better readme file

readme.md

@@ -1,21 +1,42 @@
-A program for graphing the evenness of bacterial communities using
-Pareto–Lorenz curves of the relative abundance of a set of T-RFs against the
-cumulative abundance of each T-RF. It also calculates the gini-coefficient of
-these.
+A program for graphically describing the evenness of bacterial communities using
+ Pareto–Lorenz (PL) curves, by plotting the cumulative relative abundance 
+against the cumulative proportion of each taxonomical bins (based on e.g. T-RFs
+, OTUs). The more the plotted line deviates from the 1:1 line (45° diagonal), 
+the lower the evenness of the community.
+
+For each sample individually, empty bins are removed and the remaining bins are
+ sorted in decreasing order of relative abundance. The cumulative relative 
+abundance (range 0-1) and cumulative proportion of bins (range 0-1) are 
+calculated and the data plotted so that the first (left most) data point 
+represents the contribution of the bin with the highest relative abundance. 
+Data for all samples in the imported data set are plotted on the same graph, 
+to facilitate comparisons between samples. 
+
+The program also calculates the Gini-coefficient for each community, which 
+describes the evenness of a community as the ratio of the area between the PL 
+curve and the equality line and the whole triangular area above the equality 
+line. The Gini coefficient ranges from 0 (perfect evenness) to 1 (perfect 
+unevenness). The reported Gini coefficient has been corrected for the number 
+of taxonomical units in the sample by multiplying the ratio with n/(n-1).
 
 This implements the method described in the following papers:
 
-https://www.nature.com/articles/ismej2010100
-"Possible interactions between bacterial diversity, microbial activity and
-supraglacial hydrology of cryoconite holes in Svalbard" by
-Arwyn Edwards, Alexandre M Anesio, Sara M Rassner, Birgit Sattler,
-Bryn Hubbard, William T Perkins, Michael Young & Gareth W Griffith
-in The ISME Journal volume 5, pages 150–160 (2011)
+
+["Possible interactions between bacterial diversity, microbial activity and 
+supraglacial hydrology of cryoconite holes in Svalbard" by Arwyn Edwards, 
+Alexandre M Anesio, Sara M Rassner, Birgit Sattler, Bryn Hubbard, William T 
+Perkins, Michael Young & Gareth W Griffith in The ISME Journal volume 5, 
+pages 150–160 (2011)
+https://www.nature.com/articles/ismej2010100]
+(https://www.nature.com/articles/ismej2010100)
 
 and
 
-https://doi.org/10.3389/fmicb.2016.00956
-"Can the Bacterial Community of a High Arctic Glacier Surface Escape Viral
-Control?" by Sara M. E. Rassner, Alexandre M. Anesio, Susan E. Girdwood,
-Katherina Hell, Jarishma K. Gokul, David E. Whitworth and Arwyn Edwards
-in Frontiers in Microbiology 21 June 2016
+["Can the Bacterial Community of a 
+High Arctic Glacier Surface Escape Viral Control?" by Sara M. E. Rassner, 
+Alexandre M. Anesio, Susan E. Girdwood, Katherina Hell, Jarishma K. Gokul, 
+David E. Whitworth and Arwyn Edwards in Frontiers in Microbiology 21 June 2016
+https://doi.org/10.3389/fmicb.2016.00956]
+(https://doi.org/10.3389/fmicb.2016.00956)
+
+