---
tags: EDM
---

# How to use rEDM in AWS(EC2) -MEMO-

This entry describes the preparation for running rEDM using EC2.

## Connect instance in AWS(EC2)
- Login to [EC2](https://us-east-2.console.aws.amazon.com/ec2/v2/home?region=us-east-2#Instances:)
- Make instance (This page is supporting only for Ubuntu)
- Click to "CONNECT"
- Excute following command in directory, which has .pem file

    ssh -i "hogehoge.pem" [e-mail]

## File(or Directory) import (local to AWS)

scp -i ./hogehoge.pem -r [directories] [e-mail]:~/mydir/

## Update R
- Check codename of Ubuntu

  lsb_release -cs

- Register the mirror site of the download source by adding at <b>/etc/apt/sources.list</b>

    echo -e "\n## For R package"  | sudo tee -a /etc/apt/sources.list
    echo "deb https://cran.ism.ac.jp//bin/linux/ubuntu $(lsb_release -cs)-cran35/" | sudo tee -a /etc/apt/sources.list

- cran35 means that a repository providing R 3.5.x for bionic
- Register the public key

    sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9

- And then <b>apt-get</b>

    sudo apt update
    sudo apt-get install r-base

Ref
- [Qiita -最新のRをUbuntuにインストール-](https://qiita.com/JeJeNeNo/items/43fc95c4710c668e86a2)

## rEDM installation
### Preparations in advance
- Install curl and xml and ssl on linux

    sudo apt-get install libcurl4-openssl-dev
    sudo apt-get install libxml2-dev    
    sudo apt-get install libssl-dev

### rEDM installation

install.packages(remotes)
remotes::install_github("ha0ye/rEDM")
library(rEDM)

#### !!caution!!
rEDM latest version(190422) <b>DOESN'T</b> have <b><i>twin surrogate method</i></b> by default...
So if you would like to use this method, 1. install <b>rEDM ver.0.7.1</b>, or 2. read <b>data_transformations.R</b>

Refs
- [Thiel et al., 2006](https://iopscience.iop.org/article/10.1209/epl/i2006-10147-0/pdf)
- [Nakayama et al., 2015](https://www.jstage.jst.go.jp/article/seitai/65/3/65_KJ00010198786/_pdf)

1. install rEDM ver.0.7.1

    install.packages("repmis")
    library(repmis)
    InstallOldPackages(pkgs = "rEDM", versions = "0.7.1")

2. read [data_transformations.R](/9e2Pb_-dQbSqjSWFUnQdLA)
1. create data_transformations.R by copy & paste above page
2. and then read this file

        source(data_transformations.R)

Refs
- [R パッケージ：　古いバージョンをインストールするには](https://blogs.yahoo.co.jp/igproj_fusion/20270891.html)
- [Github](https://github.com/ha0ye/rEDM)