slopes.md
In BioTIMEr: Tools to Use and Explore the 'BioTIME' Database

slopes works consistently

Code
  getLinearRegressions(x = alpham, divType = "alpha")
Output
     assemblageID     metric         slope     pvalue significance     intercept
  1             A          S -3.231300e-16 0.15830242            0     4.0000000
  2             A          N -1.085714e+00 0.49312733            0  2221.0000000
  3             A       maxN  3.428571e-01 0.57339225            0  -677.0000000
  4             A    Shannon -1.014279e-02 0.16387220            0    21.7549378
  5             A expShannon -3.860280e-02 0.15947041            0    81.5183357
  6             A    Simpson -5.747652e-03 0.17868740            0    12.2937633
  7             A invSimpson -7.518190e-02 0.16018749            0   154.9725712
  8             A        PIE -5.483465e-03 0.20734233            0    11.7832981
  9             A      DomMc  7.702476e-03 0.12601976            0   -14.8898380
  10            B          S -3.231300e-16 0.15830242            0     4.0000000
  11            B          N -3.571429e+00 0.02349824            1  7227.0000000
  12            B       maxN -3.142857e-01 0.39896494            0   645.0000000
  13            B    Shannon -8.443624e-03 0.39439070            0    18.3461137
  14            B expShannon -3.263149e-02 0.38974859            0    69.5432933
  15            B    Simpson -4.766654e-03 0.33661473            0    10.3263339
  16            B invSimpson -6.581369e-02 0.32841362            0   136.2163417
  17            B        PIE -3.214784e-03 0.48111327            0     7.2227636
  18            B      DomMc  1.384114e-02 0.34692228            0   -27.2662504
  19            C          S -3.231300e-16 0.15830242            0     4.0000000
  20            C          N -6.000000e-01 0.73091571            0  1246.0000000
  21            C       maxN -2.571429e-01 0.65825399            0   531.0000000
  22            C    Shannon  2.512677e-03 0.71407597            0    -3.7227134
  23            C expShannon  9.681283e-03 0.71058746            0   -15.6862557
  24            C    Simpson  9.383242e-04 0.75494541            0    -1.1633354
  25            C invSimpson  1.338684e-02 0.73952526            0   -23.2994890
  26            C        PIE  1.199578e-03 0.60404270            0    -1.6692828
  27            C      DomMc -2.377004e-03 0.83717092            0     5.4159374
  28            D          S -3.231300e-16 0.15830242            0     4.0000000
  29            D          N -1.885714e+00 0.18462086            0  3833.3333333
  30            D       maxN -7.714286e-01 0.38113855            0  1566.0000000
  31            D    Shannon  6.608015e-03 0.32300484            0   -11.9637075
  32            D expShannon  2.546484e-02 0.31749640            0   -47.4472840
  33            D    Simpson  2.778997e-03 0.42157180            0    -4.8679003
  34            D invSimpson  3.908144e-02 0.39448146            0   -75.0107237
  35            D        PIE  3.963670e-03 0.32464377            0    -7.2322410
  36            D      DomMc -8.736037e-03 0.44303277            0    18.2176280
  37            E          S -3.231300e-16 0.15830242            0     4.0000000
  38            E          N  2.342857e+00 0.21704733            0 -4679.6666667
  39            E       maxN  1.257143e+00 0.31596154            0 -2517.0000000
  40            E    Shannon -6.556769e-03 0.65648064            0    14.5334217
  41            E expShannon -2.556562e-02 0.64418461            0    55.2662898
  42            E    Simpson -3.569669e-03 0.66320687            0     7.9077787
  43            E invSimpson -5.106579e-02 0.61619422            0   106.4228595
  44            E        PIE -5.417667e-03 0.54732374            0    11.6489010
  45            E      DomMc  1.545518e-02 0.43815495            0   -30.5047252
  46            F          S -3.231300e-16 0.15830242            0     4.0000000
  47            F          N -2.971429e+00 0.22882036            0  6022.3333333
  48            F       maxN -6.285714e-01 0.51528960            0  1278.3333333
