diff --git a/readme.md b/readme.md index 6e30c7f..dc86f1a 100644 --- a/readme.md +++ b/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) + +