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Last data update: 2014.03.03

R: returns the null starting values used in model.test.sisters

starting.values

R Documentation

returns the null starting values used in model.test.sisters

Description

returns the null starting values used in model.test.sisters

Usage

starting.values(MODEL)

Arguments

MODEL

any one of the evolutionary models implemented by model.test.sisters except BM_2rate and OU_2rate.

Details

because nlm (and other optimization functions in R) often gets stuck on local likelihood optima, model.test.sisters uses a variety of starting parameters in combination with nlm optimization and reports the results for the best set of starting parameters as the maximum likelihood estimate. The null starting parameters have been optimized for rates of Beta and Alpha that are typically less than 1. The user can also provide their own matrix of starting parameters. This function is provided here so the user can determine if the starting parameters are suited to their particular dataset. Alternatively, values of Euclidean distances and of L can also be transformed (i.e. by dividing large values by a constant) so they lie within a range acceptable for the starting parameters.

Value

returns a matrix with the starting values. Each column is a different parameter, and the last column is NA

Author(s)

Jason T. Weir

References

Weir JT, D Wheatcroft, & T Price. 2012. The role of ecological constraint in driving the evolution of avian song frequency across a latitudinal gradient. Evolution 66, 2773-2783.

Weir JT, & D Wheatcroft. 2011. A latitudinal gradient in rates of evolution of avian syllable diversity and song length. Proceedings of the Royal Society of London, B 278, 1713-1720.

