TreEvo--abc for comparative methods

Source: R/treevo-package.R

A package for applying Approximate Bayesian Computation to estimating parameters of trait evolution in comparative analyses.

Details

Package:TreEvo
Type:Package
Version:0.3.3
Date:2012-07-02
License:GPL

Author

Brian O'Meara, Barb L. Banbury, David W. Bapst

Maintainer: David Bapst <dwbapst@gmail.com>

Examples


# example analysis, using data simulated with TreEvo

# \donttest{

set.seed(1)
# let's simulate some data, and then try to infer the parameters using ABC
# get a 20-taxon coalescent tree
tree <- rcoal(20)
# get realistic edge lengths
tree$edge.length <- tree$edge.length*20

genRateExample <- c(0.01)
ancStateExample <- c(10)

#Simple Brownian motion
simCharExample <- doSimulation(
    phy = tree, 
    intrinsicFn = brownianIntrinsic, 
    extrinsicFn = nullExtrinsic, 
    startingValues = ancStateExample, #root state
    intrinsicValues = genRateExample, 
    extrinsicValues = c(0), 
    generation.time = 100000
    )

#> Warning: You have only 22 timeSteps on the shortest branch in this dataset
#>  but should probably have a lot more if you expect change on this branch.
#>  Please consider decreasing timeStep to no more than 0.0016

# NOTE: the example analyses below sample too few particles, 
    # over too few steps, with too few starting simulations
    # - all for the sake of examples that reasonably test the functions

# Please set these values to more realistic levels for your analyses!

resultsBMExample <- doRun_prc(
  phy = tree, 
  traits = simCharExample, 
  intrinsicFn = brownianIntrinsic, 
  extrinsicFn = nullExtrinsic, 
  startingPriorsFns = "normal", 
  startingPriorsValues = list(c(mean(simCharExample[, 1]), sd(simCharExample[, 1]))), 
  intrinsicPriorsFns = c("exponential"), 
  intrinsicPriorsValues = list(10), 
  extrinsicPriorsFns = c("fixed"), 
  extrinsicPriorsValues = list(0), 
  generation.time = 100000, 
  nRuns = 2, 
  nStepsPRC = 3, 
  numParticles = 20, 
     nInitialSimsPerParam = 10, 
  jobName = "examplerun_prc", 
  stopRule = FALSE, 
  multicore = FALSE, 
  coreLimit = 1
  )

