Coerce a codiv result to a plain data frame
Usage
# S3 method for class 'codiv'
as.data.frame(x, ...)Examples
# \donttest{
sim <- simulate_codiv_data(n_hosts = 10, n_clades = 3, seed = 1)
res <- codiv(sim$host_tree, sim$symbiont_tree, sim$links,
methods = "hommola", permutations = 99)
#> Creating unique node labels
#> Of the 59 internal nodes in the symbiont tree,
#> 49 (83%) have span > 0 and <= 10% of max (0 dropped for zero span)
#> 5 (8%) have 7-500 symbiont tips (0 dropped as too large)
#> 5 (8%) have >= 3 hosts
#> Scanning 5 nodes for codiversification.
#> Scanning 5 nodes across 3 cores ...
df <- as.data.frame(res) # plain data frame for filtering / export
head(df)
#> Node_ID
#> Node_18 Node_18
#> Node_36 Node_36
#> Node_17 Node_17
#> Node_49 Node_49
#> Node_15 Node_15
#> Symbiont_Tree
#> Node_18 ((c2_h3_1:0.004661357195,c2_h3:0.004661357195)Node_24:0.01087650012,((c2_h10_1:0.001186443053,c2_h10:0.001186443053)Node_23:0.002768367124,((c2_h9_1:0.002584480569,c2_h9:0.002584480569)Node_22:0.006030454661,(c2_h2_1:0.002765316812,c2_h2:0.002765316812)Node_21:0.006452405895)Node_20:0.004002682002)Node_19:0.004072273792)Node_18;
#> Node_36 ((c3_h4_1:0.07625152206,(c3_h4_2:0.02287545662,c3_h4:0.02287545662)Node_43:0.05337606544)Node_42:0.1779202181,((c3_h3_1:0.05618300743,(c3_h3_2:0.01685490223,c3_h3:0.01685490223)Node_41:0.0393281052)Node_40:0.131093684,(c3_h2_1:0.0565443785,(c3_h2_2:0.01696331355,c3_h2:0.01696331355)Node_39:0.03958106495)Node_38:0.1319368832)Node_37:0.05085388256)Node_36;
#> Node_17 ((c2_h4_1:0.01835908762,c2_h4:0.01835908762)Node_25:0.04283787112,((c2_h3_1:0.004661357195,c2_h3:0.004661357195)Node_24:0.01087650012,((c2_h10_1:0.001186443053,c2_h10:0.001186443053)Node_23:0.002768367124,((c2_h9_1:0.002584480569,c2_h9:0.002584480569)Node_22:0.006030454661,(c2_h2_1:0.002765316812,c2_h2:0.002765316812)Node_21:0.006452405895)Node_20:0.004002682002)Node_19:0.004072273792)Node_18:0.04606688055)Node_17;
#> Node_49 (((c3_h10_1:0.007972939947,(c3_h10_2:0.002391881984,c3_h10:0.002391881984)Node_59:0.005581057963)Node_58:0.01860352654,(c3_h9_1:0.008837663511,(c3_h9_2:0.002651299053,c3_h9:0.002651299053)Node_57:0.006186364458)Node_56:0.02062121486)Node_55:0.08991485234,((c3_h8_1:0.004766214497,(c3_h8_2:0.001429864349,c3_h8:0.001429864349)Node_54:0.003336350148)Node_53:0.01112116716,(c3_h7_1:0.004478456821,(c3_h7_2:0.001343537046,c3_h7:0.001343537046)Node_52:0.003134919774)Node_51:0.01044973258)Node_50:0.1188468404)Node_49;
#> Node_15 (((c2_h4_1:0.01835908762,c2_h4:0.01835908762)Node_25:0.04283787112,((c2_h3_1:0.004661357195,c2_h3:0.004661357195)Node_24:0.01087650012,((c2_h10_1:0.001186443053,c2_h10:0.001186443053)Node_23:0.002768367124,((c2_h9_1:0.002584480569,c2_h9:0.002584480569)Node_22:0.006030454661,(c2_h2_1:0.002765316812,c2_h2:0.002765316812)Node_21:0.006452405895)Node_20:0.004002682002)Node_19:0.004072273792)Node_18:0.04606688055)Node_17:0.02968134993,(c2_h1_1:0.02884987917,c2_h1:0.02884987917)Node_16:0.06731638474)Node_15;
#> N_Symbionts Symbiont_Colless Symbiont_Sackin
#> Node_18 8 6 26
#> Node_36 9 6 30
#> Node_17 10 12 38
#> Node_49 12 4 44
#> Node_15 12 20 52
#> Host_Tree
#> Node_18 (((H2:0.01678181851,H3:0.01678181851):0.04468413943,H4:0.06146595794):1.659956878,H10:1.721422836);
#> Node_36 ((H1:0.09053719966,H4:0.09053719966):1.630885636,H10:1.721422836);
#> Node_17 (((H2:0.01678181851,H3:0.01678181851):0.04468413943,(H4:0.05480904071,H5:0.05480904071):0.006656917232):1.659956878,H10:1.721422836);
#> Node_49 (((H2:0.06146595794,H5:0.06146595794):0.5234951044,H6:0.5849610623):0.17989428,H9:0.7648553423);
#> Node_15 ((H1:0.09053719966,((H2:0.01678181851,H3:0.01678181851):0.04468413943,(H4:0.05480904071,H5:0.05480904071):0.006656917232):0.02907124172):1.630885636,H10:1.721422836);
#> N_Hosts Host_Colless Host_Sackin Hommola_r Hommola_pvalue TreeDistance
#> Node_18 4 3 9 -0.1790181 0.73 1.0000000
#> Node_36 3 1 5 -0.4922685 0.67 NaN
#> Node_17 5 3 13 -0.2492913 0.80 0.7734456
#> Node_49 4 3 9 0.5514694 0.18 0.0000000
#> Node_15 6 7 19 -0.2673787 0.72 0.8199910
#> SharedPhylogeneticInfo DifferentPhylogeneticInfo NyeSimilarity
#> Node_18 0.0000000 3.169925 0.3333333
#> Node_36 0.0000000 0.000000 0.0000000
#> Node_17 0.7369656 7.813781 1.0000000
#> Node_49 1.5849625 0.000000 1.0000000
#> Node_15 0.9708537 15.639388 1.2500000
#> JaccardRobinsonFoulds MatchingSplitDistance MatchingSplitInfoDistance
#> Node_18 1.333333 2 3.169925
#> Node_36 0.000000 0 0.000000
#> Node_17 2.000000 3 6.117787
#> Node_49 0.000000 0 0.000000
#> Node_15 3.500000 7 11.241245
#> MutualClusteringInfo
#> Node_18 0.0000000
#> Node_36 0.0000000
#> Node_17 0.4399462
#> Node_49 1.0000000
#> Node_15 0.5032583
# }