domingo, 30 de enero de 2011

Paquetes de Interés común y especifico en R....

Me he tomado la tarea de revisar la lista de paquetes (2784 paquetes!!) que actualmente se pueden utilizar en R y ser descargados por CRAN.

Los paquetes que les muestro en esta lista son básicos y  pueden ser utilizados en muchos ámbitos y en muchas disciplinas..Pero como mi formación esta interesada en la biología, también liste los paquetes que considero podrían llegar a ser de interés para muchos biólogos y estudiantes...

Los paquetes de presentan por listas de temas específicos; el nombre de cada paquete se muestra con un asterisco "*" y en el siguiente reglón, debajo del nombre se presenta la descripción de dicho paquete... 


Areal Interpolation for GIS data

CShapes Dataset and Utilities

Spatial modelling for distance sampling data

ArcGIS Geoprocessing in R via Python


Anderson-Moore Algorithm

Algorithmic Experimental Design

CGI Programming in R

Design Patterns in R to build reusable object-oriented software

Various R programming tools

The java ncbi interface to R

R/GNU Linear Programming Kit Interface

Functions and Datasets for "Introduction to Scientific Programming and Simulation Using R"


The Analysis of Biological Data

A collection of statistical tools for biologists

Provides data sets for Introduction to Statistical Data Analysis for the Life Sciences

An R package for biostatistics, public policy, and law

Statistical Methods for Quality Science


Combine multi-dimensional arrays

Tools for microarray data analysis

csv import, csv export, garbage collection,string matching and passing by reference

A Handbook of Statistical Analyses Using R (2nd Edition)

Mailmerge using R, LaTeX, and the Web

Mapping dependencies among R packages

Integration of R and Excel, (use R in Excel, read/write XLS files)

R Commander

Graphically export output to LaTeX or HTML

R to LaTeX and HTML

relax – R Editor for Literate Analysis and lateX

Generate LaTeX tables of descriptive statistics

send email from inside R

Export tables to LaTeX or HTML


Tools for testing and improving accuracy of statistical results

Another Multidimensional Analysis Package

Simple and Canonical Correspondence Analysis

Basic Statistics and Data Analysis

Significance Tests for Canonical Correlation Analysis (CCA)

Generalized Canonical Discriminant Analysis

Canonical Non-symmetrical Correspondence Analysis in R

Permutation Tests of Correlation with Repeated Measurements

Conditionally Specified Logistic Regression

Functions useful in the design and ANOVA of experiments

Descriptive statistics

Nonparametric Analysis of Covariance

Fifty-fifty MANOVA

Tools for Multivariate Nonparametrics

Introduction to Probability and Statistics Using R

Introductory Statistics with R

Inference in Logistic Regression

Lassoed principal components for testing significance of features

Generalized Shapiro-Wilk test for multivariate normality

Tests for Normality


Tools for evaluating collinearity

Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling

Using GUIs to help teach statistics to non-statistics students


Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences

ade4 Tcl/Tk Graphical User Interface

Analysis of habitat selection by animals

Analogue and weighted averaging methods for palaeoecology

Analysis of Overdispersed Data

Brownian bridge movement model for estimating the movement path of an animal using discrete 
location data

Biodemography functions

GUI for biodiversity and community ecology analysis

Predict environmental conditions from biological observations

Analyze biotic homogenization of landscapes

Forecasting mortality, fertility, migration and population data

Species distribution modeling

Dispersion models

R Package for Ecological Inference in 2x2 Tables

Dissimilarity-based functions for ecological analysis

"A practical guide to ecological modelling - using R as a simulation platform"

Ecological regression using aggregate and individual data

Palaeoecological and Palaeogeographical Analysis Tools

Ordination and Multivariate Analysis for Ecology

Multivariate Data Handling in Ecology and Biogeography

Analysis of Mark-Recapture data

statistical methods for analysing multivariate abundance data

Paleoecological Analysis

Package for Analysis of Space-Time Ecological Series

Data analysis in ecology

Functions and data for the forthcoming, A Primer of Ecology with R

R x C Ecological Inference With Optional Incorporation of Survey Information

A package for easy generation of biodiversity (species richness) or life-history traits maps using species geographical ranges

Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises

A Program to Estimate Animal Abundance and Density using Spatially-Explicit Capture-Recapture

Statistical Analysis for Environmental Data

Models and Data Sets for the Study of Species-Area Relationships

Simultaneous Confidence Intervals and Adjusted p–values for Diversity Indices

Simulation of ecological (and other) dynamic systems

SPecies Association Analysis

Interface between GRASS 6+ geographical information system and R

Community Ecology Package


adegenet: a R package for the multivariate analysis of genetic markers

A fast, unbiased and exact allelic exact test

Causal Genetic Analysis

Change point detection in genomic sequences

Data Sets and Functions, for demonstrations with expression arrays and gene sequences

