From 4846c4ee340b3a21a046ad3f704e741b448bb19e Mon Sep 17 00:00:00 2001
From: prise6 <vieille.francois@gmail.com>
Date: Mon, 27 Jul 2015 01:41:49 +0200
Subject: [PATCH] Add quick examplre and reorganize presentation

---
 README.md | 45 ++++++++++++++++++++++++++++++++-------------
 1 file changed, 32 insertions(+), 13 deletions(-)

diff --git a/README.md b/README.md
index a6ea650..d528931 100644
--- a/README.md
+++ b/README.md
@@ -13,15 +13,29 @@ As an intern in a french pharmaceutical group, i worked on this method and devel
 data(sepsis)
 # Format data
 vt.obj <- vt.data(sepsis, "survival", "THERAPY", T)
+# $table
+#            trt
+# resp        0    1     sum  
+#   0         101  188   289  
+#   1         52   129   181  
+#   sum       153  317   470  
+#   Incidence 0.34 0.407 0.385
+#
+# $rr
+# [1] 1.197059
+#
 # First step : create random forest model
 vt.for <- vt.forest("one", vt.obj, T, ntree = 500)
 # Second step : find rules in data 
-vt.trees <- vt.tree("class", vt.for, threshold = quantile(vt.for$difft, seq(.5,.8,.1)), maxdepth = 2)
+vt.trees <- vt.tree("class",
+                    vt.for, 
+                    threshold = quantile(vt.for$difft, seq(.5,.8,.1)),
+                    maxdepth = 2)
 # Print results
 vt.sbgrps <- vt.subgroups(vt.trees)
 knitr::kable(vt.sbgrps)
 ```
-|      |Subgroup                    |Subgroup size |Treatement event rate |Control event rate |Treatment sample size |Control sample size | RR (resub)| RR (snd)|
+|      |Subgroup                    |Subgroup size |Treatement \n event rate |Control event rate |Treatment sample size |Control sample size | RR (resub)| RR (snd)|
 |:-----|:---------------------------|:-------------|:---------------------|:------------------|:---------------------|:-------------------|----------:|--------:|
 |tree1 |PRAPACHE>=26.5              |157           |0.752                 |0.327              |105                   |52                  |      2.300|    1.856|
 |tree3 |PRAPACHE>=26.5 & AGE>=51.74 |120           |0.897                 |0.31               |78                    |42                  |      2.894|    1.991|
@@ -38,11 +52,17 @@ Most of the package use Reference Class programing (in R). Feel free to create y
 
 I got a *WARNING* when Checking package for "cheking PDF version of manual" because of my version of LaTeX. Need to fix it.
 
-## To-do list
 
-* Description and help
-* Vignette example
-* ...
+## Help & Documentation
+
+_Vignette is not finished ..._
+
+See [full-example](http://htmlpreview.github.io/?https://github.com/prise6/aVirtualTwins/blob/dev/inst/doc/full-example.html)
+
+or when installed : 
+``` r
+vignette("full-example", package = "aVirtualTwins")
+```
 
 ## Install
 
@@ -55,14 +75,13 @@ devtools::install_github("prise6/aVirtualTwins@dev")
 library(aVirtualTwins)
 ```
 
-## Help
 
-* _Vignette is really not finished ..._
+## To-do list
+
+* More description
+* Finish full-example vignette
+* Link to my simulation
+* ...
 
-See [full-example](http://htmlpreview.github.io/?https://github.com/prise6/aVirtualTwins/blob/dev/inst/doc/full-example.html)
 
-or when installed : 
-``` r
-vignette("full-example", package = "aVirtualTwins")
-```