  49            F    Shannon -2.569709e-03 0.51268337            0     6.5354102
  50            F expShannon -1.000002e-02 0.51605470            0    24.0366679
  51            F    Simpson -1.340213e-03 0.49619976            0     3.4361451
  52            F invSimpson -1.928566e-02 0.50881398            0    42.6457206
  53            F        PIE -1.145575e-04 0.96734196            0     0.9881616
  54            F      DomMc  3.867156e-03 0.72148009            0    -7.2037333
  55            G          S -3.231300e-16 0.15830242            0     4.0000000
  56            G          N -7.714286e-01 0.37779156            0  1588.6666667
  57            G       maxN  1.142857e-01 0.79429474            0  -218.0000000
  58            G    Shannon -2.522603e-03 0.57010856            0     6.4334201
  59            G expShannon -9.973337e-03 0.56343713            0    23.9550388
  60            G    Simpson -1.302904e-03 0.55776144            0     3.3572440
  61            G invSimpson -1.988473e-02 0.53165210            0    43.7966564
  62            G        PIE -9.106016e-04 0.68827531            0     2.5887860
  63            G      DomMc  4.201681e-03 0.60924469            0    -7.8557190
  64            H          S -3.231300e-16 0.15830242            0     4.0000000
  65            H          N  1.714286e+00 0.34035262            0 -3411.3333333
  66            H       maxN  1.142857e-01 0.80472616            0  -217.6666667
  67            H    Shannon  4.191228e-03 0.33744336            0    -7.0696837
  68            H expShannon  1.626469e-02 0.33567459            0   -28.8158919
  69            H    Simpson  2.282941e-03 0.31905187            0    -3.8552402
  70            H invSimpson  3.248526e-02 0.31089303            0   -61.5391930
  71            H        PIE  1.181638e-03 0.37077264            0    -1.6185918
  72            H      DomMc -4.928107e-03 0.41164195            0    10.4936117

Code
  getLinearRegressions(x = betam, divType = "beta")
Output
     assemblageID           metric        slope     pvalue significance
  1             A      JaccardDiss  0.016326531 0.57339225            0
  2             A MorisitaHornDiss  0.020438356 0.62482173            0
  3             A   BrayCurtisDiss  0.001239032 0.96196422            0
  4             B      JaccardDiss -0.079455782 0.15064420            0
  5             B MorisitaHornDiss -0.090499580 0.15637235            0
  6             B   BrayCurtisDiss -0.080403596 0.11808705            0
  7             C      JaccardDiss -0.048979592 0.02131164            1
  8             C MorisitaHornDiss -0.080526810 0.09006650            0
  9             C   BrayCurtisDiss -0.065059033 0.05670431            0
  10            D      JaccardDiss  0.027210884 0.32616424            0
  11            D MorisitaHornDiss  0.005105450 0.88851018            0
  12            D   BrayCurtisDiss  0.008434437 0.77210602            0
  13            E      JaccardDiss -0.066666667 0.13470194            0
  14            E MorisitaHornDiss -0.095237006 0.08766297            0
  15            E   BrayCurtisDiss -0.086136153 0.09335691            0
  16            F      JaccardDiss  0.048979592 0.02131164            1
  17            F MorisitaHornDiss  0.070812332 0.13020623            0
  18            F   BrayCurtisDiss  0.059920630 0.06497971            0
  19            G      JaccardDiss  0.022040816 0.76450766            0
  20            G MorisitaHornDiss  0.020545808 0.82369684            0
  21            G   BrayCurtisDiss  0.032524487 0.68064142            0
  22            H      JaccardDiss  0.041360544 0.46161451            0
  23            H MorisitaHornDiss  0.011387456 0.83756354            0
  24            H   BrayCurtisDiss  0.019660543 0.70643863            0
       intercept
  1   -32.095238
  2   -40.522856
  3    -1.819232
  4   160.577778
  5   182.739180
  6   162.475029
  7    99.333333
  8   162.673482
  9   131.604069
  10  -54.000000
  11   -9.598164
  12  -16.257195
  13  135.000000
  14  192.456862
  15  174.151364
  16  -97.809524
  17 -141.851661
  18 -119.897270
  19  -43.628571
  20  -40.716682
  21  -64.779047
  22  -82.596825