Data Sets and Functions, supplementary to DAAG

Gene by Environment Interaction and Conditional Gene Tests for Nuclear Families

Gene set analysis

Identification of Periodically Expressed Genes

Simulation and analysis of spatial structure of population genetics data

Detection of structure from multilocus genetic data

Population Genetics

Plot publication-grade gene and genome maps

Statistical Analysis Tools for High Dimension Molecular Data (HDMD)

Bayesian investigation of Hardy-Weinberg Equilibrium via estimation and testing

Objective Bayesian Testing for the Hardy-Weinberg Equilibrium Problem

Graphical tests for Hardy-Weinberg equilibrium

Identifying functional polymorphisms in genetic association studies

Spatially explicit population genetic simulations

Exact tests for Linkage Disequilibrium and Hardy-Weinberg Equilibrium

Detect gene-gene interactions using multifactor dimensionality reduction

Software for constructing genetic maps in outcrossing species

Functions to facilitate power and sensitivity analyses for genetic studies of natrual popualtions

Population and Evolutionary Genetics Analysis System

Statistical and Population Genetics

Tools for mapping of quantitative traits of genetically related individuals

An individual-based population genetic simulation environment

Simulation and visualization of restriction enzyme cutting pattern from DNA sequences


adephylo: exploratory analyses for the phylogenetic comparative method

Analyses of Phylogenetic Treeshape

Analyses of Phylogenetics and Evolution

Explore life histories

Distance Between Phylogenetic Histories

diversitree: comparative phylogenetic tests of diversification

methods for analyzing introgression between divergent lineages

Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

Mapping Transitions in Continuous Character Evolution

Modeling evolution in paleontological time-series

Classification using biological pathways as prior knowledge

Phylogenetic analysis in R

Basic functions for phylogenetic analysis

Phylogenetic Clustering (Phyloclustering)

Base package for phylogenetic structures and comparative data

Integrating phylogenetics and climatic niche modelling

R packge for simulating biological sequence evolution

Phylogenetic tools for ecologists

R tools for integrating phylogenies and ecology

Modelling and analysis of real-time PCR data

Biological Sequences Retrieval and Analysis

Statistical shape analysis

Estimating diversification rate changes and mass extinction events in phylogenies


Simulating trees under the birth-death model


Treemap visualization

Methods for Tree-based Local Adaptive Thresholding

Spatial analysis of animal track data


Miscellaneous plotting and utility functions


Interactive Biplots in R

GUI for Basic image operations

Biplot of Multivariate Data Based on Principal Components Analysis

R graphics device using cairo graphics library for creating high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG, PostScript) and display (X11 and Win32) output

Plot a correlogram

Data Analysis And Graphics data and functions

Graphic Extensions for Categorical Data

iPlots - interactive graphics for R

Plot a genome scan

Data and Functions from the book R Graphics

3D Scatter Plot

Functions for plotting graphical shapes, colors

Por ultimo, dos cositas:

La primera es que debo presentar disculpas por presentar información corta de cada paquete en ingles (ya que pues, el blog se llama "R para chibchombianos" y se supone debería escribir o explicar la mayoría de cosas en español, para la gente que no es muy afín con el ingles), pero es que el problema es que eran demasiados paquetes como uds pueden observar. De todos modos, no esta tan difícil entender la descripción de cada paquete y espero les guste.

Lo segundo es que quisiera felicitar a dos grandes amigas (SUSY ECHEVERRIA LONDOÑO Y ADRIANA MARCELA MORALES GUERRERO) por su nuevo articulo de divulgación científica titulado " cuantos somos y como no cuantificamos?" publicado en la revista- evolución, historia de la vida- de la  Asociación colombiana para el avance de la ciencias. Este trabajo tiene como tema principal los métodos de  delimitación  de especie y fue publicado en conjunto con DANIEL RAFAEL MIRANDA ESQUIVEL a quien también expreso mis felicitaciones...

Espero les guste este post y el articulo mencionado..
hasta la próxima.....

4 comentarios:

  1. Un paquete que sería genial agregar a la lista sería el paquete "agricolae". Es un paquete con análisis estadísticos y otras funcionalidades para experimentación en agricultura o mejoramiento genético de plantas.

  2. Muchas gracias por su aporte.
    Pienso que si!! definitivamente, talvez haga falta agregar muchísimos paquetes a la lista que pueden ser muy importantes!!
    (De hecho talvez todos sean importantes)
    Pero pues la lista esta larga y el espacio limitado!!

  3. Gracias amigo por tomarte el trabajo para facilitarnos a los que estamos en el cuento del R

  4. hola! una ayuda adicional por favor: como subir candisc o cualquiera de ellos a R para su utilización. gracias