Constructing a curve for the user-specified lognormal prior using Beast2 parameters

Usage

lognormalBeast(
  M,
  S,
  meanInRealSpace = TRUE,
  offset = 0,
  from = NULL,
  to = NULL,
  by = 0.05
)

Arguments

M: Mean of the lognormal density in Beast2.
S: Standard deviation of the lognormal density in Beast2.
meanInRealSpace: Whether to plot the mean on the real- or log-space (i.e., apply log(M) before plotting). Please see under details.
offset: Hard lower bound.
from, to, by: Starting and ending point to calculate considering the offset as zero. That is, from will affect produce a starting point of (offset + from) and an ending point of (offset + to). By sets the step size of the sequence from `from` to `to` each `by` steps.

Value

A matrix of two columns consisting of the x and y values of the lognormal density.

Details

This function creates a matrix of x,y values given parameters of a lognormal density as specified in the program Beast2. It's main purpose is for plotting but other uses such as similarity quantification are available. Please note that the value of mean depends on whether we expect it to be in real or log space. Please refer to Heath (2015) for more info: Heath, T. A. (2015). Divergence Time Estimation using BEAST v2.

Examples


# Generate a matrix for the lognormal density with mean 1 and standard deviation 1, with mean
# in real space, and spanning values in x from 0 to 10
lognormalBeast(M = 1, S = 1, meanInRealSpace = TRUE, from = 0, to = 10)
#>            x           y
#>   [1,]  0.00 0.000000000
#>   [2,]  0.05 0.089778281
#>   [3,]  0.10 0.281590189
#>   [4,]  0.15 0.439837180
#>   [5,]  0.20 0.546267871
#>   [6,]  0.25 0.610455304
#>   [7,]  0.30 0.644203257
#>   [8,]  0.35 0.656928789
#>   [9,]  0.40 0.655444168
#>  [10,]  0.45 0.644527295
#>  [11,]  0.50 0.627496077
#>  [12,]  0.55 0.606648294
#>  [13,]  0.60 0.583573823
#>  [14,]  0.65 0.559370868
#>  [15,]  0.70 0.534794832
#>  [16,]  0.75 0.510361006
#>  [17,]  0.80 0.486415781
#>  [18,]  0.85 0.463186358
#>  [19,]  0.90 0.440815686
#>  [20,]  0.95 0.419387175
#>  [21,]  1.00 0.398942280
#>  [22,]  1.05 0.379493072
#>  [23,]  1.10 0.361031261
#>  [24,]  1.15 0.343534692
#>  [25,]  1.20 0.326972024
#>  [26,]  1.25 0.311306100
#>  [27,]  1.30 0.296496371
#>  [28,]  1.35 0.282500627
#>  [29,]  1.40 0.269276229
#>  [30,]  1.45 0.256780967
#>  [31,]  1.50 0.244973652
#>  [32,]  1.55 0.233814513
#>  [33,]  1.60 0.223265447
#>  [34,]  1.65 0.213290165
#>  [35,]  1.70 0.203854259
#>  [36,]  1.75 0.194925229
#>  [37,]  1.80 0.186472449
#>  [38,]  1.85 0.178467127
#>  [39,]  1.90 0.170882238
