Differences

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--- r-lequin [2008/01/24 13:21] – heidi
+++ r-lequin [2009/01/17 10:55] (current) – heidi
@@ Line 1: / Line 1: @@
 ====== R-lequin ======
-{{matrix_pairwise_fst.png?220}} {{matrix_hapdistance_between-within_pop_and_groups.png?220}}  {{mismatchdistribution.png?220}} \\
+{{pairwisediffmatrix_03-10-08_at_14-09-16.png?220}}  {{micdiplhapdistmatrix_withinbetweencompleteexpanded2_03-10-08_at_15-41-55.png?220}} {{sumallelicsizerange_18-11-08_at_13-25-55.png?220}}
+\\
-**R-lequin is an R interface for the graphical display of Arlequin outputs. It should add value and help interpreting results from large Arlequin analyses.**
+\\
+**R-lequin is a collection of R functions to parse a XML output file of ARLEQUIN version 3.12. R-lequin extracts data and produces graphics. R is an ideal programming language for parsing XML files and for graphic creation because it provides a lot of graphical  techniques and a XML package containing tools for parsing and generating XML within R. The graphics should help to get an impression and to interpret the results produced by ARLEQUIN.\\
+R-lequin is a tool to enhance the user friendliness and the readability of the ARLEQUIN output.
+**
 \\
 ===== R code for graphics =====
-  * {{master_r-lequin.doc}}
+=== Documentations: ===
+{{master_r-lequin.pdf|}}\\
+{{r-lequin_graphic_description.pdf|}}
 \\
-  * [[general commands]]
+  * **[[general commands]]**
-  * lines:
+=== lines: ===
     * [[mismatch distribution]]
     * [[heterozygosity]]
-    * [[expected/observed haplotype]] (with CI)
+    * Haplotype:
-      * save graphic as a .png file
+      * [[expected/observed haplotype]] (with CI)
+        * save graphic as a .png file
+      * [[Haplotype frequencies in population]]
     * [[Allelic size range]] (lines with different colors)
-  * matrix:
+    * [[Molecular diversity indexes]]
+=== matrix: ===
     * [[Fst Matrix]]
       * read data from a HTML file
       * read data from a XML file
       * move legend
-    * [[haplotype distance]] (line by line input)
+    * haplotype distance:
-      * improved: matrix rotated, more labels
+      * [[haplotype distance]] (line by line input)
-    * [[haplotype distance between/within two populations]]
+        * improved: matrix rotated, more labels
-      * with mixed data from several populations
+      * [[haplotype distance between/within two populations]]
-    * [[haplotype distance between/within populations and groups]] (multiple plots in one graphic)
+        * with mixed data from several populations
-  * bar:
+    * [[Tau]]
+    * multiple plots in one graphic:
+      * [[haplotype distance between/within populations and groups]]
+      * [[Population average pairwise difference]]
+=== bar: ===
     * [[Allelic size range]]
     * [[relative Fis per locus]]
     * [[expected/observed haplotype]] (with CI)
-  * points:
+=== points: ===
     * [[Population assignment test]]
-  * XML:
+=== XML: ===
     * [[read data between XML tags]]
+      * [[half matrix]] data
+      * [[full matrix]] data
+      * [[table]] data
 \\
 ===== Arlequin output file changes (HTML to XML) =====
-**Delete:**
+=== Delete: ===
   * <html>, <head>, <style>, <body> and <PRE> tags
-  * the space (&nbsp;) in the empty <A> tag
+  * the space (&nbsp;) in the empty <A> tag or replace it with the space code: &#xAO;
 \\
-**Insert:**
+=== Insert: ===
   * XML declaration on top of the output file: <code>
 <?xml version="1.0" encoding="ISO-8859-1"?>
@@ Line 80: / Line 73: @@
 \\
-**example:**
+  * no sample names/population names with wihte space, use '_' instead
+\\
+=== example: ===
    * {{html_-_bsp_arlequinfile.doc|Arlequinfile HTML}}
    * {{xml_-_bsp_arlequinfile.doc|Arlequinfile XML}}
@@ Line 88: / Line 84: @@
 ===== tutorials =====
   * {{r_tutorial.pdf|small introduction to R}}
@@ Line 97: / Line 94: @@
   * [[http://addictedtor.free.fr/graphiques/thumbs.php|graph gallery]]
 \\
-  * [[xml_presentation|xml presentation]]
+  * [[xml_presentation|XML]]