Updated the README.

README.Rmd

@@ -0,0 +1,38 @@
+---
+title: "CKMRsim"
+output: github_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+This package implements Monte Carlo methods
+(including efficient importance sampling approaches) for assessing the false positive and false
+negative rates expected when using a particular set of genetic markers for pairwise relationship inference. It also
+provides functions implemented in C++ for computing likelihood ratios for different 
+relationships between all pairs of individuals in a data set.  
+
+CKMRsim can be installed with devtools.  It requires that development tools be installed on your
+system to allow compilation of C++ via RCpp.
+```{r, eval=FALSE}
+devtools::install_github("eriqande/CKMRsim", build_vignettes = TRUE)
+```
+
+After this, the various vignettes can be accessed and read like this:
+```{r, eval=FALSE}
+vignette("CKMRsim-example-1")
+
+vignette("CKMRsim-example-2-microsatellites")
+
+vignette("CKMRsim-simulating-linked-markers")
+
+vignette("CKMRsim-writing-geno-error-funcs")
+```
+
+In order to pursue simulations in the face of physical linkage, you must download
+and install the external dependency, Mendel version 16.  For Windows and Mac OS X, 
+CKMRsim will look for the Mendel binary in its default install location. So download
+it from [http://software.genetics.ucla.edu/mendel](http://software.genetics.ucla.edu/mendel) and do a default install.
+Note that you need to register with your email in order to download Mendel.
+

README.md

@@ -1,21 +1,36 @@
-# CKMRsim
+CKMRsim
+================
 
-[![DOI](https://zenodo.org/badge/55812404.svg)](https://zenodo.org/badge/latestdoi/55812404)
+This package implements Monte Carlo methods (including efficient
+importance sampling approaches) for assessing the false positive and
+false negative rates expected when using a particular set of genetic
+markers for pairwise relationship inference. It also provides functions
+implemented in C++ for computing likelihood ratios for different
+relationships between all pairs of individuals in a data set.
 
+CKMRsim can be installed with devtools. It requires that development
+tools be installed on your system to allow compilation of C++ via RCpp.
 
-This is an R package in development.  Not much else here now.
+``` r
+devtools::install_github("eriqande/CKMRsim", build_vignettes = TRUE)
+```
 
-NOTES:
+After this, the various vignettes can be accessed and read like this:
 
-When you define a pedigree for gene dropping, individuals 1 and 2 are the focal
-individauls of the pair and they must have observed parents (because MENDEL output
-is hard to parse otherwise...).  Hence PO must look like:
-```
-  Kid Pa Ma Sex Observed
-1   1  2  3   1        1
-2   2  4  5   1        1
-3   3  0  0   2        0
-4   4  0  0   1        0
-5   5  0  0   2        0
+``` r
+vignette("CKMRsim-example-1")
+
+vignette("CKMRsim-example-2-microsatellites")
+
+vignette("CKMRsim-simulating-linked-markers")
+
+vignette("CKMRsim-writing-geno-error-funcs")
 ```
-instead of having just three lines.
+
+In order to pursue simulations in the face of physical linkage, you must
+download and install the external dependency, Mendel version 16. For
+Windows and Mac OS X, CKMRsim will look for the Mendel binary in its
+default install location. So download it from
+<http://software.genetics.ucla.edu/mendel> and do a default install.
+Note that you need to register with your email in order to download
+Mendel.

vignettes/CKMRsim-simulating-linked-markers.Rmd

@@ -28,8 +28,11 @@ library(tidyverse)
 
 ## Prerequisites
 
-INCLUDE STUFF HERE ABOUT HOW TO DOWNLOAD MENDEL AND WHERE IT SHOULD BE INSTALLED TO.
-NOTE THAT I NEED TO FIGURE THAT OUT ON WINDOZE.
+In order to pursue simulations in the face of physical linkage, you must download
+and install the external dependency, Mendel version 16.  For Windows and Mac OS X, 
+CKMRsim will look for the Mendel binary in its default install location. So download
+it from [http://software.genetics.ucla.edu/mendel](http://software.genetics.ucla.edu/mendel) and do a default install.
+Note that you need to register with your email in order to download Mendel.
 
 ## An Example