plot.indelmiss {indelmiss}

Plot parameter estimates from the model fit

Description

Plotting command for use on an object of class "indelmiss". Will draw two plots: one with the estimates for the rates and the other for the "missingness" parameter. plot.indelmiss() calls plotp and plotrates.

Usage

## S3 method for class 'indelmiss'
plot(x, model = NULL, ci = TRUE, cil = 95, ...)

Arguments

x

An object of class "indelmiss".

model

One of "M1", "M2", "M3", or "M4".

ci

TRUE plots confidence intervals around the estimates.

cil

Confidence interval level.

...

Any further commands to plot.

Value

Draws two plots: one with the estimates for the rates and the other for the "missingness" parameter.

Author(s)

Utkarsh J. Dang and G. Brian Golding

[e-mail]

See Also

See also indelrates, plotrates and plotp.

Examples

indel <- indelrates(datasource = "simulation", seed = 1, taxa = 5,
             mu = 1, nu = 5, phyl = 5000,  pmiss = 0, toi = 1, 
             bgtype="ancestornodes", bg = c(7, 9), 
             zerocorrection = TRUE, rootprob="maxlik",  
             modelnames = c("M1", "M2", "M3", "M4"),
             optmethod = "nlminb")
print(indel)
plot(indel, model="M4")