  23  -22.412783
  24  -39.018592

Code
  getLinearRegressions(x = alpham, divType = "alpha", pThreshold = 0.01)
Output
     assemblageID     metric         slope     pvalue significance     intercept
  1             A          S -3.231300e-16 0.15830242            0     4.0000000
  2             A          N -1.085714e+00 0.49312733            0  2221.0000000
  3             A       maxN  3.428571e-01 0.57339225            0  -677.0000000
  4             A    Shannon -1.014279e-02 0.16387220            0    21.7549378
  5             A expShannon -3.860280e-02 0.15947041            0    81.5183357
  6             A    Simpson -5.747652e-03 0.17868740            0    12.2937633
  7             A invSimpson -7.518190e-02 0.16018749            0   154.9725712
  8             A        PIE -5.483465e-03 0.20734233            0    11.7832981
  9             A      DomMc  7.702476e-03 0.12601976            0   -14.8898380
  10            B          S -3.231300e-16 0.15830242            0     4.0000000
  11            B          N -3.571429e+00 0.02349824            0  7227.0000000
  12            B       maxN -3.142857e-01 0.39896494            0   645.0000000
  13            B    Shannon -8.443624e-03 0.39439070            0    18.3461137
  14            B expShannon -3.263149e-02 0.38974859            0    69.5432933
  15            B    Simpson -4.766654e-03 0.33661473            0    10.3263339
  16            B invSimpson -6.581369e-02 0.32841362            0   136.2163417
  17            B        PIE -3.214784e-03 0.48111327            0     7.2227636
  18            B      DomMc  1.384114e-02 0.34692228            0   -27.2662504
  19            C          S -3.231300e-16 0.15830242            0     4.0000000
  20            C          N -6.000000e-01 0.73091571            0  1246.0000000
  21            C       maxN -2.571429e-01 0.65825399            0   531.0000000
  22            C    Shannon  2.512677e-03 0.71407597            0    -3.7227134
  23            C expShannon  9.681283e-03 0.71058746            0   -15.6862557
  24            C    Simpson  9.383242e-04 0.75494541            0    -1.1633354
  25            C invSimpson  1.338684e-02 0.73952526            0   -23.2994890
  26            C        PIE  1.199578e-03 0.60404270            0    -1.6692828
  27            C      DomMc -2.377004e-03 0.83717092            0     5.4159374
  28            D          S -3.231300e-16 0.15830242            0     4.0000000
  29            D          N -1.885714e+00 0.18462086            0  3833.3333333
  30            D       maxN -7.714286e-01 0.38113855            0  1566.0000000
  31            D    Shannon  6.608015e-03 0.32300484            0   -11.9637075
  32            D expShannon  2.546484e-02 0.31749640            0   -47.4472840
  33            D    Simpson  2.778997e-03 0.42157180            0    -4.8679003
  34            D invSimpson  3.908144e-02 0.39448146            0   -75.0107237
  35            D        PIE  3.963670e-03 0.32464377            0    -7.2322410
  36            D      DomMc -8.736037e-03 0.44303277            0    18.2176280
  37            E          S -3.231300e-16 0.15830242            0     4.0000000
  38            E          N  2.342857e+00 0.21704733            0 -4679.6666667
  39            E       maxN  1.257143e+00 0.31596154            0 -2517.0000000
  40            E    Shannon -6.556769e-03 0.65648064            0    14.5334217
  41            E expShannon -2.556562e-02 0.64418461            0    55.2662898
  42            E    Simpson -3.569669e-03 0.66320687            0     7.9077787
  43            E invSimpson -5.106579e-02 0.61619422            0   106.4228595
  44            E        PIE -5.417667e-03 0.54732374            0    11.6489010
  45            E      DomMc  1.545518e-02 0.43815495            0   -30.5047252
  46            F          S -3.231300e-16 0.15830242            0     4.0000000
  47            F          N -2.971429e+00 0.22882036            0  6022.3333333
  48            F       maxN -6.285714e-01 0.51528960            0  1278.3333333
  49            F    Shannon -2.569709e-03 0.51268337            0     6.5354102
