R-Librarys.R

## Curated stuff:
## * MetaCran: http://www.r-pkg.org/
## * List of Packages gathered by Garret G.: https://github.com/rstudio/RStartHere
## * List of popular packages https://awesome-r.com/
## * List of DataScience R tutorials https://github.com/ujjwalkarn/DataScienceR
## * List of machine elearning tutorials by subject: https://ujjwalkarn.github.io/Machine-Learning-Tutorials/

## Reproducible package management for R:
install.packages("devtools")
install.packages("tidyverse")
library(devtools)

#devtools::install_github("rstudio/packrat")
# More info @ http://rstudio.github.io/packrat/

## great RStudio Addins
install.packages("radiant", repos = "http://vnijs.github.io/radiant_miniCRAN/", type = 'binary')
install.packages("addinslist") # an AddIn that serves as AddIn Browser and Manager
install.packages("ggThemeAssist") # ggplot2 theme assistance
devtools::install_github("jennybc/jadd") # Convenience function for developing and debuging functions
devtools::install_github("tjmahr/WrapRmd") #  a tool to convienently wrap long RMD texts with R code
devtools::install_github("MangoTheCat/tidyshiny") # Interactively manipulate data with the tidyr package using this handy shiny gadget.

## great RStudio Markdown Templates
install.packages("rmdformats") # great templates for RMD files

## great bioconductor packages
#EBIImage - Image Processing: source("http://bioconductor.org/biocLite.R"), biocLite("EBImage")

## cran packages recommended by a blogger
x <- c(
  ## Data Import and Manipulation
  "broom", # Convert statistical analysis objects from R into tidy format
  'XML', # tools for parsing and generating XML
  'foreign', # functions for reading and writing data stored by Minitab, S, SAS, SPSS...
  'lubridate', # makes it easier to work with dates and times by providing functions to identify and parse date-time data
  'stringr', # makes it easier to work with strings
  'sqldf', # for running SQL statements on R data frames, optimized for convenience
  'RCurl', # general network (HTTP/HTTPS/FTP/...) client interface for R
  'rjson', # converts R object into JSON objects and vice-versa
  'xlsx', # provides R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats
  'tidyr', # an evolution of reshape2. It's designed specifically for data tidying (not general reshaping or aggregating) and works well with dplyr data pipelines
  'dplyr', # a fast, consistent tool for working with data frame like objects, both in memory and out of memory
  'httr', # provides useful tools for working with HTTP
  'data.

', # Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all
  
  ## Exploratory Data Analysis and Visualization
  'ggplot2', # an implementation of the Grammar of Graphics
  'RColorBrewer', # provides palettes for drawing nice maps shaded according to a variable
  'ellipse', # functions for drawing ellipses and ellipse-like confidence regions
  'animation', # a gallery of animations in statistics and utilities to create animations
  'shiny', # elegant and powerful web framework for building interactive web applications using R
)

## my own installed packages on my system
y = c(
  "arm",
  
  #### Graphics devices
  "Cairo","cairoDevice",
  "svglite", # fast SVG graphics device - Hadlyverse
  
  "car",     # mostly used: car::recode
  "caTools",
  
  ## testing, asserting and validating tools
  "validate", # awesome package for rule based checking of data, very sophistcated and mature
  "assertr", # assert tool especially optimized for data checking, plays well with dplyr
  "ensurer", # Ensure Values at Runtime, plays well with dplyr
  "testthat", # r unit test framework "hadleyverse", could be also great for data checking
  "asserthat", # r unit test framework "hadleyverse", could be also great for data checking
  
  ## knitr suite
  "knitr", # literate programming for R
  #"printr" # yet to be released to CRAN; companion package to knitr by its creator
  "pander", # An R Pandoc Writer
  "sparkTable", # create sparklines, sparkhistograms, sparktables for shiny and knitr docs
  "formattable", # Awesome package to conditionally format tables by renkun-ken 