Examples


starting.values(MODEL = "OU_linear")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(EvoRAG)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/EvoRAG/starting.values.Rd_%03d_medium.png", width=480, height=480)
> ### Name: starting.values
> ### Title: returns the null starting values used in model.test.sisters
> ### Aliases: starting.values
> ### Keywords: Brownian Motion Ornstein Uhlenbeck
> 
> ### ** Examples
> 
> 
> starting.values(MODEL = "OU_linear")
        [,1]   [,2]  [,3]   [,4] [,5]
  [1,] 10.00  0.010 1e-02  0.010   NA
  [2,] 10.00  0.010 1e-01  0.010   NA
  [3,] 10.00  0.010 5e-01  0.010   NA
  [4,] 10.00  0.010 1e+00  0.010   NA
  [5,] 10.00  0.010 5e+00  0.010   NA
  [6,] 10.00  0.010 1e+01  0.010   NA
  [7,] 10.00  0.100 1e-02  0.010   NA
  [8,] 10.00  0.100 1e-01  0.010   NA
  [9,] 10.00  0.100 5e-01  0.010   NA
 [10,] 10.00  0.100 1e+00  0.010   NA
 [11,] 10.00  0.100 5e+00  0.010   NA
 [12,] 10.00  0.100 1e+01  0.010   NA
 [13,] 10.00  0.010 1e-02  0.100   NA
 [14,] 10.00  0.010 1e-01  0.100   NA
 [15,] 10.00  0.010 5e-01  0.100   NA
 [16,] 10.00  0.010 1e+00  0.100   NA
 [17,] 10.00  0.010 5e+00  0.100   NA
 [18,] 10.00  0.010 1e+01  0.100   NA
 [19,] 10.00  0.001 1e-02  0.001   NA
 [20,] 10.00  0.001 1e-01  0.001   NA
 [21,] 10.00  0.001 5e-01  0.001   NA
 [22,] 10.00  0.001 1e+00  0.001   NA
 [23,] 10.00  0.001 5e+00  0.001   NA
 [24,] 10.00  0.001 1e+01  0.001   NA
 [25,] 10.00 -0.010 1e-02  0.010   NA
 [26,] 10.00 -0.010 1e-01  0.010   NA
 [27,] 10.00 -0.010 5e-01  0.010   NA
 [28,] 10.00 -0.010 1e+00  0.010   NA
 [29,] 10.00 -0.010 5e+00  0.010   NA
 [30,] 10.00 -0.010 1e+01  0.010   NA
 [31,] 10.00 -0.100 1e-02  0.010   NA
 [32,] 10.00 -0.100 1e-01  0.010   NA
 [33,] 10.00 -0.100 5e-01  0.010   NA
 [34,] 10.00 -0.100 1e+00  0.010   NA
 [35,] 10.00 -0.100 5e+00  0.010   NA
 [36,] 10.00 -0.100 1e+01  0.010   NA
 [37,] 10.00 -0.010 1e-02  0.100   NA
 [38,] 10.00 -0.010 1e-01  0.100   NA
 [39,] 10.00 -0.010 5e-01  0.100   NA
 [40,] 10.00 -0.010 1e+00  0.100   NA
 [41,] 10.00 -0.010 5e+00  0.100   NA
 [42,] 10.00 -0.010 1e+01  0.100   NA
 [43,] 10.00 -0.001 1e-02  0.001   NA
 [44,] 10.00 -0.001 1e-01  0.001   NA
 [45,] 10.00 -0.001 5e-01  0.001   NA
 [46,] 10.00 -0.001 1e+00  0.001   NA
 [47,] 10.00 -0.001 5e+00  0.001   NA
 [48,] 10.00 -0.001 1e+01  0.001   NA
 [49,] 10.00  0.010 1e-02 -0.010   NA
 [50,] 10.00  0.010 1e-01 -0.010   NA
 [51,] 10.00  0.010 5e-01 -0.010   NA
 [52,] 10.00  0.010 1e+00 -0.010   NA
 [53,] 10.00  0.010 5e+00 -0.010   NA
 [54,] 10.00  0.010 1e+01 -0.010   NA
 [55,] 10.00  0.100 1e-02 -0.010   NA
 [56,] 10.00  0.100 1e-01 -0.010   NA
 [57,] 10.00  0.100 5e-01 -0.010   NA
