plotGradient.ci: Plot evolutionary rates and their confidence regions across a...

In EvoRAG: Evolutionary Rates Across Gradients

Description

Takes the output from bootstrap.test for the BM_linear model and plots how evolutionary rates and their confidence regions change across the gradient.

Usage

plotGradient.ci(bootstraps1, bootstraps2=c("FALSE"), Lmin, Lmax, ylim, 
   MLE = FALSE, MLE1, MLE2, xlab="Gradient") 

Arguments

bootstraps1	the raw bootstraps output by bootstrap.test
bootstraps2	same as bootstraps1, but for an optional second dataset.
Lmin	minimum gradient value for graph
Lmax	maximum gradient value for graph
ylim	maximum y-axis value
MLE	Logical. If MLE=TRUE, then the maximum likelihood values are plotted. If MLE=FALSE, then the mean bootstrap values are plotted.
MLE1	A list of the maximum likelihood parameter values for dataset 1
MLE2	A list of the maximum likelihood parameter values for dataset 2, if a second dataset provided
xlab	A title for the x-axis.

Details

Currently, only works for the BM_linear model.

Value

A plot of the bootstrap 95

Author(s)

Jason T. Weir

See Also

bootstrap.test

Examples

## Not run: 
  ###simulate data
  set.seed(seed = 3)
  TIME = runif(n=200, min = 0, max = 10)
  GRAD = runif(n=200, min = 0, max = 60)
  DATA1 <- sim.sisters(GRAD, TIME, parameters = c(0.1, 0.065), model=c("BM_linear"))

  ###Find the MLE of model parameters
  RESULT <- model.test.sisters(DIST=DATA1[,3], TIME=DATA1[,2], 
     GRAD=DATA1[,1], models=c("BM_linear"))
  intercept <- as.numeric(RESULT[5,1])
  slope <- as.numeric(RESULT[6,1])
  model = c("BM_linear")
  parameters=c(intercept, slope)

  ###Run the bootstrap
  RR <- bootstrap.test(DIST=DATA1[,3], TIME=DATA1[,2],
     GRAD=DATA1[,1], model = "BM_linear", parameters, meserr1=0, 
	 meserr2=0, N = c(100))
  summary <- RR$summary #to show only the summary. 
  bootstraps <- RR$bootstraps #to obtain the bootstraps
  
  ###Plot data
  plotGradient.ci(bootstraps1=bootstraps, 
     bootstraps2= c("FALSE"), Lmin=0, Lmax=60, ylim=c(0,10), 
     MLE=TRUE, MLE1=c(0.1, 0.065), MLE2=c(0,0), xlab="Latitude")
  
## End(Not run)#end dontrun

EvoRAG documentation built on May 2, 2019, 8:57 a.m.