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

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 #!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

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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

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#!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

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#!/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

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

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library(EpiNow)
library(EpiSoon)
library(data.table)

#1. Input a vector of Rt estimates, and vector to initialise cases, and a generation time
initial_cases <- 100
initial_date <- as.Date("2020-03-01")
rts <- c(rep(2, 20), (2 - 1:15 * 0.1), rep(0.5, 10))

## Simulating cases

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# Packages -----------------------------------------------------------------
require(data.table, quietly = TRUE) 
require(future, quietly = TRUE)
## Require for data and nowcasting
# require(EpiNow, quietly = TRUE)
# require(NCoVUtils, quietly = TRUE)

## Required for forecasting
# require(future.apply, quietly = TRUE)

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#!bin/bash

## This requires java and bfg to be installed
## bfg: https://rtyley.github.io/bfg-repo-cleaner/
## Assumes that the repo is in the current directory

## Remove all .rds and .png from the Git history
java -jar bfg.jar --delete-files "*.rds" $1
java -jar bfg.jar --delete-files "*.png" $1

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sudo docker pull jcrodriguez1989/rco

mkdir rco_results

sudo docker run -v /rco_results:/rco_results -e RCO_PKG=getTBinR jcrodriguez1989/rco

cd rco_results