You can order each matrix by any column you choose like: a<-matrix(rnorm(20),ncol=2) > a[order(a[,1]),] #orders by column 1 [,1] [,2] [1,] -1.86523489 -1.6920270 [2,] -0.94488744 0.2815087 [3,] 0.02380494 0.2491136 [4,] 0.37295795 0.8156993 [5,] 0.55533366 -0.7053233 [6,] 0.79799294 -0.8224082 [7,] 0.80497452 0.4260842 [8,] 1.12438976 -0.1567863 [9,] 1.29213037 -1.6783762 [10,] 1.33496542 0.7807943
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