  ## Templates for RStudio/knitr RMDMarkdown format
  "rmdformats", # html_clean and html_docco template
  
  ## Table generation packages
  "huxtable",  ### my new favorite - htmlTable++
  "tangram", ### grammar of tables - from hmisc creator
  "desctable",  ### my new favorite - DescTools/tableone for the tidyverse
  "tableone", ### great for Table 1, works well for Propensity Score analytics
  "moonBook",     # great for Table1 creation for medical papers
  "ztable",       # great for table creation for medical papers
  "compareGroups", ### great for Table 1
  "htmlTable", ### great for creating tables like in top medical journals, does not summarize only helps with formating
  "DescTools", ### prefect for describtive stats, great tools for plotting and descriptive stats
  "stargazer", # great table output for model objects
  "pixiedust", # a grammar for formatting tables.
  "tables",       # has an interesting interface for producing summary statistics. It looks complex but powerful.
  "formattable",

  "ompr", # DSL for MODEL MIXED-INTEGER LINEAR PROGRAMS
  "ompr.ROI", # DSL for MODEL MIXED-INTEGER LINEAR PROGRAMS

  ## Image processing
  "imager", # imager: an R package for image processing
  
  ## Shiny and Shiny addons -- check out shiny.rstudio.com
  "shiny",      # essential - R web framework
  "flexdashboard" # Easy interactive dashboards for R - works well with htmlwidgets
  "shinyAce",   # code editor
  "shinyjs", # javascript in shiny made easy
  "shinythemes", # a collection of Shiny themes for the theme argument of bootstrapPage, fluidPage, navbarPage, or fixedPage
  "shinydashboard", # a dashboard framework, much more options than flexdashboard, but also more features
  
  ## htmlwidgtes framework for JS/D3 widgets in Shiny and  knitr
  "htmlwidgets" , #htmlwidgtes
  "trelliscopejs" # great for exploratory analysis
  "DiagrammeR",
  "threejs",
  "DT",
  "d3heatmap",
  "networkD3", # great for static and interactive network graphics
  "visNetwork", # great for static and interactive network graphics
  "dygraphs",
  "leaflet",
  "rgl", # 3D plotting WebGL widget 
  #https://github.com/timelyportfolio/timelineR # timelines in R
  
  "mindr" # mindmaps in markdown!
  
  ##
  "corrr", # tidy woking with correlations
  
  ## data structures
  "data.tree", # General Purpose Hierarchical Data Structure
  
  ## Graph Database utilities
  "tidygraph" # verbs and a tidy API for working with graphs
  "igraph", # igraph is a collection of network analysis and viz tools
  "RNeo4j", # Neo4j R driver
  # OrientDB - ???
  "networkD3",  # htmlwidget: great for static and interactive network graphics
  "visNetwork", # htmlwidget: great for static and interactive network graphics
  "ggraph", "ggnetwork", # ggplot2 extensions for graphs
  
  ## clustering
  "cluster", ## main functions: agnes and daisy
  "fpc", ## check validity of clusters: clusterboot function; kmeansruns
  "heatmaply", ## sophisticated heatmap ploting
  
  ## data reading and munging packages - tidyverse
  "tidyverse"
  "janitor", # great for cleaning data 
  "dplyr",  # DSL for data work - hadleyverse
  "wrapr", # great for NSE with dplyr, simplifies NSE programming quite a lot!
  "tidyr", # great for data munging - hadleyverse
  "purrr",     # functional programming for lists - hadleyverse
  "broom", # Convert statistical analysis objects from R into tidy format
  "forcats", # working with factors 
  "lubridate", # working with dates
  "magrittr",  # %>%
  "jsonlite", # jsonlite: A Robust, High Performance JSON Parser and Generator for R
  "tidyjson", # a grammar for reading in deterministically json data into a data frame
  "yaml", # Methods to convert R data to YAML and back; works well with data.tree package
  "readr", # great for data IO of text files - hadleyverse
  "readxl", # for data IO of excel files, still buggy and unreliable - hadleyverse
  "janitor", # must have when reading in excel files with the readxl package
  "openxlsx", # great for data IO of excel files
  "XLConnect", # for reading in Excel - at the moment the most reliable. Backbone: Java
  "rvest", # convenient webscraping - hadleyverse
  "haven", # great for data IO of SPSS, SAS, STATA im/export - hadleyverse
  "import", # from the creator of magrittr: great for importing
  "dummies", # for easy creation of dummy variables
  "feather", # high speed data reading andd writing format
  'doMC' # for multi-core processing
  
