Last data update: 2014.03.03

R: Graph genomic clines fit to data
Cline.plotR Documentation

Graph genomic clines fit to data

Description

A quick way to summarize and view the results of Cline.fit

Usage

Cline.plot(cfit)

Arguments

cfit

An object: the output of Cline.fit.

Details

Creates up to sixteen graphs, depending on which models are fit to the data. For each fitted model, fitted clines are graphed first. For two-parameter models, a bivariate graph of parameter estimates is plotted next (this is left blank for four-parameter models). Finally, a Q-Q plot of squared Mahalanobis distances vs. CHi-squared quantiles is graphed. Putative outlier markers are indicated in red.

Author(s)

Benjamin M. Fitzpatrick

References

Fitzpatrick, B. M. 2012. Alternative forms for genomic clines. In prep

See Also

See gcline.fn for the basic fitting function. Cline.plot provides an easy way to visualize the output of Cline.fit.

Examples

	
data(Bluestone)
BS.fit <- Cline.fit(Bluestone[,1:12],model=c("logit.logistic","Barton"))
Cline.plot(BS.fit)

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(HIest)
Loading required package: nnet
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/HIest/Cline.plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Cline.plot
> ### Title: Graph genomic clines fit to data
> ### Aliases: Cline.plot
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> 	
> data(Bluestone)
> BS.fit <- Cline.fit(Bluestone[,1:12],model=c("logit.logistic","Barton"))

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> Cline.plot(BS.fit)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>