From b6bd60c66b236a230059158b1c04e05bd45b63c6 Mon Sep 17 00:00:00 2001
From: Chee Yee Lim <cheeyee.lim@gmail.com>
Date: Thu, 3 Dec 2015 22:27:13 +0000
Subject: [PATCH] Fixed section links

---
 README.md | 52 ++++++++++++++++++++++++++--------------------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/README.md b/README.md
index b2133c6..f5ca867 100644
--- a/README.md
+++ b/README.md
@@ -1,26 +1,26 @@
--   Brief introduction
--   Installation
--   Input data format
--   Output format
--   Useful functions in BoolTraineR
--   Example workflows
-    -   Inferring model without an initial model
-        -   Full workflow
-        -   Initial setup
-        -   Data preparation
-        -   Run model training
-    -   Inferring model with an initial model
-        -   Full workflow
-        -   Initial setup
-        -   Data preparation
-        -   Run model training
-    -   Extending model with more genes
-        -   Full workflow
-        -   Initial setup
-        -   Data preparation
-        -   Add extra genes to the initial Boolean model
-        -   Estimate initial state for the extra genes
-        -   Run model training
+-   [Brief introduction](#brief-introduction)
+-   [Installation](#installation)
+-   [Input data format](#input-data-format)
+-   [Output format](#output-format)
+-   [Useful functions in BoolTraineR](#useful-functions-in-booltrainer)
+-   [Example workflows](#example-workflows)
+    -   [Inferring model without an initial model](#inferring-model-without-an-initial-model)
+        -   [Full workflow](#full-workflow)
+        -   [Initial setup](#initial-setup)
+        -   [Data preparation](#data-preparation)
+        -   [Run model training](#run-model-training)
+    -   [Inferring model with an initial model](#inferring-model-with-an-initial-model)
+        -   [Full workflow](#full-workflow-1)
+        -   [Initial setup](#initial-setup-1)
+        -   [Data preparation](#data-preparation-1)
+        -   [Run model training](#run-model-training-1)
+    -   [Extending model with more genes](#extending-model-with-more-genes)
+        -   [Full workflow](#full-workflow-2)
+        -   [Initial setup](#initial-setup-2)
+        -   [Data preparation](#data-preparation-2)
+        -   [Add extra genes to the initial Boolean model](#add-extra-genes-to-the-initial-boolean-model)
+        -   [Estimate initial state for the extra genes](#estimate-initial-state-for-the-extra-genes)
+        -   [Run model training](#run-model-training-2)
 
 <!---
     rmarkdown::pdf_document:
@@ -262,7 +262,7 @@ final_model = model_train(cdata = fcdata, ddata = fddata, max_varperrule = 4,
 plotBM(final_model)
 ```
 
-![](vignettes/booltrainer_files/figure-markdown_github/unnamed-chunk-17-1.png)
+![](booltrainer_files/figure-markdown_github/unnamed-chunk-17-1.png)
 
 Inferring model with an initial model
 -------------------------------------
@@ -373,7 +373,7 @@ final_model = model_train(cdata = fcdata, ddata = fddata, bmodel = bmodel, istat
 plotBM(final_model)
 ```
 
-![](vignettes/booltrainer_files/figure-markdown_github/unnamed-chunk-23-1.png)
+![](booltrainer_files/figure-markdown_github/unnamed-chunk-23-1.png)
 
 Extending model with more genes
 -------------------------------
@@ -526,4 +526,4 @@ final_model = model_train(cdata = fcdata, ddata = fddata, bmodel = grown_bmodel,
 plotBM(final_model)
 ```
 
-![](vignettes/booltrainer_files/figure-markdown_github/unnamed-chunk-31-1.png)
+![](booltrainer_files/figure-markdown_github/unnamed-chunk-31-1.png)