  50            F expShannon -1.000002e-02 0.51605470            0    24.0366679
  51            F    Simpson -1.340213e-03 0.49619976            0     3.4361451
  52            F invSimpson -1.928566e-02 0.50881398            0    42.6457206
  53            F        PIE -1.145575e-04 0.96734196            0     0.9881616
  54            F      DomMc  3.867156e-03 0.72148009            0    -7.2037333
  55            G          S -3.231300e-16 0.15830242            0     4.0000000
  56            G          N -7.714286e-01 0.37779156            0  1588.6666667
  57            G       maxN  1.142857e-01 0.79429474            0  -218.0000000
  58            G    Shannon -2.522603e-03 0.57010856            0     6.4334201
  59            G expShannon -9.973337e-03 0.56343713            0    23.9550388
  60            G    Simpson -1.302904e-03 0.55776144            0     3.3572440
  61            G invSimpson -1.988473e-02 0.53165210            0    43.7966564
  62            G        PIE -9.106016e-04 0.68827531            0     2.5887860
  63            G      DomMc  4.201681e-03 0.60924469            0    -7.8557190
  64            H          S -3.231300e-16 0.15830242            0     4.0000000
  65            H          N  1.714286e+00 0.34035262            0 -3411.3333333
  66            H       maxN  1.142857e-01 0.80472616            0  -217.6666667
  67            H    Shannon  4.191228e-03 0.33744336            0    -7.0696837
  68            H expShannon  1.626469e-02 0.33567459            0   -28.8158919
  69            H    Simpson  2.282941e-03 0.31905187            0    -3.8552402
  70            H invSimpson  3.248526e-02 0.31089303            0   -61.5391930
  71            H        PIE  1.181638e-03 0.37077264            0    -1.6185918
  72            H      DomMc -4.928107e-03 0.41164195            0    10.4936117

Code
  getLinearRegressions(x = betam, divType = "beta", pThreshold = 0.01)
Output
     assemblageID           metric        slope     pvalue significance
  1             A      JaccardDiss  0.016326531 0.57339225            0
  2             A MorisitaHornDiss  0.020438356 0.62482173            0
  3             A   BrayCurtisDiss  0.001239032 0.96196422            0
  4             B      JaccardDiss -0.079455782 0.15064420            0
  5             B MorisitaHornDiss -0.090499580 0.15637235            0
  6             B   BrayCurtisDiss -0.080403596 0.11808705            0
  7             C      JaccardDiss -0.048979592 0.02131164            0
  8             C MorisitaHornDiss -0.080526810 0.09006650            0
  9             C   BrayCurtisDiss -0.065059033 0.05670431            0
  10            D      JaccardDiss  0.027210884 0.32616424            0
  11            D MorisitaHornDiss  0.005105450 0.88851018            0
  12            D   BrayCurtisDiss  0.008434437 0.77210602            0
  13            E      JaccardDiss -0.066666667 0.13470194            0
  14            E MorisitaHornDiss -0.095237006 0.08766297            0
  15            E   BrayCurtisDiss -0.086136153 0.09335691            0
  16            F      JaccardDiss  0.048979592 0.02131164            0
  17            F MorisitaHornDiss  0.070812332 0.13020623            0
  18            F   BrayCurtisDiss  0.059920630 0.06497971            0
  19            G      JaccardDiss  0.022040816 0.76450766            0
  20            G MorisitaHornDiss  0.020545808 0.82369684            0
  21            G   BrayCurtisDiss  0.032524487 0.68064142            0
  22            H      JaccardDiss  0.041360544 0.46161451            0
  23            H MorisitaHornDiss  0.011387456 0.83756354            0
  24            H   BrayCurtisDiss  0.019660543 0.70643863            0
       intercept
  1   -32.095238
  2   -40.522856
  3    -1.819232
  4   160.577778
  5   182.739180
  6   162.475029
  7    99.333333
  8   162.673482
  9   131.604069
  10  -54.000000
  11   -9.598164
  12  -16.257195
  13  135.000000
  14  192.456862
  15  174.151364
  16  -97.809524
  17 -141.851661
  18 -119.897270
  19  -43.628571
  20  -40.716682
  21  -64.779047
  22  -82.596825
  23  -22.412783
  24  -39.018592