Documentation fixes

README.md

@@ -1,10 +1,8 @@
 GeostatInversion
 ================
 
-[![GeostatInversion](http://pkg.julialang.org/badges/GeostatInversion_0.4.svg)](http://pkg.julialang.org/?pkg=GeostatInversion&ver=0.4) [![GeostatInversion](http://pkg.julialang.org/badges/GeostatInversion_0.5.svg)](http://pkg.julialang.org/?pkg=GeostatInversion&ver=0.5)
-
+[![GeostatInversion](http://pkg.julialang.org/badges/GeostatInversion_0.5.svg)](http://pkg.julialang.org/?pkg=GeostatInversion&ver=0.5)
 [![Build Status](https://travis-ci.org/madsjulia/GeostatInversion.jl.svg?branch=master)](https://travis-ci.org/madsjulia/GeostatInversion.jl)
-
 [![Coverage Status](https://coveralls.io/repos/madsjulia/GeostatInversion.jl/badge.svg?branch=master)](https://coveralls.io/r/madsjulia/GeostatInversion.jl?branch=master)
 
 This package provides methods for inverse analysis using parameter fields that are represented using geostatistical (stochastic) methods.
@@ -24,22 +22,39 @@ Two versions of PCGA are implemented in this package
 
 The RGA method, `rga`, can use either of these approaches using the keyword argument. That is, by doing `rga(...; pcgafunc=GeostatInversion.pcgadirect)` or `rga(...; pcgafunc=GeostatInversion.pcgalsqr)`.
 
-GeostatInversion is a module of MADS.
+GeostatInversion is a module of [MADS](http://madsjulia.github.io/Mads.jl).
+
+Example
+-------
+
+```julia
+import GeostatInversion
+
+Ns = map(x->round(Int, 25 * x), 1 + rand(N))
+k0 = randn()
+dk = rand()
+beta = -2 - rand()
+k = GeostatInversion.FFTRF.powerlaw_structuredgrid(Ns, k0, dk, beta)
+```
 
 MADS
 ====
 
-MADS is an open-source [Julia](http://julialang.org) code designed as an integrated high-performance computational framework performing a wide range of model-based analyses:
+[MADS](http://madsjulia.github.io/Mads.jl) (Model Analysis & Decision Support) is an integrated open-source high-performance computational (HPC) framework in [Julia](http://julialang.org).
+MADS can execute a wide range of data- and model-based analyses:
 
 * Sensitivity Analysis
 * Parameter Estimation
 * Model Inversion and Calibration
 * Uncertainty Quantification
-* Model Selection and Averaging
-* Decision Support
+* Model Selection and Model Averaging
+* Model Reduction and Surrogate Modeling
+* Machine Learning and Blind Source Separation
+* Decision Analysis and Support
 
-MADS utilizes adaptive rules and techniques which allows the analyses to be performed with minimum user input.
-The code provides a series of alternative algorithms to perform each type of model analyses.
+MADS has been tested to perform HPC simulations on a wide-range multi-processor clusters and parallel enviromentls (Moab, Slurm, etc.).
+MADS utilizes adaptive rules and techniques which allows the analyses to be performed with a minimum user input.
+The code provides a series of alternative algorithms to execute each type of data- and model-based analyses.
 
 Documentation
 =============
@@ -49,42 +64,41 @@ All the available MADS modules and functions are described at [madsjulia.github.
 Installation
 ============
 
-After starting Julia, execute:
-
-```
+```julia
 Pkg.add("GeostatInversion")
 ```
 
-Installation of MADS behind a firewall
+Installation behind a firewall
 ------------------------------
 
-Julia uses git for package management. Add in the `.gitconfig` file in your home directory:
+Julia uses git for the package management.
+To install Julia packages behind a firewall, add the following lines in the `.gitconfig` file in your home directory:
 
-```
+```git
 [url "https://"]
         insteadOf = git://
 ```
 
 or execute:
 
-```
+```bash
 git config --global url."https://".insteadOf git://
 ```
 
 Set proxies:
 
-```
+```bash
 export ftp_proxy=http://proxyout.<your_site>:8080
 export rsync_proxy=http://proxyout.<your_site>:8080
 export http_proxy=http://proxyout.<your_site>:8080
 export https_proxy=http://proxyout.<your_site>:8080
 export no_proxy=.<your_site>
 ```
 
-For example, if you are doing this at LANL, you will need to execute the 
+For example, if you are doing this at LANL, you will need to execute the
 following lines in your bash command-line environment:
 
-```
+```bash
 export ftp_proxy=http://proxyout.lanl.gov:8080
 export rsync_proxy=http://proxyout.lanl.gov:8080
 export http_proxy=http://proxyout.lanl.gov:8080
@@ -97,20 +111,28 @@ MADS examples
 
 In Julia REPL, do the following commands:
 
-`import Mads`
+```julia
+import Mads
+```
 
 To explore getting-started instructions, execute:
 
-`Mads.help()`
+```julia
+Mads.help()
+```
 
 There are various examples located in the `examples` directory of the `Mads` repository.
 
 For example, execute
 
-`include(Mads.madsdir * "/../examples/contamination/contamination.jl")`
+```julia
+include(Mads.madsdir * "/../examples/contamination/contamination.jl")
+```
 
-to perform various analyses related to contaminant transport, or execute
+to perform various example analyses related to groundwater contaminant transport, or execute
 
-`include(Mads.madsdir * "/../examples/bigdt/bigdt.jl")`
+```julia
+include(Mads.madsdir * "/../examples/bigdt/bigdt.jl")
+```
 
-to perform BIG-DT analysis
+to perform Bayesian Information Gap Decision Theory (BIG-DT) analysis.