Monotonic Spline

Description

Fits a monotonic cubic spline to the data provided, using the penalized constrained least squares method from the mgcv package.

Usage

makespline(x, y, newX=NULL, nKnots = 6, lower_bound = 10^-3)

Arguments

Details

This uses the pcls function from the mgcv package to produce the fit. The montonicity constraint is enforced using mono.con from the same package. The lower_bound argument is only used on the rare occasions when the fitting function becomes negative or arbitrarily close to zero. If this does occur lower_bound is added everywhere to ensure that no one length is given essentially infinite weighting.

Value

Returns a vector of values containing the value of the fit at each point newX.

Author(s)

Matthew D. Young myoung@wehi.edu.au.

References

Package mgcv. In particular this function is a modification of an example given in the man page for pcls.

Examples

y <- c( rbinom(50,p=0.4,size=1), rbinom(50,p=0.6,size=1) )
x <- 1:100
plot(x,y)
p <- makespline(x,y)
lines(x,p)

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(goseq)
Loading required package: BiasedUrn
Loading required package: geneLenDataBase

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/goseq/makespline.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makespline
> ### Title: Monotonic Spline
> ### Aliases: makespline
> 
> ### ** Examples
> 
> 
> y <- c( rbinom(50,p=0.4,size=1), rbinom(50,p=0.6,size=1) )
> x <- 1:100
> plot(x,y)
> p <- makespline(x,y)
Warning message:
In pcls(G) : initial point very close to some inequality constraints
> lines(x,p)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>