updated broken links

Documentation/evolve/evolve.Rmd

@@ -11,6 +11,6 @@ Put simply, my genetic algorithm works as follows:
 
 It is used like this: ``GATOC.evolve(fasta_file, vcf_file, parameters)``. ``parameters`` is a hash of symbol keys that point to values used in the sub-methods of GATOC. Each parameter has a default value, shown in the ``opts`` hash. The parameters are described in the annotation of [GATOC.evolve](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/lib/GATOC.rb).
 
-The flow chart below shows the key inputs and outputs for GATOC.evolve. For more detail on some of the sub methods see [new_population](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/new_population.md) and [select](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/select.md).
+The flow chart below shows the key inputs and outputs for GATOC.evolve. For more detail on some of the sub methods see [new_population](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/new_population/new_population.md) and [select](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/select/select.md).
 
 ![Image](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/algorithm_flowcharts/evolve.png?raw=true)

Documentation/evolve/evolve.html

@@ -153,7 +153,7 @@ <h1>GATOC.evolve</h1>
 
 <p>It is used like this: <code>GATOC.evolve(fasta_file, vcf_file, parameters)</code>. <code>parameters</code> is a hash of symbol keys that point to values used in the sub-methods of GATOC. Each parameter has a default value, shown in the <code>opts</code> hash. The parameters are described in the annotation of <a href="https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/lib/GATOC.rb">GATOC.evolve</a>.</p>
 
-<p>The flow chart below shows the key inputs and outputs for GATOC.evolve. For more detail on some of the sub methods see <a href="https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/new_population.md">new_population</a> and <a href="https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/select.md">select</a>.</p>
+<p>The flow chart below shows the key inputs and outputs for GATOC.evolve. For more detail on some of the sub methods see <a href="https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/new_population/new_population.md">new_population</a> and <a href="https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/select/select.md">select</a>.</p>
 
 <p><img src="https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/algorithm_flowcharts/evolve.png?raw=true" alt="Image"/></p>
 

Documentation/evolve/evolve.md

@@ -11,6 +11,6 @@ Put simply, my genetic algorithm works as follows:
 
 It is used like this: ``GATOC.evolve(fasta_file, vcf_file, parameters)``. ``parameters`` is a hash of symbol keys that point to values used in the sub-methods of GATOC. Each parameter has a default value, shown in the ``opts`` hash. The parameters are described in the annotation of [GATOC.evolve](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/lib/GATOC.rb).
 
-The flow chart below shows the key inputs and outputs for GATOC.evolve. For more detail on some of the sub methods see [new_population](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/new_population.md) and [select](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/select.md).
+The flow chart below shows the key inputs and outputs for GATOC.evolve. For more detail on some of the sub methods see [new_population](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/new_population/new_population.md) and [select](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/select/select.md).
 
 ![Image](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/algorithm_flowcharts/evolve.png?raw=true)

README.md

@@ -76,7 +76,7 @@ To run [algorithm_test.rb](https://github.com/edwardchalstrey1/fragmented_genome
 
 When running the algorithm with real data, a new ruby script will be needed to call ``GATOC.evolve``
 
-For a detailed look at how the algorithm works see [Documentation/evolve](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/evolve.md)
+For a detailed look at how the algorithm works see [Documentation/evolve](https://github.com/edwardchalstrey1/fragmented_genome_with_snps/blob/master/Documentation/evolve/evolve.md)
 
 Assesing the Genetic Algorithm's performance
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