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Maths

R, RCommander and RStudio

General information

R 3.3.3 is a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.

RStudio an RCommander are a graphical front ends for R.

Installed packages

abind, ape, biomformat, cummeRbund, DCGL, DESeq2, DEXSeq, e1071, edgeR, FactoMineR, GEOquery, lavaan, metagenomeSeq, mnormt, optparse, psych, randomForest, Rcmdr, RColorBrewer, ReactomePA, RUVSeq, vegan, WGCNA, xlsx.

Please, ask if you need any more.

How to use it

To use R in the queue scripts execute:

/software/bin/R CMD BATCH  R-input-file.R

to execute RStudio you must connect to Txinparta or Katramila with X2Go and execute

rstudio

to execute RCommander you must connect to Txinparta or Katramila with X2Go and execute R. Then inside R load

library(Rcmdr)

More information

R web page.

rstudio web page.

R-3.2

Información general

R is ‘GNU S’, a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.

Paquetes Instalados

lavaan, mnormt, psych, Rcmdr, abind, e1071, xlsx, biocLite(),FactoMineR

Si se requiere alguno más, por favor, haznoslo saber.

Cómo usar

Para usar R-3.2  ejecutar:

/software/R-3.2.0/bin/R CMD BATCH input.R

Más información

http://cran.r-project.org/

CPLEX

Información general

CPLEX proporciona algoritmos matemáticos robustos, permite resolver problemas con millones de variables y restricciones. Versión 12.6.3.

Características

  • Automatic and dynamic algorithm parameter control
    IBM ILOG CPLEX Optimizer automatically determines “smart” settings for a wide range of algorithm parameters, usually resulting in optimal linear programming solution performance. However, for a more hands-on approach, dozens of parameters may be manually adjusted, including algorithmic strategy controls, output information controls, optimization duration limits, and numerical tolerances.
  • Fast, automatic restarts from an advanced basis
    Large problems can be modified, and then solved again in a fraction of the original solution time.
  • A variety of problem modification options, such as:
    – The ability to add and delete variables
    – The ability to add and delete constraints
    – The ability to modify objective, right-hand side, bound and matrix coefficients
    – The ability to change constraint types
  • A wide variety of input/output options, such as:
    – Problem files: read/write MPS files, IBM ILOG CPLEX Optimizer LP files, MPS basis and revise files, binary problem/basis files
    – Log files: session information and various solution reports
    – Solution files: ASCII and binary solution files
    – IBM ILOG CPLEX Optimizer messages: Each message type (such as RESULTS, WARNINGS or ERRORS) can be directed to specified files, or completely suppressed.
  • Post solution information and analysis, including:
    – Objective function value
    – Solution variable and slack values
    – Constraint dual values (shadow prices)
    – Variable reduced costs
    – Right-hand side, objective function, and bound sensitivity ranges
    – Basic variables and constraints
    – Solution infeasibilities (if any exist)
    – Iteration/node count, solution time, process data
    – Infeasibility (IIS) finder for diagnosing problem infeasibilities
    – Feasibility optimizer for automatic correction of infeasible models

Cómo usar

Para usar CPLEX ejecutar:

/software/bin/cplex/cplex

Benchmark

Hemos realizado un pequeño benchmark usando COIN-OR, ver la página de COIN-OR.

Más información

Página web de CPLEX.

Matplotlib

Información general

Librerías para cálculo matemático con Python. Se han instalado también las librerías numphy y el intérprete ipython.

Se ha requerido recompilar python, se deben usar ejecutando

/software/bin/python

/software/bin/ipython

Más información

Página web de Matplotlib.

Página web de Numpy.

Página web de ipython.

Grace

Información general

Está instalada la versión 5.1.19. Grace es un herramienta WYSIWYG (What you see is what you get, es decir, Lo que Ves es lo que Consigues) para hacer gráficos en dos dimensiones de datos numéricos.

Para ejecutarlo hay que utilizar el comando:

xmgrace

Más información

Más información y documentación en la página web de Grace.

Octave

Versión 3.2.3 en Itanium, Opteron y Péndulo y 3.2.4 en Xeon del programa matemático de cálculo numérico.
(más…)

scilab