List of 58 matrices of model seeding parameters.

Description

The performance of modFit (package FME) with the pseudorandom parameter search algorithm (package FME, pseudoOptim) used to estimated model parameter values, is sensitive to the choice of initial seeding values. We have provided the fitted parameters returned from our simulations to be used as initial seeding parameters.

Usage

data(ParamSeeds)

Format

A list of 58 matrices. Each matrix has columns corresponding to the parameters of the matching model in ModelSet. Each row is set of potential seeding parameters

Details

For each model, each initial parameter guess (i.e. each row of the model matrix in ParamRanges) is evaluated by to modCost. The parameter guess returning the lowest cost is used as the seeding value in modFit. If the user wishes to input alternative initial seeding parameter values, then for each model and parameter, all values must be finite (not NA or NaN), and within the upper and lower bounds set in ParamRanges. Column names must match parameter names (params) in the corresponding model in ModelSet (i.e. models argument in DivEMaster).

References

Laydon, D., Melamed, A., Sim, A., Gillet, N. A., Sim, K., Darko, S., Kroll, S., Douek, D. C., Price, D., Bangham, C. R. M., Asquith, B., Quantification of HTLV-1 clonality and TCR diversity, PLOS Comput. Biol. 2014

Examples

data(ParamSeeds)

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(DivE)
Loading required package: deSolve

Attaching package: 'deSolve'

The following object is masked from 'package:graphics':

    matplot

Loading required package: FME
Loading required package: rootSolve
Loading required package: coda
Loading required package: rgeos
rgeos version: 0.3-19, (SVN revision 524)
 GEOS runtime version: 3.5.0-CAPI-1.9.0 r4084 
 Linking to sp version: 1.2-3 
 Polygon checking: TRUE 

Loading required package: sp
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/DivE/ParamSeeds.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ParamSeeds
> ### Title: List of 58 matrices of model seeding parameters.
> ### Aliases: ParamSeeds
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ParamSeeds)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>