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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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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

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#  Get required packages - managed using pacman ---------------------------
# This installs packages if they are missing and otherwise loads them.
if (!require(pacman)) install.packages("pacman"); library(pacman)
p_load("tidyverse")
p_load("fs")
p_load("data.table")
p_load("lubridate")
p_load("purrr")
p_load("furrr")

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## For password management
git config --global user.email "s.e.abbott12@gmail.com"
git config --global user.name "Sam Abbott"
git config --global credential.helper cache
git remote set-url origin https://github.com/USERNAME/REPOSITORY.git

# github settings
# developer settings
# create access token and copy
# git pull/push

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# Install and load the package --------------------------------------------
if(!require(pacman))install.packages("pacman")

pacman::p_load('dplyr', 'ggplot2', 'getTBinR')
pacman::p_load_gh('thomasp85/patchwork') 
pacman::p_load_gh('bbc/bbplot')

# Look at available datasets\ ---------------------------------------------

available_datasets

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# Install and load the package --------------------------------------------
#Use install.packages(c("getTBinR", "dplyr", "getTBinR")) to get required packages
library(getTBinR) #TB data + visualisations
library(dplyr) # For data manipulation
library(ggplot2) # For additional visualisations etc.
#For storyboards - install with commented out code
# install.packages("devtools")
# devtools::install_github("thomasp85/patchwork")