Update paper.md

paper.md

@@ -58,6 +58,7 @@ To facilitate comparisons within a set of clusterings, the *CluSim* package prov
  
 
 ![Evaluating clustering comparisons w.r.t. random models.](paperfigures/CluSimFig1.png)
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 **Evaluating clustering comparisons w.r.t. random models.** A comparison using the Rand Index between the classification of cancer types and clustering labels derived using Hierarchical Clustering on gene expression data ($0.5$, red). above, Pairwise comparisons between samples from the Permutation model (blue, see [@Hubert1985adjrand]) with mean $0.44$ (black). below, Pairwise comparisons between samples from the one-sided model with a Fixed Number of Clusters (blue, see [@Gates2017impact]) with mean $0.59$ (black). The Permutation model suggests Hierarchical Clustering is more similar to the ground truth than a random clustering, while the one-sized fixed number of clusterings model, the more appropriate model for this scenario, reveals that the result is less similar than random clusterings.
 
  
@@ -67,6 +68,7 @@ In the second example, we identify the loci of gene-tree heterogeneity in an ana
  
 
 ![Element-centric comparisons of phylogenetic dendrograms.](paperfigures/CluSimFig2.png)
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 **Element-centric comparisons of phylogenetic dendrograms**. **a**, An example phylogenetic tree for the $37$ mammals from [@Song2012mammalphylogeny]. **b**, The average element-centric similarity between $424$-gene trees for different scaling parameters reveals few conflicts near the roots (left, $r<0$), while decreasing similarity for increasing $r$ suggests greater conflicts towards the leaves (left, $r>0$). **c**, The element-centric frustration highlights the 5 taxa previously identified with structural discrepancies (bats, shrews, and hedgehog, blue, [@Mirarab2014astral]), and the 3 taxa with the smallest bootstrapping support in the maximum-pseudolikelihood coalescent tree (pig, guinea pig, kangaroo rat, purple, [@Song2012mammalphylogeny]).
 
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