#> The effective timeStep for this tree will be 0.0035,
#>      as a proportion of tree height (root to furthest tip)...
#> Rescaling edge lengths relative to maximum tip-to-root distance...
#> The smallest edge length on the input tree is 0.0028
#>    (This is 79000 in the same TreeYears units
#>       as used for the input generation.time ( = 1e+05))
#> Warning: Tree has rescaled branches shorter than generation.time/TreeYears
#>     No trait evolution will be simulated on these branches and
#>     thus ML summary statistic functions may fail or produce unexpected results.
#> Given generation time, a total of 1387 generations are
#>      expected to occur over this tree
#> Number of initial simulations to be performed (nInitialSims) not given
#>     Number of initial simulations will thus be the
#>     product of the number of free parameters multiplied by 10
#>     ( = 20 initial simulations)
#> Beginning PRC Run 1 out of a total of 2...
#> Number of initial simulations set to 20
#> Doing initial simulations...
#> Initial simulations took 11.931 seconds
#> Finding distribution of distances...
#> Beginning partial rejection control algorithm...
#> 
#> STARTING DATA GENERATION STEP 1
#> Successes   Attempts   Distance   starting_1  intrinsic_1  
#> 1           40         240        11         0.1                   
#> 2           40         260        8.8         0.086                   
#> 3           40         240        10         0.058                   
#> 4           40         170        9         0.049                   
#> 5           40         68        9.2         0.019                   
#> 6           40         250        9.1         0.078                   
#> 7           40         71        9.4         0.023                   
#> 8           40         84        9.9         0.02                   
#> 9           40         200        10         0.08                   
#> 10           40         120        11         0.025                   
#> 11           40         97        10         0.033                   
#> 12           40         260        10         0.086                   
#> 13           40         210        9.6         0.055                   
#> 14           40         110        11         0.031                   
#> 15           40         90        9.8         0.008                   
#> 16           40         190        9.8         0.062                   
#> 17           40         220        11         0.051                   
#> 18           40         76        9.4         0.0079                   
#> 19           40         200        9.9         0.069                   
#> 20           40         160        9.8         0.062                   
#> 21           40         12        8.8         0.013                   
#> 22           40         270        10         0.12                   
#> 23           40         200        10         0.047                   
#> 24           40         260        9.4         0.1                   
#> 25           40         240        9.8         0.091                   
#> 26           40         100        11         0.019                   
#> 27           40         38        9.6         0.027                   
#> 
#> STARTING DATA GENERATION STEP 2
#> Successes   Attempts   Distance   starting_1  intrinsic_1  
#> 1           40         190        10         0.053                   
#> 2           40         190        11         0.049                   
#> 3           40         160        11         0.055                   
#> 4           40         180        9.9         0.043                   
#> 5           40         100        10         0.03                   
#> 6           40         110        8.9         0.023                   
#> 7           40         66        9.8         0.019                   
#> 8           40         170        9.6         0.059                   
#> 9           40         150        10         0.037                   
#> 10           40         190        10         0.062                   
#> 11           40         170        10         0.055                   
#> 12           40         150        11         0.045                   
#> 13           40         100        9.5         0.0043                   
#> 14           40         120        11         0.05                   
#> 15           40         180        10         0.066                   
#> 16           40         110        9.7         0.029                   
#> 17           40         12        9.9         0.015                   
#> 18           40         23        8.8         0.012                   
#> 19           40         30        9.9         0.016                   
#> 20           40         200        10         0.056                   
#> 21           40         150        11         0.059                   
#> 22           40         74        8.7         0.021                   
#> 23           40         120        11         0.047                   
#> 24           40         190        9.6         0.039                   
#> 25           40         70        9.5         0.0063                   
#> 
#> STARTING DATA GENERATION STEP 3
#> Successes   Attempts   Distance   starting_1  intrinsic_1  
#> 1           48         120        11         0.046                   
#> 2           48         120        11         0.051                   
#> 3           48         82        10         0.039                   
#> 4           48         15        8.7         0.013                   
#> 5           48         32        9.8         0.018                   
#> 6           48         75        10         0.017                   
#> 7           48         32        10         0.0098                   
#> 8           48         46        8.8         0.0082                   
#> 9           48         61        8.9         0.018                   
#> 10           48         19        10         0.01                   
#> 11           48         78        9.3         0.022                   
#> 12           48         33        9.6         0.015                   
#> 13           48         100        8.9         0.034                   
#> 14           48         110        10         0.0041                   
#> 15           48         110        9.6         0.054                   
#> 16           48         110        9.6         0.031                   
#> 17           48         140        9.8         0.037                   
#> 18           48         29        9.9         0.017                   
#> 19           48         40        8.6         0.019                   
#> 20           48         110        9.7         0.035                   
#> 21           48         120        10         0.028                   
#> 22           48         56        9.9         0.0088                   
#> Collection of simulation particles under PRC completed in 29 seconds...
#> Run finished...
#> ...
#> 
#> Beginning PRC Run 2 out of a total of 2...
#> Number of initial simulations set to 20
#> Doing initial simulations...
#> Initial simulations took 12.287 seconds
#> Finding distribution of distances...
#> Beginning partial rejection control algorithm...
#> 
#> STARTING DATA GENERATION STEP 1
#> Successes   Attempts   Distance   starting_1  intrinsic_1  