 [58,] 10.00  0.100 1e+00 -0.010   NA
 [59,] 10.00  0.100 5e+00 -0.010   NA
 [60,] 10.00  0.100 1e+01 -0.010   NA
 [61,] 10.00  0.010 1e-02 -0.100   NA
 [62,] 10.00  0.010 1e-01 -0.100   NA
 [63,] 10.00  0.010 5e-01 -0.100   NA
 [64,] 10.00  0.010 1e+00 -0.100   NA
 [65,] 10.00  0.010 5e+00 -0.100   NA
 [66,] 10.00  0.010 1e+01 -0.100   NA
 [67,] 10.00  0.001 1e-02 -0.001   NA
 [68,] 10.00  0.001 1e-01 -0.001   NA
 [69,] 10.00  0.001 5e-01 -0.001   NA
 [70,] 10.00  0.001 1e+00 -0.001   NA
 [71,] 10.00  0.001 5e+00 -0.001   NA
 [72,] 10.00  0.001 1e+01 -0.001   NA
 [73,] 10.00 -0.010 1e-02 -0.010   NA
 [74,] 10.00 -0.010 1e-01 -0.010   NA
 [75,] 10.00 -0.010 5e-01 -0.010   NA
 [76,] 10.00 -0.010 1e+00 -0.010   NA
 [77,] 10.00 -0.010 5e+00 -0.010   NA
 [78,] 10.00 -0.010 1e+01 -0.010   NA
 [79,] 10.00 -0.100 1e-02 -0.010   NA
 [80,] 10.00 -0.100 1e-01 -0.010   NA
 [81,] 10.00 -0.100 5e-01 -0.010   NA
 [82,] 10.00 -0.100 1e+00 -0.010   NA
 [83,] 10.00 -0.100 5e+00 -0.010   NA
 [84,] 10.00 -0.100 1e+01 -0.010   NA
 [85,] 10.00 -0.010 1e-02 -0.100   NA
 [86,] 10.00 -0.010 1e-01 -0.100   NA
 [87,] 10.00 -0.010 5e-01 -0.100   NA
 [88,] 10.00 -0.010 1e+00 -0.100   NA
 [89,] 10.00 -0.010 5e+00 -0.100   NA
 [90,] 10.00 -0.010 1e+01 -0.100   NA
 [91,] 10.00 -0.001 1e-02 -0.001   NA
 [92,] 10.00 -0.001 1e-01 -0.001   NA
 [93,] 10.00 -0.001 5e-01 -0.001   NA
 [94,] 10.00 -0.001 1e+00 -0.001   NA
 [95,] 10.00 -0.001 5e+00 -0.001   NA
 [96,] 10.00 -0.001 1e+01 -0.001   NA
 [97,] 10.00  0.010 1e-02  0.010   NA
 [98,]  1.00  0.010 1e-01  0.010   NA
 [99,]  1.00  0.010 5e-01  0.010   NA
[100,]  1.00  0.010 1e+00  0.010   NA
[101,]  1.00  0.010 5e+00  0.010   NA
[102,]  1.00  0.010 1e+01  0.010   NA
[103,]  1.00  0.100 1e-02  0.010   NA
[104,]  1.00  0.100 1e-01  0.010   NA
[105,]  1.00  0.100 5e-01  0.010   NA
[106,]  1.00  0.100 1e+00  0.010   NA
[107,]  1.00  0.100 5e+00  0.010   NA
[108,]  1.00  0.100 1e+01  0.010   NA
[109,]  1.00  0.010 1e-02  0.100   NA
[110,]  1.00  0.010 1e-01  0.100   NA
[111,]  1.00  0.010 5e-01  0.100   NA
[112,]  1.00  0.010 1e+00  0.100   NA
[113,]  1.00  0.010 5e+00  0.100   NA
[114,]  1.00  0.010 1e+01  0.100   NA
[115,]  1.00  0.001 1e-02  0.001   NA
[116,]  1.00  0.001 1e-01  0.001   NA
[117,]  1.00  0.001 5e-01  0.001   NA
[118,]  1.00  0.001 1e+00  0.001   NA
[119,]  1.00  0.001 5e+00  0.001   NA
[120,]  1.00  0.001 1e+01  0.001   NA
[121,]  1.00 -0.010 1e-02  0.010   NA
[122,]  1.00 -0.010 1e-01  0.010   NA
[123,]  1.00 -0.010 5e-01  0.010   NA
[124,]  1.00 -0.010 1e+00  0.010   NA
[125,]  1.00 -0.010 5e+00  0.010   NA
[126,]  1.00 -0.010 1e+01  0.010   NA
[127,]  1.00 -0.100 1e-02  0.010   NA
[128,]  1.00 -0.100 1e-01  0.010   NA
[129,]  1.00 -0.100 5e-01  0.010   NA
