How to get various bits of software

• JAGS
• LaTeX
• Quatro
• R and Rstudio
• RMark on a Mac wiithout an emulator
• SAS

JAGS

• To have a cross-platform engine for the BUGS language
• To be extensible, allowing users to write their own functions, distributions and samplers.
• To be a plaftorm for experimentation with ideas in Bayesian modelling

JAGS is available for Macintosh, Windoze, and Linux platforms.

Most people use R to use JAGS and so R and Rstudio should be installed on your machine as outlined elsewhere on this page.

1. Install R and RStudio on your machine as noted elsewhere on this page.

2. Install the packages as listed in the R installation instrucitons plus the following packages
        R2Jags,    coda,     digest
   Don't forget to check the box on installing dependencies when installing the packages.

3. Download and install the latest version of JAGS from JAGS Website.

   To test that the installation is working on a Macintosh, open a Terminal window, and simply type jags If you get a message similar to
       Welcome to JAGS 4.x.x on Tue Feb 10 20:35:14 2015
   then you are ok.

LaTeX

A brief introduction is available at https://rpubs.com/YaRrr/SweaveIntro

LaTeX is available for Macintosh, Windoze, and Linux platforms.

Download the LaTeX program from:

• Windows: http://miktex.org/download
• Macintosh: https://tug.org/mactex/mactex-download.html

Quatro

A Quatro script mixes R code and text to create a living document. Great for reproducible research and breaking the copy-and-paste paradigm when using MSWord. Visit the Quatro installation page for details.

R (and Rstudio)

1. Download the latest verson of R for your machine from The R Project for Statistical Computing or the local (SFU) mirror site.

2. Install R using the downloaded files. You will need administrator privlidges for your machine.
   Additional (technical) information is available at: R Installation and Administration but you likely won't need this.

   If you are running Windoze, you should delete any earlier versions of R from previous installations. If you running a Macintosh, newer versions of R automatically overwrite older versions of R

3. Create a personal (package) library. There are many extensions (packages) available for R. The default location for these packages will require administrative access everytime you update a package. Additionally, when you update to a new version of R, you will lose your installed packages unless you have a personal library.

   Here are instruction for Windoze and Macintosh machines. If you have a Unix machine that is not a Macintosh, the instructions will be similar to that from the Macintosh.

   • Creating a personal library (Macintosh computer).
   • Creating a personal library (Windoze 10 computers).
   • Creating a personal library (Windoze 7 computers). Instructions for Windoze 8 are similar.
     Note that you do NOT have to use the H: drive as illustrated in the instructions. Most people install their personal library on the C: drive.
   • Creating a personal library (Windoze XP computer).

   Many corporate and goernment environments "lockdown" computers so users cannot install packages following the step above.
   Here are instruction on how to install packages when you do not have administrative access to your Windoze machine.

4. Download Rstudio, an integrated development environment for running R, from the Rstudio website.

5. Install Rstudio. You will need adminstrative access to your machine.

6. Install the following packages into your personal library using R or Rstudio (you only need to this with either method).
   
         AICcmodavg,    arm,    binom,    boot,    car,    data.table,    devtools,    dplyr,    emmeans,    EnvStats,    GGally,    ggplot2,    ggforce,    ggfortify,    ggmap,
         gplots,    gmodels,    gridExtra,    hms,    Kendall,    knitr,    lme4,    lmerTest,    lmtest,    lubridate,    multcomp,    multcompView,
         nlme,    plyr,    pwr,    randtests,    readxl,    reshape2,    rkt,    sf    sp    SiZer,    survey    tidyverse    trend
   
   Instructions on installing packages ONE AT A TIME using R are availble on this video.
   Instructions on installing packages ONE AT A TIME using Rstudio are available on this video
   BE SURE TO CHECK THE BOX ASKING TO INSTALL DEPENDENCIES as some packages depend on other packages.

   You can install ALL of the above packages by copying and pasting the following into the R console once you open RStudio
   

   package.set <- c("AICcmodavg","arm",
                    "binom",     "boot",
                    "car",       'data.table',
                     "devtools",'dplyr',
                     "emmeans", "EnvStats",
                    "GGally",    "ggplot2",   
                    "ggforce",   "ggmap",
                    "ggfortify", "gplots",
                    "gmodels",   "gridExtra",
                    "hms",      
                    "Kendall",   "knitr",
                    "lme4",       "lmerTest",
                    "lmtest",     "lubridate",  
                    "multcomp",   "multcompView",
                    "nlme",       "plyr",
                    "pwr",        "randtests",
                    "readxl",     "reshape2",
                    "rkt",        "sf",
                    'sp',        "spData",
                    "SiZer",
                    "survey",   'tidyverse',
                    "trend")
   
   install.packages(package.set)
   

You are now ready to use R and Rstudio. There are many useful on-line manuals on the R site along with much contributed documentation.

CodeSchool has a brief introduction to R that is useful.

The short reference card here is also useful

RMark on a Mac without an emulator

The MARK program consists of two separate parts -- the user graphical interface which uses Windoze application program interfaces (API) and so can run only under Windoze, and an optimization engine which then actually the model and returns the results to the interface. RMark call the optimization engine only. Consequently, with some work, it is possible to install only the optimiztion engine on the Macintosh and run RMark natively on a Macintosh without the need for a virtualization engine such as VirtualBox.

The following instructions were created by Simon Bonner and follow the thread at Installing MARK on a Macintosh

had to change my shell to zsh before running Bonner's scripts

1. Install home-brew
   

   /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

2. Install gcc
   

   brew install gcc

3. Install Mark
   

   brew tap sjbonner/tap
   
   brew install mark-on-mac

4. Check MARK - should return /usr/local/bin
   

   which mark

5. Check that mark runs - should return "no input file...."
   

   mark

SAS