Get the new update script
	curl --fail https://raw.githubusercontent.com/epiforecasts/covid-rt-estimates/master/bin/update-via-ssh.sh > update-via-ssh.sh

	# Run the update script
	bash update-via-ssh.sh ~/.ssh/id_rsa azureuser@$1 github-username-here github-pat-here