[130,]  1.00 -0.100 1e+00  0.010   NA
[131,]  1.00 -0.100 5e+00  0.010   NA
[132,]  1.00 -0.100 1e+01  0.010   NA
[133,]  1.00 -0.010 1e-02  0.100   NA
[134,]  1.00 -0.010 1e-01  0.100   NA
[135,]  1.00 -0.010 5e-01  0.100   NA
[136,]  1.00 -0.010 1e+00  0.100   NA
[137,]  1.00 -0.010 5e+00  0.100   NA
[138,]  1.00 -0.010 1e+01  0.100   NA
[139,]  1.00 -0.001 1e-02  0.001   NA
[140,]  1.00 -0.001 1e-01  0.001   NA
[141,]  1.00 -0.001 5e-01  0.001   NA
[142,]  1.00 -0.001 1e+00  0.001   NA
[143,]  1.00 -0.001 5e+00  0.001   NA
[144,]  1.00 -0.001 1e+01  0.001   NA
[145,]  1.00  0.010 1e-02 -0.010   NA
[146,]  1.00  0.010 1e-01 -0.010   NA
[147,]  1.00  0.010 5e-01 -0.010   NA
[148,]  1.00  0.010 1e+00 -0.010   NA
[149,]  1.00  0.010 5e+00 -0.010   NA
[150,]  1.00  0.010 1e+01 -0.010   NA
[151,]  1.00  0.100 1e-02 -0.010   NA
[152,]  1.00  0.100 1e-01 -0.010   NA
[153,]  1.00  0.100 5e-01 -0.010   NA
[154,]  1.00  0.100 1e+00 -0.010   NA
[155,]  1.00  0.100 5e+00 -0.010   NA
[156,]  1.00  0.100 1e+01 -0.010   NA
[157,]  1.00  0.010 1e-02 -0.100   NA
[158,]  1.00  0.010 1e-01 -0.100   NA
[159,]  1.00  0.010 5e-01 -0.100   NA
[160,]  1.00  0.010 1e+00 -0.100   NA
[161,]  1.00  0.010 5e+00 -0.100   NA
[162,]  1.00  0.010 1e+01 -0.100   NA
[163,]  1.00  0.001 1e-02 -0.001   NA
[164,]  1.00  0.001 1e-01 -0.001   NA
[165,]  1.00  0.001 5e-01 -0.001   NA
[166,]  1.00  0.001 1e+00 -0.001   NA
[167,]  1.00  0.001 5e+00 -0.001   NA
[168,]  1.00  0.001 1e+01 -0.001   NA
[169,]  1.00 -0.010 1e-02 -0.010   NA
[170,]  1.00 -0.010 1e-01 -0.010   NA
[171,]  1.00 -0.010 5e-01 -0.010   NA
[172,]  1.00 -0.010 1e+00 -0.010   NA
[173,]  1.00 -0.010 5e+00 -0.010   NA
[174,]  1.00 -0.010 1e+01 -0.010   NA
[175,]  1.00 -0.100 1e-02 -0.010   NA
[176,]  1.00 -0.100 1e-01 -0.010   NA
[177,]  1.00 -0.100 5e-01 -0.010   NA
[178,]  1.00 -0.100 1e+00 -0.010   NA
[179,]  1.00 -0.100 5e+00 -0.010   NA
[180,]  1.00 -0.100 1e+01 -0.010   NA
[181,]  1.00 -0.010 1e-02 -0.100   NA
[182,]  1.00 -0.010 1e-01 -0.100   NA
[183,]  1.00 -0.010 5e-01 -0.100   NA
[184,]  1.00 -0.010 1e+00 -0.100   NA
[185,]  1.00 -0.010 5e+00 -0.100   NA
[186,]  1.00 -0.010 1e+01 -0.100   NA
[187,]  1.00 -0.001 1e-02 -0.001   NA
[188,]  1.00 -0.001 1e-01 -0.001   NA
[189,]  1.00 -0.001 5e-01 -0.001   NA
[190,]  1.00 -0.001 1e+00 -0.001   NA
[191,]  1.00 -0.001 5e+00 -0.001   NA
[192,]  1.00 -0.001 1e+01 -0.001   NA
[193,]  0.01  0.010 1e-03  0.010   NA
[194,]  0.01  0.010 1e-01  0.010   NA
[195,]  0.01  0.010 5e-01  0.010   NA
[196,]  0.10  0.010 1e-02  0.010   NA
[197,]  0.10  0.010 1e-01  0.010   NA
[198,]  0.10  0.010 5e-01  0.010   NA
[199,]  0.50  0.010 1e-02  0.010   NA
[200,]  0.50  0.010 1e-01  0.010   NA