#>  [40,]  1.95 0.163692446
#>  [41,]  2.00 0.156874019
#>  [42,]  2.05 0.150404746
#>  [43,]  2.10 0.144263846
#>  [44,]  2.15 0.138431884
#>  [45,]  2.20 0.132890686
#>  [46,]  2.25 0.127623257
#>  [47,]  2.30 0.122613707
#>  [48,]  2.35 0.117847173
#>  [49,]  2.40 0.113309754
#>  [50,]  2.45 0.108988443
#>  [51,]  2.50 0.104871067
#>  [52,]  2.55 0.100946230
#>  [53,]  2.60 0.097203259
#>  [54,]  2.65 0.093632155
#>  [55,]  2.70 0.090223546
#>  [56,]  2.75 0.086968643
#>  [57,]  2.80 0.083859205
#>  [58,]  2.85 0.080887493
#>  [59,]  2.90 0.078046245
#>  [60,]  2.95 0.075328637
#>  [61,]  3.00 0.072728256
#>  [62,]  3.05 0.070239074
#>  [63,]  3.10 0.067855420
#>  [64,]  3.15 0.065571956
#>  [65,]  3.20 0.063383656
#>  [66,]  3.25 0.061285787
#>  [67,]  3.30 0.059273887
#>  [68,]  3.35 0.057343749
#>  [69,]  3.40 0.055491406
#>  [70,]  3.45 0.053713112
#>  [71,]  3.50 0.052005332
#>  [72,]  3.55 0.050364725
#>  [73,]  3.60 0.048788135
#>  [74,]  3.65 0.047272577
#>  [75,]  3.70 0.045815229
#>  [76,]  3.75 0.044413419
#>  [77,]  3.80 0.043064619
#>  [78,]  3.85 0.041766434
#>  [79,]  3.90 0.040516593
#>  [80,]  3.95 0.039312948
#>  [81,]  4.00 0.038153457
#>  [82,]  4.05 0.037036185
#>  [83,]  4.10 0.035959297
#>  [84,]  4.15 0.034921048
#>  [85,]  4.20 0.033919783
#>  [86,]  4.25 0.032953929
#>  [87,]  4.30 0.032021989
#>  [88,]  4.35 0.031122542
#>  [89,]  4.40 0.030254236
#>  [90,]  4.45 0.029415782
#>  [91,]  4.50 0.028605956
#>  [92,]  4.55 0.027823591
#>  [93,]  4.60 0.027067575
#>  [94,]  4.65 0.026336850
#>  [95,]  4.70 0.025630406
#>  [96,]  4.75 0.024947280
#>  [97,]  4.80 0.024286554
#>  [98,]  4.85 0.023647353
#>  [99,]  4.90 0.023028838
#> [100,]  4.95 0.022430213
#> [101,]  5.00 0.021850715
#> [102,]  5.05 0.021289614
#> [103,]  5.10 0.020746215
#> [104,]  5.15 0.020219852
#> [105,]  5.20 0.019709889
#> [106,]  5.25 0.019215716
#> [107,]  5.30 0.018736751
#> [108,]  5.35 0.018272437
#> [109,]  5.40 0.017822239
#> [110,]  5.45 0.017385647
#> [111,]  5.50 0.016962171
#> [112,]  5.55 0.016551341
#> [113,]  5.60 0.016152709
#> [114,]  5.65 0.015765843
#> [115,]  5.70 0.015390329
#> [116,]  5.75 0.015025771
#> [117,]  5.80 0.014671790
#> [118,]  5.85 0.014328019
#> [119,]  5.90 0.013994109
#> [120,]  5.95 0.013669723
#> [121,]  6.00 0.013354538
#> [122,]  6.05 0.013048244
#> [123,]  6.10 0.012750543
#> [124,]  6.15 0.012461147
#> [125,]  6.20 0.012179782
#> [126,]  6.25 0.011906183
#> [127,]  6.30 0.011640095
#> [128,]  6.35 0.011381274
#> [129,]  6.40 0.011129482
#> [130,]  6.45 0.010884494
#> [131,]  6.50 0.010646092
#> [132,]  6.55 0.010414065
