diff --git a/README.md b/README.md index 9108bd1..148de02 100644 --- a/README.md +++ b/README.md @@ -20,35 +20,36 @@ MixSIAR incorporates several years of advances in Bayesian mixing model theory s The MixSIAR package can be run as a GUI with `mixsiar_gui()`, or as a sequence of R commands (`.R` script). The GUI depends on the `gWidgetsRGtk2` package in R. MixSIAR GUI has been tested and runs on [Windows](#windows), [Mac OS X](#mac-os-x), and [Linux](#linux). -If you want to build the vignettes, you'll need to install "pandoc". [R Studio] comes bundled with pandoc, or you can visit http://pandoc.org/installing.html. +If you want to build the vignettes, you'll need to install [pandoc]. Alternatively, [R Studio] comes bundled with pandoc. #### Windows 1. Download and install/update [R]. 2. Download and install [JAGS]. -3. Open R. -4. Install GTK+ dependent packages: +3. (Optional) If you want to build the vignettes, install [pandoc] or [R Studio]. +4. Open R. +5. Install GTK+ dependent packages: ``` install.packages(c("gWidgets", "RGtk2", "gWidgetsRGtk2", "devtools")) ``` -5. Load `RGtk2`. You will be prompted to install GTK+. **Follow the automatic prompts and do not interrupt the GTK+ installation!**: +6. Load `RGtk2`. You will be prompted to install GTK+. **Follow the automatic prompts and do not interrupt the GTK+ installation!**: ``` library(RGtk2) ``` -6. Restart R and run: +7. Restart R and run: ``` library(devtools) devtools::install_github("brianstock/MixSIAR", dependencies = TRUE, - build_vignettes = TRUE) # FALSE if no pandoc + build_vignettes = TRUE) # FALSE if no pandoc/R Studio ``` -7. Load MixSIAR and run GUI: +8. Load MixSIAR and run GUI: ``` library(MixSIAR) @@ -59,25 +60,26 @@ If you want to build the vignettes, you'll need to install "pandoc". [R Studio] 1. Download and install/update [R]. 2. Download and install [JAGS]. -3. Open R. -4. Install GTK+ dependent R packages: +3. (Optional) If you want to build the vignettes, install [pandoc] or [R Studio]. +4. Open R. +5. Install GTK+ dependent R packages: ``` install.packages(c("gWidgets", "RGtk2", "gWidgetsRGtk2", "devtools")) ``` -5. Close R. -6. Download and install the newest [GTK+ framework]. -7. Install the latest X11 application, [xQuartz]. -8. Open R and run: +6. Close R. +7. Download and install the newest [GTK+ framework]. +8. Install the latest X11 application, [xQuartz]. +9. Open R and run: ``` library(devtools) devtools::install_github("brianstock/MixSIAR", dependencies = TRUE, - build_vignettes = TRUE) # FALSE if no pandoc + build_vignettes = TRUE) # FALSE if no pandoc/R Studio ``` -9. Load MixSIAR and run GUI: +10. Load MixSIAR and run GUI: ``` library(MixSIAR) @@ -89,24 +91,25 @@ If you want to build the vignettes, you'll need to install "pandoc". [R Studio] 1. Download and install/update [R]. 2. Download and install [JAGS]. Or, from the terminal: `sudo apt-get install jags r-cran-rjags`. 3. Download and install [GTK+ framework]. From the terminal: `sudo apt-get install libgtk2.0-dev`. -4. Check if GTK+ is installed correctly. Open R, install and load the `RGtk2` package with: +4. (Optional) If you want to build the vignettes, install [pandoc] or [R Studio]. +5. Check if GTK+ is installed correctly. Open R, install and load the `RGtk2` package with: ``` install.packages("RGtk2") library(RGtk2) ``` -5. Install and load devtools, then install MixSIAR: +6. Install and load devtools, then install MixSIAR: ``` install.packages("devtools") library(devtools) devtools::install_github("brianstock/MixSIAR", dependencies = TRUE, - build_vignettes = TRUE) # FALSE if no pandoc + build_vignettes = TRUE) # FALSE if no pandoc and pandoc-citeproc ``` -6. Load MixSIAR and run GUI: +7. Load MixSIAR and run GUI: ``` library(MixSIAR) @@ -149,6 +152,7 @@ For a detailed description of the math underlying these models, see: Finally... yes, a paper introducing MixSIAR is in the works and will be forthcoming shortly. +[pandoc]:https://github.com/jgm/pandoc/releases/ [GTK+ framework]:http://r.research.att.com/#other [xQuartz]:http://xquartz.macosforge.org/landing/ [R Studio]:https://www.rstudio.com/products/rstudio/download/