Last data update: 2014.03.03

R: Generates a random sample of the unknowns for a linear...
 Xsample R Documentation

## Generates a random sample of the unknowns for a linear inverse problem

### Description

Given an inverse input list, randomly samples the unknowns, using an MCMC method

### Usage

```Xsample(lim, exact = NULL, ...)
```

### Arguments

 `lim ` a list that contains the linear inverse model specification, as generated by function `setup.limfile`. `exact ` if not `NULL`, a vector containing the numbers of the equations to be solved exactly; if `NULL`, all equations are considered exact. `... ` extra parameters passed to function `xsample` from package`limSolve`.

### Details

For overdetermined LIM problems, the inverse equations may be split up in equations which have to be exactly met and other equations which have to be approximated.

`exact` is a vector with the exact equations

The default settings of `xsample` will often not do. For instance, the default consists of 3000 iterations (`iter`) and a jump length of `jmp` of 0.1. You may need to increase one of those to ensure that the entire solution space has been adequately sampled.

### Value

a 2-columned vector containing the minimum (column 1) and maximum (column 2) of each unknown.

### Author(s)

Karline Soetaert <karline.soetaert@nioz.nl>

### References

Van den Meersche K, Soetaert K, Van Oevelen D (2009). xsample(): An R Function for Sampling Linear Inverse Problems. Journal of Statistical Software, Code Snippets, 30(1), 1-15.

`Varranges` which estimates the ranges of inverse variables

`Plotranges` to plot the ranges

function `xsample` from package`limSolve`

### Examples

```# sample solution space
xs <- Xsample(LIMRigaAutumn, iter = 500, jmp = 5)
# remove flows that are invariable (sd=0)
xs <- xs[ ,-which(apply(xs, 2, sd) == 0 )]
#pairs plot
pairs(xs, gap = 0, pch = ".", upper.panel = NULL)
```

### 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.
'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(LIM)
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/LIM/Xsample.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Xsample
> ### Title: Generates a random sample of the unknowns for a linear inverse
> ###   problem
> ### Aliases: Xsample
> ### Keywords: optimize utilities
>
> ### ** Examples
> # sample solution space
>   xs <- Xsample(LIMRigaAutumn, iter = 500, jmp = 5)
>   # remove flows that are invariable (sd=0)
>   xs <- xs[ ,-which(apply(xs, 2, sd) == 0 )]
>   #pairs plot
>   pairs(xs, gap = 0, pch = ".", upper.panel = NULL)
>
>
>
>
>
> dev.off()
null device
1
>

```