#> [133,]  6.60 0.010188210
#> [134,]  6.65 0.009968333
#> [135,]  6.70 0.009754246
#> [136,]  6.75 0.009545768
#> [137,]  6.80 0.009342725
#> [138,]  6.85 0.009144949
#> [139,]  6.90 0.008952276
#> [140,]  6.95 0.008764553
#> [141,]  7.00 0.008581626
#> [142,]  7.05 0.008403352
#> [143,]  7.10 0.008229590
#> [144,]  7.15 0.008060204
#> [145,]  7.20 0.007895064
#> [146,]  7.25 0.007734044
#> [147,]  7.30 0.007577022
#> [148,]  7.35 0.007423879
#> [149,]  7.40 0.007274504
#> [150,]  7.45 0.007128786
#> [151,]  7.50 0.006986618
#> [152,]  7.55 0.006847899
#> [153,]  7.60 0.006712529
#> [154,]  7.65 0.006580413
#> [155,]  7.70 0.006451458
#> [156,]  7.75 0.006325575
#> [157,]  7.80 0.006202676
#> [158,]  7.85 0.006082679
#> [159,]  7.90 0.005965502
#> [160,]  7.95 0.005851066
#> [161,]  8.00 0.005739296
#> [162,]  8.05 0.005630119
#> [163,]  8.10 0.005523463
#> [164,]  8.15 0.005419260
#> [165,]  8.20 0.005317442
#> [166,]  8.25 0.005217945
#> [167,]  8.30 0.005120707
#> [168,]  8.35 0.005025667
#> [169,]  8.40 0.004932766
#> [170,]  8.45 0.004841948
#> [171,]  8.50 0.004753157
#> [172,]  8.55 0.004666339
#> [173,]  8.60 0.004581444
#> [174,]  8.65 0.004498420
#> [175,]  8.70 0.004417220
#> [176,]  8.75 0.004337795
#> [177,]  8.80 0.004260099
#> [178,]  8.85 0.004184090
#> [179,]  8.90 0.004109722
#> [180,]  8.95 0.004036955
#> [181,]  9.00 0.003965747
#> [182,]  9.05 0.003896060
#> [183,]  9.10 0.003827854
#> [184,]  9.15 0.003761094
#> [185,]  9.20 0.003695741
#> [186,]  9.25 0.003631763
#> [187,]  9.30 0.003569124
#> [188,]  9.35 0.003507792
#> [189,]  9.40 0.003447734
#> [190,]  9.45 0.003388919
#> [191,]  9.50 0.003331316
#> [192,]  9.55 0.003274898
#> [193,]  9.60 0.003219633
#> [194,]  9.65 0.003165496
#> [195,]  9.70 0.003112458
#> [196,]  9.75 0.003060494
#> [197,]  9.80 0.003009577
#> [198,]  9.85 0.002959684
#> [199,]  9.90 0.002910789
#> [200,]  9.95 0.002862869
#> [201,] 10.00 0.002815902
# The same as above but with an offset of 10, that is, the curve starts at 10 as if it was 0
# to values will start in (offset + from) and finish in (offset + to)
lognormalBeast(M = 1, S = 1, meanInRealSpace = TRUE, offset = 10, from = 0, to = 10)
#>            x           y
#>   [1,] 10.00 0.000000000
#>   [2,] 10.05 0.089778281
#>   [3,] 10.10 0.281590189
#>   [4,] 10.15 0.439837180
#>   [5,] 10.20 0.546267871
#>   [6,] 10.25 0.610455304
#>   [7,] 10.30 0.644203257
#>   [8,] 10.35 0.656928789
#>   [9,] 10.40 0.655444168
#>  [10,] 10.45 0.644527295
#>  [11,] 10.50 0.627496077
#>  [12,] 10.55 0.606648294
#>  [13,] 10.60 0.583573823
#>  [14,] 10.65 0.559370868
