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Rsolnp specifications

Information


Unique identifier OMICS_15890
Name Rsolnp
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 1.16
Stability Stable
Requirements
stats, parallel, R(≥2.10.0), truncnorm
Source code URL https://cran.r-project.org/src/contrib/Rsolnp_1.16.tar.gz
Maintained Yes

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Maintainer


  • person_outline Alexios Ghalanoss

Rsolnp citations

 (5)
library_books

On the testing of Hardy‐Weinberg proportions and equality of allele frequencies in males and females at biallelic genetic markers

2017
Genet Epidemiol
PMCID: 5813254
PMID: 29071737
DOI: 10.1002/gepi.22079

[…] g coefficients. No closed form expressions for the ML estimators of the parameters were found. ML estimators were therefore obtained by maximizing the likelihood function numerically, using R‐package Rsolnp (Ghalanos & Theussl, ). Maximization respected the nonlinear constraint −min(pA,pB)/(1−min(pA,pB))≤ρm≤1 for males; the analogous constraint was used for females with ρm replaced by ρf. The LR s […]

library_books

Evaluation of the Effect of a Continuous Treatment: A Machine Learning Approach with an Application to Treatment for Traumatic Brain Injury

2015
PMCID: 4744663
PMID: 26059721
DOI: 10.1002/hec.3189

[…] ator as L(r^j)=1V∑v=1V1nv∑i∈v−logr^j,v¯(ti,xi)We consider estimator candidates of the form r^α(t,x)=∑jαjr^j(t,x)We choose α to minimise L(r^α) with the constraint that α j≥0 and ∑jαj=1. We use the ‘rsolnp’ package in R to perform the optimisation (Ghalanos and Theussl, ). […]

library_books

Assessment of Weighted Quantile Sum Regression for Modeling Chemical Mixtures and Cancer Risk

2015
Cancer Inform
PMCID: 4431483
PMID: 26005323
DOI: 10.4137/CIN.S17295

[…] the nonlinear function in equation , subject to the linear constraint ∑i=1cwi=1 and the bounds wi∈[0,1]. The nonlinear optimization was performed in R using the function solnp found in the package Rsolnp. The algorithm employed belongs to the class of indirect solvers and implements the augmented Lagrange multiplier method with a sequential quadratic programing interior algorithm.For each of th […]

library_books

Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle

2014
Mol Syst Biol
PMCID: 4300491
PMID: 25527639
DOI: 10.15252/msb.20145654

[…] nfortunately, these constraints define a non-convex optimization domain. Still, powerful numerical solvers for concave functions exist. In our case, we used the ipopt solver (Wächter & Biegler, ) and Rsolnp (version 1.14, http://cran.r-project.org/src/contrib/Archive/Rsolnp/Rsolnp_1.14.tar.gz). Transition probabilities might become very small or even 0, which may cause problems for the optimizatio […]

library_books

Confidence Intervals for Population Allele Frequencies: The General Case of Sampling from a Finite Diploid Population of Any Size

2014
PLoS One
PMCID: 3897575
PMID: 24465792
DOI: 10.1371/journal.pone.0085925

[…] study, the “Minimize” and “Maximize” functions in Mathematica v5.0 are used to compute and , but corresponding functions may be used in other software packages, such as the “solnp” function in the “Rsolnp” R package. A % CI for can then be defined as the interval . Supporting Webpage 1 provides Mathematica code that can be used to calculate for the butterfly case study examined (http://rpubs.c […]

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