  # cat data analysis
  "vcd",    # great for categorical data analysis
  
  "epibasix", # epi helper package
  "epicalc", # epi helper package (print_logistic), not anymore maintained
  "epiR", # epi helper package
  "epitools", # epi helper package
  
  # excat statistics
  "exact2x2", # exact methods
  "exactci", # exact methods
  
  "extracat",
  "ez",
  "gdata",
  
  ## ggplot2 and general plotting packages
  # A web page listing all ggplot2 extensions:  http://www.ggplot2-exts.org/
  "ggplot2", # see packages "cowplot" (plot_grid)
  "ggrepel",             # extension: for direct labeling
  "ggforce",             # extension: contextual zoom -> facet_zoom ; sinaplot -> geom_sina
  "ggbeeswarm",          # extension: awesome beeswarm plots
  "gganimate", "tweenr", # extension: easy animations of ggplot2 plots
  "ggloop",              # extension: Create 'ggplot2' Plots in a Loop
  "ggthemes","ggthemr",  # great themes for ggplot2
  "ggsci",               # plotting scales and palettes of scientific journals 
  "ggTimeSeries",        # great for time series or time related data! Innovative viz!
  "ggpubr"               # easy 'ggplot2' Based Publication Ready Plots
  
  "viridis", # academic and aestethic proven color palette
  
  # great ploting packages for special purposes
  "tabplot",   # Tableplot, a Visualization of Large Datasets 
  "plotluck", # fantastic and crazy simple way of beautiful automatic plotting for exploratory purposes with formulat interface
  "survminer", # ggplot2 based beautiful and 'ready-to-publish' survival curves with tables
  "rms",      # survplot and estimates
  "survMisc",  # also survival plotting
  "trelliscopejs" # great for exploratory analysis
  "GGally", # GGally - some special plots using ggplot2  
  "likert", # great for visualizing likert scales
  "dotwhisker", # Better than coefplot, Visualizing regression coefficients - very nice!, plays well with dplyr and broom
  "visreg", # great for visualizing a regression result
  "corrplot", "corrgram", # visualizing correlation matrices 
  "forestplot", # Advanced Forest Plot Using 'grid' Graphics
  "venneuler", # creating Venn and Euler diagramms 
  "dendextend", # create package for various viz of dendograms
  "plotROC", # create for plotting ROC curves
  "DiagrammeR", # excellent Diagram lib
  
  "ggfortify", # Define fortify and autoplot functions to allow ggplot2 to handle some popular R packages.,
  "cowplot", # great for multi-panel figures with ggplot2 - plot_grid; save_ggplot3
  "ggdendro",  "ggRandomForests", 
  "ggmcmc", # has gg_pairs function
  "plotly", # good plots
  "ggvis", # next gen ggplot2, early dev
  "plotly", # plotly API - offline dynamic viz gen.
  "timeline", # timeline: Timelines for a Grammar of Graphics
  "sjPlot", # package for plotting of forest plots and interaction term of GLMs
  "moonBook", # for plotting forests plots and survival curves
  "googleVis",
  "latticeExtra",
  "Gmisc",
  "gmodels",
  "granova","granovaGG",
  "gridExtra",
  "gtable",
  "gtools",
  "Hmisc",
  
  "scatterplot3d", # great 3d plotting library
  "plot3D", #
  "rgl", # 3D plotting including the WebGL htmlwidget
  