[201,]  0.50  0.010 5e-01  0.010   NA
[202,]  0.01  0.100 1e-02  0.100   NA
[203,]  0.01  0.100 1e-01  0.100   NA
[204,]  0.01  0.100 5e-01  0.100   NA
[205,]  0.10  0.100 1e-02  0.100   NA
[206,]  0.10  0.100 1e-01  0.100   NA
[207,]  0.10  0.100 5e-01  0.100   NA
[208,]  0.50  0.100 1e-02  0.100   NA
[209,]  0.50  0.100 1e-01  0.100   NA
[210,]  0.50  0.100 5e-01  0.100   NA
[211,]  0.01  0.100 1e-02  0.010   NA
[212,]  0.01  0.100 1e-01  0.010   NA
[213,]  0.01  0.100 5e-01  0.010   NA
[214,]  0.10  0.100 1e-02  0.010   NA
[215,]  0.10  0.100 1e-01  0.010   NA
[216,]  0.10  0.100 5e-01  0.010   NA
[217,]  0.50  0.100 1e-02  0.010   NA
[218,]  0.50  0.100 1e-01  0.010   NA
[219,]  0.50  0.100 5e-01  0.010   NA
[220,]  0.01  0.100 1e-02  0.010   NA
[221,]  0.01  0.100 1e-01  0.010   NA
[222,]  0.01  0.100 5e-01  0.010   NA
[223,]  0.10  0.100 1e-02  0.010   NA
[224,]  0.10  0.100 1e-01  0.010   NA
[225,]  0.10  0.100 5e-01  0.010   NA
[226,]  0.50  0.100 1e-02  0.010   NA
[227,]  0.50  0.100 1e-01  0.010   NA
[228,]  0.50  0.100 5e-01  0.010   NA
[229,]  0.01 -0.010 1e-02 -0.010   NA
[230,]  0.01 -0.010 1e-01 -0.010   NA
[231,]  0.01 -0.010 5e-01 -0.010   NA
[232,]  0.10 -0.010 1e-02 -0.010   NA
[233,]  0.10 -0.010 1e-01 -0.010   NA
[234,]  0.10 -0.010 5e-01 -0.010   NA
[235,]  0.50 -0.010 1e-02 -0.010   NA
[236,]  0.50 -0.010 1e-01 -0.010   NA
[237,]  0.50 -0.010 5e-01 -0.010   NA
[238,]  0.01 -0.100 1e-02 -0.100   NA
[239,]  0.01 -0.100 1e-01 -0.100   NA
[240,]  0.01 -0.100 5e-01 -0.100   NA
[241,]  0.10 -0.100 1e-02 -0.100   NA
[242,]  0.10 -0.100 1e-01 -0.100   NA
[243,]  0.10 -0.100 5e-01 -0.100   NA
[244,]  0.50 -0.100 1e-02 -0.100   NA
[245,]  0.50 -0.100 1e-01 -0.100   NA
[246,]  0.50 -0.100 5e-01 -0.100   NA
[247,]  0.01 -0.100 1e-02 -0.010   NA
[248,]  0.01 -0.100 1e-01 -0.010   NA
[249,]  0.01 -0.100 5e-01 -0.010   NA
[250,]  0.10 -0.100 1e-02 -0.010   NA
[251,]  0.10 -0.100 1e-01 -0.010   NA
[252,]  0.10 -0.100 5e-01 -0.010   NA
[253,]  0.50 -0.100 1e-02 -0.010   NA
[254,]  0.50 -0.100 1e-01 -0.010   NA
[255,]  0.50 -0.100 5e-01 -0.010   NA
[256,]  0.01 -0.100 1e-02 -0.010   NA
[257,]  0.01 -0.100 1e-01 -0.010   NA
[258,]  0.01 -0.100 5e-01 -0.010   NA
[259,]  0.10 -0.100 1e-02 -0.010   NA
[260,]  0.10 -0.100 1e-01 -0.010   NA
[261,]  0.10 -0.100 5e-01 -0.010   NA
[262,]  0.50 -0.100 1e-02 -0.010   NA
[263,]  0.50 -0.100 1e-01 -0.010   NA
[264,]  0.50 -0.100 5e-01 -0.010   NA
[265,]  0.01  0.010 1e-02 -0.010   NA
[266,]  0.01  0.010 1e-01 -0.010   NA
[267,]  0.01  0.010 5e-01 -0.010   NA
[268,]  0.10  0.010 1e-02 -0.010   NA
[269,]  0.10  0.010 1e-01 -0.010   NA
[270,]  0.10  0.010 5e-01 -0.010   NA
[271,]  0.50  0.010 1e-02 -0.010   NA