#>  [15,] 10.70 0.534794832
#>  [16,] 10.75 0.510361006
#>  [17,] 10.80 0.486415781
#>  [18,] 10.85 0.463186358
#>  [19,] 10.90 0.440815686
#>  [20,] 10.95 0.419387175
#>  [21,] 11.00 0.398942280
#>  [22,] 11.05 0.379493072
#>  [23,] 11.10 0.361031261
#>  [24,] 11.15 0.343534692
#>  [25,] 11.20 0.326972024
#>  [26,] 11.25 0.311306100
#>  [27,] 11.30 0.296496371
#>  [28,] 11.35 0.282500627
#>  [29,] 11.40 0.269276229
#>  [30,] 11.45 0.256780967
#>  [31,] 11.50 0.244973652
#>  [32,] 11.55 0.233814513
#>  [33,] 11.60 0.223265447
#>  [34,] 11.65 0.213290165
#>  [35,] 11.70 0.203854259
#>  [36,] 11.75 0.194925229
#>  [37,] 11.80 0.186472449
#>  [38,] 11.85 0.178467127
#>  [39,] 11.90 0.170882238
#>  [40,] 11.95 0.163692446
#>  [41,] 12.00 0.156874019
#>  [42,] 12.05 0.150404746
#>  [43,] 12.10 0.144263846
#>  [44,] 12.15 0.138431884
#>  [45,] 12.20 0.132890686
#>  [46,] 12.25 0.127623257
#>  [47,] 12.30 0.122613707
#>  [48,] 12.35 0.117847173
#>  [49,] 12.40 0.113309754
#>  [50,] 12.45 0.108988443
#>  [51,] 12.50 0.104871067
#>  [52,] 12.55 0.100946230
#>  [53,] 12.60 0.097203259
#>  [54,] 12.65 0.093632155
#>  [55,] 12.70 0.090223546
#>  [56,] 12.75 0.086968643
#>  [57,] 12.80 0.083859205
#>  [58,] 12.85 0.080887493
#>  [59,] 12.90 0.078046245
#>  [60,] 12.95 0.075328637
#>  [61,] 13.00 0.072728256
#>  [62,] 13.05 0.070239074
#>  [63,] 13.10 0.067855420
#>  [64,] 13.15 0.065571956
#>  [65,] 13.20 0.063383656
#>  [66,] 13.25 0.061285787
#>  [67,] 13.30 0.059273887
#>  [68,] 13.35 0.057343749
#>  [69,] 13.40 0.055491406
#>  [70,] 13.45 0.053713112
#>  [71,] 13.50 0.052005332
#>  [72,] 13.55 0.050364725
#>  [73,] 13.60 0.048788135
#>  [74,] 13.65 0.047272577
#>  [75,] 13.70 0.045815229
#>  [76,] 13.75 0.044413419
#>  [77,] 13.80 0.043064619
#>  [78,] 13.85 0.041766434
#>  [79,] 13.90 0.040516593
#>  [80,] 13.95 0.039312948
#>  [81,] 14.00 0.038153457
#>  [82,] 14.05 0.037036185
#>  [83,] 14.10 0.035959297
#>  [84,] 14.15 0.034921048
#>  [85,] 14.20 0.033919783
#>  [86,] 14.25 0.032953929
#>  [87,] 14.30 0.032021989
#>  [88,] 14.35 0.031122542
#>  [89,] 14.40 0.030254236
#>  [90,] 14.45 0.029415782
#>  [91,] 14.50 0.028605956
#>  [92,] 14.55 0.027823591
#>  [93,] 14.60 0.027067575
#>  [94,] 14.65 0.026336850
#>  [95,] 14.70 0.025630406
#>  [96,] 14.75 0.024947280
#>  [97,] 14.80 0.024286554
#>  [98,] 14.85 0.023647353
#>  [99,] 14.90 0.023028838
#> [100,] 14.95 0.022430213
#> [101,] 15.00 0.021850715
#> [102,] 15.05 0.021289614
#> [103,] 15.10 0.020746215
#> [104,] 15.15 0.020219852
#> [105,] 15.20 0.019709889
#> [106,] 15.25 0.019215716
#> [107,] 15.30 0.018736751
#> [108,] 15.35 0.018272437
