Preparation of R Environment

1. The following two applications should be installed depending on OS（Windows, Mac OSX (later than 9.5), or Linux). The following explanation is mainly for Windows and Mac users.

(1) R environment : https://cran.ism.ac.jp/index.html

(2) RStudio Desktop: https://www.rstudio.com/products/rstudio/download/

2. Installation of the necessary libraries from Rstudio (vegan，scatterplot3d, picante, GUniFrac, SYNCSA) and confirmation of library loading

Installation of R environment

Visit CRAN.

https://cran.ism.ac.jp/index.html

A Windows user can find and download "R-3.4.1-win.exe" by following the link "Download R for Windows" at "Download and Install R" or directly by the following link.

https://cran.ism.ac.jp/bin/windows/base/

A Mac OSX user can find and download "***.pkg" file depending on OSX version by following the link "Download R for (Mac) OS X" at "Download and Install R". The way to check the version of OSX is here.

For either Windows or OSX, R can be easily installed by following the guidance, which appears when clicking the downloaded file (installer). If the "R" folder is generated at Program folder (or Application folder), or "R" shortcut appears at Desktop, it indicates the success in the installation processes.

Installation of Rstudio desktop

Visit Rstudio download website.

https://www.rstudio.com/products/rstudio/download/#download

From ”Installers", download the installer that fits with your OS, and install Rstudio desktop following the guidance of the installer. The launching appearance of R or Rstudio desktop (Rstudio hearafter) can be checked from the following website (in Japanese).

R と R Studioのインストール

Installation of libraries and confirmation of loading the libraries

Setting Rstudio desktop's proxy

Internet access might be via proxy server in some institutes. In this case, the pre-arrangement on R is necessary before installing R libraries. If any proxy is not set, or you have used R environment under the proxy setting but never used Rstudio, the following arrangement is not necessary.

Launch Rstudio via double click of its shortcut. On the lower left window (= "Console" window), type the following command and press the Return key.

file.edit('~/.Renviron')

Then, on the upper left window (= "Editor" window), an empty file (if this file didn't exist before) or some texts (if it already exists) will appear. Add the following three lines and save the file. This is the example when hogehoge1.ac.jp, hogehoge2.ac.jp, and hogehoge3.ac.jp are http, https, and ftp proxy, respectively, with port number 8080. Note that "http://" etc should not be omitted. If you cannot catch the point, talk with the system administrator.

http_proxy=http://hogehoge1.ac.jp:8080

https_proxy=https://hogehoge2.ac.jp:8080

ftp_proxy=ftp://hogehoge.ac.jp:8080

After saving the information, R studio should be once quit and then relaunched. Then, typing the following command on "Console" window and pressing the Return key tells if the proxy setting is loaded or not.

Sys.getenv(c("http_proxy", "https_proxy", "ftp_proxy"))

The guidance above is based on the information at the official website.

https://support.rstudio.com/hc/en-us/articles/200488488-Configuring-R-to-Use-an-HTTP-or-HTTPS-Proxy

Installation of the necessary libraries from Rstudio and confirmation of library loading

From the tool bar of Rstudio: Tools>Install Packages..., type "vegan" in the empty form, check ”Install dependencies”, and click Install. Then, the package "vegan" can be installed. If the installation has been succeeded, the package (library) vegan and dependent libraries will be loaded by typing the following command on the Console (and press the Return key), without any error messages (warning messages are not problem).

library(vegan)

After vegan is installed, install picante, scatterplot3d, GUniFrac, SYNCSA with the same method.

If the explanation above is not enough, you can also check the following guidance. The GUI (Graphical User Interface) depends on OS version and Windows, MacOSX, or Linux, but it's just a minor difference.

When vegan is successfully installed, install picante, scatterplot3d, GUniFrac, SYNCSA with the same method.