Anaconda Python needs cleaning every once in a while

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As a user of Anaconda python I have been receiving (Ubuntu) system warnings of low free space in my home directory. Investigating what was causing this I found out that Anaconda python had several versions of each package. The overall size of the pkgs directory was 14+ GB. After cleaning it is about 3GB.

The second largest directory was my mail in Thunderbird.

So it would be wise, especially if you are limited in disk space, to clean Anaconda. The commands I used are as follows:

 
conda clean --all
conda update conda
# just to make sure nothing is broken and
# your environment is updated
source activate <your-environment>
conda update --all
conda clean --all

Assorted links – Data Science with R

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last updated: 2015-08-29

References & Most helpful commands

Tutorials & Handy packages

Hands-on dplyr tutorial for faster data manipulation in R Interactive Visualizations From R Using Rcharts rMaps – Interactive Maps from R (github repo) (requires “devtools” from cran)
Using R for Psychological Research – Personality Project, William Revelle
DataCamp courses
Try R by Code School (on codeschool)
Introduction to R, Leada

Visualization Packages

see Assorted links – Data Visualization (to be published later)

Papers

Tidy Data, Hadley Wickham [PDF]

Journals

Big Data & Society – Open-access journal

Hacks for better productivity

Sublime and R

Using Sublime Text 2 for R Using R in Sublime Text 3

Books

Video (training) courses

Introduction to Data Science with R, Garrett Grolemund, O’Reilly Media

Lists of Resources by others

Data Mining

Scraping Twitter and Web Data Using R – Pablo Barbera

Numerical Analysis
Interoperability
Data Sources

see Assorted links – Data sources (To be published later)

If you’d like to contribute to this list, please leave them in the comments below.

Map of Universities offering Data Science degrees

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Below is a nice map created by Ali Rebaie of universities offering degrees in Data Science based on data from this github repo. Contribute using this Google spreadsheet.

[via Ali Rebaie]

Miroculus uses Data Science for Early Detection of Cancer

Video

Miroculus

Rscript to customize the R environment

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A while ago I published a post on how to install some basic packages in R. This post goes further by sharing with you an Rscript (as part of another Ubuntu customization script) to install many popular R packages.

I’ve written the Rscript to be run after a fresh installation of Ubuntu. The Rscript is called by the Ubuntu customization script (yet to be published) and should install some basic and popular R packages.

Below is a Gist. For the repo click here.

####################################
## R environment customization script
# to automate package installation
# repo is maintained at http://bit.ly/r-customize-script
####################################
## To run execute in a terminal:
# Rscript r-customize.R # depends on R being installed
####################################
## Some relevant links
# Rstudio's Quick list of useful R packages: http://bit.ly/useful_R_packages
####################################
## Basic packages
#################
install.packages("devtools")
library(devtools) # to install from source (eg; github)
install.packages("downloader")
install.packages("checkpoint")
install.packages("rJava")
install.packages("xlsxjars")
install.packages("xlsx")
install.packages("data.table")
install.packages(c("Hmisc", "jpeg"))
install.packages("RJSONIO") # also required for "WDI"
# DataTables see: https://rstudio.github.io/DT/
# installs an R interface to the Js DataTables
# will ask to select a server
if (!requireNamespace('htmlwidgets') || packageVersion('htmlwidgets') <= '0.3.2')
install_github('ramnathv/htmlwidgets')
install_github('rstudio/DT')
install.packages("xtable")
# Web scraping
##############
install.packages("XML") # read & create XML docs
install.packages("rvest") # XML & httr wrappers to make it easy to download & manipulate html & xml.
install.packages(c("httr", "rjson")) # required for "Rfacebook"
install.packages("jsonlite")
install.packages("RCurl")
## Data Wrangling
#################
install.packages(c("dplyr", "reshape2"))
install.packages("tidyr")
install.packages("sqldf") # Manipulate R data frames using SQ
## Swirl
# Learn R, in R. http://swirlstats.com
install.packages("swirl")
# install_github("swirldev/swirl") # latest development version
# Visualization
###############
install.packages("ggplot2")
install.packages("ggvis")
install.packages("gridExtra")
# R interface to dygraphs
if (!requireNamespace('htmlwidgets'))
install_github('ramnathv/htmlwidgets')
install_github('rstudio/dygraphs')
# Shiny Apps
install_github('rstudio/shinyapps')
# download("https://github.com/rstudio/shinyapps/archive/master.tar.gz&quot;, "shinyapps.tar.gz")
# install.packages("shinyapps.tar.gz", repos = NULL, type = "source")
# Plotly
install_github("ropensci/plotly")
# download("https://github.com/ropensci/plotly/archive/master.tar.gz&quot;, "plotly.tar.gz")
# install.packages("plotly.tar.gz", repos = NULL, type = "source")
install.packages("maptools") # for shapefiles
# install.packages("rgeos") # required by maptools
# rMaps (still under development) # https://rmaps.github.io/
# rCharts required for some (experimental) features
if (!requireNamespace('rCharts'))
install_github('ramnathv/rCharts@dev')
install_github('ramnathv/rMaps')
# Google Vis
install.packages("googleVis")
## Leaftlet
# R package to create interactive web-maps based on the Leaflet JavaScript library
install.packages("leafletR")
# install_github("chgrl/leafletR")
install_github("rstudio/leaflet") # by Rstudio
# Documents
###########
# for Knitr
install.packages("yaml"); install.packages("htmltools"); install.packages("rmarkdown")
# Slidify & Libraries
install_github('ramnathv/slidify')
install_github('ramnathv/slidifyLibraries')
# Spatial & GIS
###############
install.packages("sp") # classes and methods for spatial data
install.packages("maptools") # Tools for Reading and Handling Spatial Objects
install.packages("maps") # Draw Geographical Maps
install.packages("ggmap") # Spatial Visualization with Google Maps and OpenStreetMap
install.packages("raster")
install.packages("mapdata")
install.packages("mapproj")
install.packages("gpclib")
install.packages("rdgal")
install.packages("Rgooglemaps")
install.packages("rgeos")
install.packages("rasterVis")
# Connections
#############
# API's
install.packages("streamR") # Access to Twitter Streaming API via R # github: https://github.com/pablobarbera/streamR
install.packages("Rfacebook") # provides an interface to the Facebook API
# Connect to Databases
install.packages("DBI") # database interface (DBI) definition for communication between R and relational database management systems
install.packages("RMySQL") # DBI-compliant Interface to MySQL and MariaDB Databases
install.packages("dbConnect") # Provides a graphical user interface to connect with databases that use MySQL
# Data scources
install.packages("Quandl")
install.packages("WDI") #github.com/vincentarelbundock/WDI
# Big Data
##########
# Packages to deal with datasets larger than RAM
install.packages("bigmemory") # Manage massive matrices with shared memory and memory-mapped files
# Medical packages
install.packages("oro.dicom")
# Machine Learning & Predictive Modeling
########################################
## caret – Classification And REgression Training
install.packages("caret")
install.packages("e1071") # needed when fitting a model in caret

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