Sam Abbott seabbs

## regional-secondary.R
# load required packages
library(EpiNow2)
library(future.apply)
library(purrr)
library(data.table)


warning("This gist is depreciated. Please use the following development repository: https://github.com/seabbs/regional-secondary.git")
# extract priors from a posterior and update fitting args
extract_secondary_priors <- function(posterior) {

## forecast-covid-deaths-from-covid-cases.R
# set number of cores to use fitting the model
# no benefit on runtime if cores > chains which is set to 4 by default
options(mc.cores = 4)

# Packages ----------------------------------------------------------------
# install.packages(c("data.table", "remotes", "ggplot2"))
# remotes::install_github("epiforecasts/EpiNow2")
# remotes::install_github("epiforecasts/covidregionaldata")
library(data.table)
library(ggplot2)

## 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)

## epinow2-covid-rt-national.R
# packages
# install.packages(c("data.table", "remotes", "EpiNow2"))
library(data.table)
library(EpiNow2)
library(covidregionaldata)

# target country (must be present in ECDC data)
country <- "france"

# set number of cores to use fitting the model

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

## 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

## 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

## set-up-epinow2.sh
#!bin/bash

sudo apt-get update
sudo apt-get install -y docker.io

sudo docker login docker.pkg.github.com
sudo docker pull docker.pkg.github.com/epiforecasts/epinow2/epinow2:latest
sudo docker tag docker.pkg.github.com/epiforecasts/epinow2/epinow2:latest epinow2


## 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

## deploy_pages.sh

git subtree split --squash --prefix docs -b gh-pages
git push -f origin gh-pages:gh-pages
git branch -D gh-pages
	# load required packages
	library(EpiNow2)
	library(future.apply)
	library(purrr)
	library(data.table)


	warning("This gist is depreciated. Please use the following development repository: https://github.com/seabbs/regional-secondary.git")
	# extract priors from a posterior and update fitting args
	extract_secondary_priors <- function(posterior) {
	# set number of cores to use fitting the model
	# no benefit on runtime if cores > chains which is set to 4 by default
	options(mc.cores = 4)

	# Packages ----------------------------------------------------------------
	# install.packages(c("data.table", "remotes", "ggplot2"))
	# remotes::install_github("epiforecasts/EpiNow2")
	# remotes::install_github("epiforecasts/covidregionaldata")
	library(data.table)
	library(ggplot2)
	# 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
	# install.packages(c("data.table", "remotes", "EpiNow2"))
	library(data.table)
	library(EpiNow2)
	library(covidregionaldata)

	# target country (must be present in ECDC data)
	country <- "france"

	# set number of cores to use fitting the model
	#!bin/bash
	cd /home/azureuser/covid-rt-estimates
	git add --all
	git commit -m "update estimates"
	git push
	#!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
	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

	sudo apt-get update
	sudo apt-get install -y docker.io

	sudo docker login docker.pkg.github.com
	sudo docker pull docker.pkg.github.com/epiforecasts/epinow2/epinow2:latest
	sudo docker tag docker.pkg.github.com/epiforecasts/epinow2/epinow2:latest epinow2
	#!/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

	git subtree split --squash --prefix docs -b gh-pages
	git push -f origin gh-pages:gh-pages
	git branch -D gh-pages