#> [109,] 15.40 0.017822239
#> [110,] 15.45 0.017385647
#> [111,] 15.50 0.016962171
#> [112,] 15.55 0.016551341
#> [113,] 15.60 0.016152709
#> [114,] 15.65 0.015765843
#> [115,] 15.70 0.015390329
#> [116,] 15.75 0.015025771
#> [117,] 15.80 0.014671790
#> [118,] 15.85 0.014328019
#> [119,] 15.90 0.013994109
#> [120,] 15.95 0.013669723
#> [121,] 16.00 0.013354538
#> [122,] 16.05 0.013048244
#> [123,] 16.10 0.012750543
#> [124,] 16.15 0.012461147
#> [125,] 16.20 0.012179782
#> [126,] 16.25 0.011906183
#> [127,] 16.30 0.011640095
#> [128,] 16.35 0.011381274
#> [129,] 16.40 0.011129482
#> [130,] 16.45 0.010884494
#> [131,] 16.50 0.010646092
#> [132,] 16.55 0.010414065
#> [133,] 16.60 0.010188210
#> [134,] 16.65 0.009968333
#> [135,] 16.70 0.009754246
#> [136,] 16.75 0.009545768
#> [137,] 16.80 0.009342725
#> [138,] 16.85 0.009144949
#> [139,] 16.90 0.008952276
#> [140,] 16.95 0.008764553
#> [141,] 17.00 0.008581626
#> [142,] 17.05 0.008403352
#> [143,] 17.10 0.008229590
#> [144,] 17.15 0.008060204
#> [145,] 17.20 0.007895064
#> [146,] 17.25 0.007734044
#> [147,] 17.30 0.007577022
#> [148,] 17.35 0.007423879
#> [149,] 17.40 0.007274504
#> [150,] 17.45 0.007128786
#> [151,] 17.50 0.006986618
#> [152,] 17.55 0.006847899
#> [153,] 17.60 0.006712529
#> [154,] 17.65 0.006580413
#> [155,] 17.70 0.006451458
#> [156,] 17.75 0.006325575
#> [157,] 17.80 0.006202676
#> [158,] 17.85 0.006082679
#> [159,] 17.90 0.005965502
#> [160,] 17.95 0.005851066
#> [161,] 18.00 0.005739296
#> [162,] 18.05 0.005630119
#> [163,] 18.10 0.005523463
#> [164,] 18.15 0.005419260
#> [165,] 18.20 0.005317442
#> [166,] 18.25 0.005217945
#> [167,] 18.30 0.005120707
#> [168,] 18.35 0.005025667
#> [169,] 18.40 0.004932766
#> [170,] 18.45 0.004841948
#> [171,] 18.50 0.004753157
#> [172,] 18.55 0.004666339
#> [173,] 18.60 0.004581444
#> [174,] 18.65 0.004498420
#> [175,] 18.70 0.004417220
#> [176,] 18.75 0.004337795
#> [177,] 18.80 0.004260099
#> [178,] 18.85 0.004184090
#> [179,] 18.90 0.004109722
#> [180,] 18.95 0.004036955
#> [181,] 19.00 0.003965747
#> [182,] 19.05 0.003896060
#> [183,] 19.10 0.003827854
#> [184,] 19.15 0.003761094
#> [185,] 19.20 0.003695741
#> [186,] 19.25 0.003631763
#> [187,] 19.30 0.003569124
#> [188,] 19.35 0.003507792
#> [189,] 19.40 0.003447734
#> [190,] 19.45 0.003388919
#> [191,] 19.50 0.003331316
#> [192,] 19.55 0.003274898
#> [193,] 19.60 0.003219633
#> [194,] 19.65 0.003165496
#> [195,] 19.70 0.003112458
#> [196,] 19.75 0.003060494
#> [197,] 19.80 0.003009577
#> [198,] 19.85 0.002959684
#> [199,] 19.90 0.002910789
#> [200,] 19.95 0.002862869
#> [201,] 20.00 0.002815902