#> 1           40         320        8.9         0.12                   
#> 2           40         3        9         0.013                   
#> 3           40         160        9.2         0.065                   
#> 4           40         24        9.4         0.014                   
#> 5           40         74        9.1         0.024                   
#> 6           40         100        8.8         0.04                   
#> 7           40         67        9.1         0.0056                   
#> 8           40         230        9.3         0.078                   
#> 9           40         200        9.1         0.056                   
#> 10           40         50        9.9         0.015                   
#> 11           40         300        9.5         0.093                   
#> 12           40         340        10         0.16                   
#> 13           40         310        9.2         0.14                   
#> 14           40         8.7        9         0.012                   
#> 15           40         26        9.9         0.021                   
#> 16           40         38        11         0.013                   
#> 17           40         300        10         0.084                   
#> 18           40         86        10         0.025                   
#> 19           40         14        10         0.013                   
#> 20           40         110        9.2         0.022                   
#> 21           40         3.7        10         0.0099                   
#> 22           40         280        10         0.15                   
#> 23           40         70        10         0.018                   
#> 24           40         170        10         0.057                   
#> 25           40         53        9.7         0.02                   
#> 26           40         16        11         0.017                   
#> 
#> STARTING DATA GENERATION STEP 2
#> Successes   Attempts   Distance   starting_1  intrinsic_1  
#> 1           40         190        9.1         0.0019                   
#> 2           40         160        10         0.037                   
#> 3           40         160        9.5         0.05                   
#> 4           40         160        9.3         0.043                   
#> 5           40         160        9.1         0.046                   
#> 6           40         35        9.6         0.019                   
#> 7           40         46        9.4         0.016                   
#> 8           40         47        10         0.019                   
#> 9           40         120        9.9         0.04                   
#> 10           40         6.4        10         0.0094                   
#> 11           40         66        10         0.024                   
#> 12           40         73        10         0.022                   
#> 13           40         210        8.8         0.048                   
#> 14           40         76        9.4         0.024                   
#> 15           40         130        9.9         0.0029                   
#> 16           40         94        10         0.0041                   
#> 17           40         140        9.4         0.0027                   
#> 18           40         9.6        8.8         0.015                   
#> 19           40         44        9.1         0.018                   
#> 20           40         68        8.7         0.0062                   
#> 21           40         32        10         0.0084                   
#> 22           40         140        9.1         0.035                   
#> 23           40         96        11         0.031                   
#> 24           40         41        9.3         0.0067                   
#> 25           40         170        8.7         0.051                   
#> 26           40         210        11         0.064                   
#> 27           40         170        9.1         0.0026                   
#> 28           40         37        9.6         0.0097                   
#> 29           40         5        9.1         0.015                   
#> 30           40         130        8.9         0.0049                   
#> 31           40         110        11         0.024                   
#> 32           40         180        8.8         0.043                   
#> 
#> STARTING DATA GENERATION STEP 3
#> Successes   Attempts   Distance   starting_1  intrinsic_1  
#> 1           40         160        9.2         0.068                   
#> 2           40         99        9.4         0.027                   
#> 3           40         49        10         0.0062                   
#> 4           40         34        9.2         0.016                   
#> 5           40         28        9.1         0.021                   
#> 6           40         17        9.3         0.0094                   
#> 7           40         61        10         0.02                   
#> 8           40         77        9.9         0.0047                   
#> 9           40         100        9.2         0.029                   
#> 10           40         140        9.6         0.049                   
#> 11           40         92        9.2         0.032                   
#> 12           40         43        9         0.0081                   
#> 13           40         33        8.8         0.021                   
#> 14           40         34        10         0.015                   
#> 15           40         93        9.2         0.028                   
#> 16           40         93        9.3         0.0047                   
#> 17           40         44        9.1         0.017                   
#> 18           40         120        10         0.03                   
#> 19           40         30        10         0.012                   
#> 20           40         130        10         0.036                   
#> 21           40         30        11         0.015                   
#> 22           40         56        9         0.027                   
#> 23           40         13        10         0.015                   
#> 24           40         46        10         0.019                   
#> 25           40         150        8.7         0.064                   
#> 26           40         10        9.1         0.018                   
#> 27           40         160        9.4         0.052                   
#> 28           40         150        10         0.03                   
#> 29           40         43        10         0.0085                   
#> 30           40         110        9.4         0.03                   
#> 31           40         46        9.6         0.018                   
#> 32           40         95        10         0.0048                   
#> 33           40         140        10         0.03                   
#> 34           40         86        9.4         0.026                   
#> 35           40         25        9.7         0.0096                   
#> 36           40         130        10         0.0037                   
#> 37           40         130        9.5         0.03                   
#> 38           40         63        10         0.028                   
#> Collection of simulation particles under PRC completed in 24 seconds...
#> Run finished...
#> ...
#> 
#> Function completed in 180 seconds.
# }