[272,]  0.50  0.010 1e-01 -0.010   NA
[273,]  0.50  0.010 5e-01 -0.010   NA
[274,]  0.01  0.100 1e-02 -0.100   NA
[275,]  0.01  0.100 1e-01 -0.100   NA
[276,]  0.01  0.100 5e-01 -0.100   NA
[277,]  0.10  0.100 1e-02 -0.100   NA
[278,]  0.10  0.100 1e-01 -0.100   NA
[279,]  0.10  0.100 5e-01 -0.100   NA
[280,]  0.50  0.100 1e-02 -0.100   NA
[281,]  0.50  0.100 1e-01 -0.100   NA
[282,]  0.50  0.100 5e-01 -0.100   NA
[283,]  0.01  0.100 1e-02 -0.010   NA
[284,]  0.01  0.100 1e-01 -0.010   NA
[285,]  0.01  0.100 5e-01 -0.010   NA
[286,]  0.10  0.100 1e-02 -0.010   NA
[287,]  0.10  0.100 1e-01 -0.010   NA
[288,]  0.10  0.100 5e-01 -0.010   NA
[289,]  0.50  0.100 1e-02 -0.010   NA
[290,]  0.50  0.100 1e-01 -0.010   NA
[291,]  0.50  0.100 5e-01 -0.010   NA
[292,]  0.01  0.100 1e-02 -0.010   NA
[293,]  0.01  0.100 1e-01 -0.010   NA
[294,]  0.01  0.100 5e-01 -0.010   NA
[295,]  0.10  0.100 1e-02 -0.010   NA
[296,]  0.10  0.100 1e-01 -0.010   NA
[297,]  0.10  0.100 5e-01 -0.010   NA
[298,]  0.50  0.100 1e-02 -0.010   NA
[299,]  0.50  0.100 1e-01 -0.010   NA
[300,]  0.50  0.100 5e-01 -0.010   NA
[301,]  0.01 -0.010 1e-02  0.010   NA
[302,]  0.01 -0.010 1e-01  0.010   NA
[303,]  0.01 -0.010 5e-01  0.010   NA
[304,]  0.10 -0.010 1e-02  0.010   NA
[305,]  0.10 -0.010 1e-01  0.010   NA
[306,]  0.10 -0.010 5e-01  0.010   NA
[307,]  0.50 -0.010 1e-02  0.010   NA
[308,]  0.50 -0.010 1e-01  0.010   NA
[309,]  0.50 -0.010 5e-01  0.010   NA
[310,]  0.01 -0.100 1e-02  0.100   NA
[311,]  0.01 -0.100 1e-01  0.100   NA
[312,]  0.01 -0.100 5e-01  0.100   NA
[313,]  0.10 -0.100 1e-02  0.100   NA
[314,]  0.10 -0.100 1e-01  0.100   NA
[315,]  0.10 -0.100 5e-01  0.100   NA
[316,]  0.50 -0.100 1e-02  0.100   NA
[317,]  0.50 -0.100 1e-01  0.100   NA
[318,]  0.50 -0.100 5e-01  0.100   NA
[319,]  0.01 -0.100 1e-02  0.010   NA
[320,]  0.01 -0.100 1e-01  0.010   NA
[321,]  0.01 -0.100 5e-01  0.010   NA
[322,]  0.10 -0.100 1e-02  0.010   NA
[323,]  0.10 -0.100 1e-01  0.010   NA
[324,]  0.10 -0.100 5e-01  0.010   NA
[325,]  0.50 -0.100 1e-02  0.010   NA
[326,]  0.50 -0.100 1e-01  0.010   NA
[327,]  0.50 -0.100 5e-01  0.010   NA
[328,]  0.01 -0.100 1e-02  0.010   NA
[329,]  0.01 -0.100 1e-01  0.010   NA
[330,]  0.01 -0.100 5e-01  0.010   NA
[331,]  0.10 -0.100 1e-02  0.010   NA
[332,]  0.10 -0.100 1e-01  0.010   NA
[333,]  0.10 -0.100 5e-01  0.010   NA
[334,]  0.50 -0.100 1e-02  0.010   NA
[335,]  0.50 -0.100 1e-01  0.010   NA
[336,]  0.50 -0.100 5e-01  0.010   NA
>     
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

returns the null starting values used in model.test.sisters

Description

Usage

Arguments

Details

Value

Author(s)

References

See Also

Examples

Results