  "simmer", # Discrete event simulation with nice viz; plays well with dplyr
  
  # Meta research - Meta Analysis - Open Science
  "meta",
  "MAVIS", # a shiny app for Meta-Analysis
  "metagear", # Research Synthesis Tools for Systematic Reviews and Meta-Analysis
  "metafor", # comprehensive collection of functions for conducting meta-analyses in R.
  "meta", # meta analysis package
  "compute.es", # Compute Effect Sizes
  "MAVIS", # MAVIS: Meta Analysis via Shiny
  
  "minerva", # implementation of MIC
  
  # Survival Analysis
  "survMisc", # great survival misc functions
  
  "installr", # great tool for installing R and other necessary tools
  
  "lme4", # linear mixed effects
  "multcomp", # handling multiple comparison
  
  "lubridate", # easy working with dates - hadleyverse
  
  "MASS",
  
  # QUality Control
  "MethComp",
  "qcc",
  
  # Propensity Score tools
  # shiny::runGitHub("LaurenSamuels/VisualPruner")
  "optmatch", "twang", 
  "Matching","MatchIt",
  "PSAboot","PSAgraphics",
  "multilevelPSA",
  "TriMatch",
  
  # Single/Multiple Imputation
  "VIM", # vizualising missing data patterns and imputing missing data with fast algorithms
  "mice","Amelia","mi" # multiple imputation tools, Amelia for longitudinal data
  "missMDA", # great for single imputation, however, unstable
    
  "mosaic", # some handy extension to stat functions, e.g. formula interface, etc.
  
  "packrat", # facilitates Reproduceable Research - Package Versioning by RStudio
  "checkpoint", # facilitates Reproduceable Research - Package Versioning by Revolution Analytics
  
  ## Building APIs with R
  "plumber", # easy creation of R webservice by just code decoration 
  "fiery", "routr", # a web-server and web-socket server and routr for routing of HTTP and WebSocket in R, great for web service dev
  "jug", # small web development framework for R, make building APIs for your code as easy as possible
  
  ## Machine Learning and Statistical Modeling
  "h2o", # create MachienLearning libarary, AutoML
  "rpart", # decesion trees
  "rpart.plot",
  "party", # 
  "randomForest",
  "rpart",
  "rpart.plot",
  "xgboost", # high speed gbm implementation
  'gbm', # Generalized Boosted Regression Models
  'glmnet', # lasso and elastic-net regularized generalized linear models
  'geepack', # GEE: alternative to Linear Mixed Models for correlated data i.e. time series, clustered cohorts, ...
  'contrast', 'multcomp', # great for contrasts in linear models: contrast:contrast function and 
  # multcomp:glht function. Like the lincom command in Stata
  'tree', # classification and regression trees
  'randomForest', # classification and regression based on a forest of trees using random inputs
  'mclust', # Normal Mixture Modeling for Model-Based Clustering, Classification, and Density Estimation
  'car', # Companion to Applied Regression. Esp. useful for ANOVA tables.
  'lme4', # linear mixed-effects models using S4 classes
  'mvtnorm', # multivariate Normal and t Distributions
  # specially useful:
  #   * car::recode()             --> for easy recoding of any variables
  #   * car::linear.hypothesis()  --> like 'lincom' command in Stata, alterantive is survey::svycontrast()
  'rms', # regression modelling tools
  # specially useful:
  #   * rms::datadist()           --> like 'adjust' command in Stata      
  
  ## Text mining, string distances, NLP
  'tm', # a framework for text mining applications within R
  "stringdist", # Approximate String Matching and String Distance Functions
  
  "pwr", # Power Analysis
  
  # rOpenScience and rOpenHealth Packages
  "rentrez", # talk with NCBI entrez using R
  "RISmed", # talk with NCBI entrez using R
  "rclinicaltrials", # an interface to clinicaltrails.gov - fetches studies meta-data and study data 
  "rcrossref", # crossref API
  "fulltext", # download fulltext articles using R,
  "BerlinData", # BerlinData: Easy access to Berlin related data
  "rHealthDataGov", # This package provides an R interface to the HealthData.gov data API
  "rsnps", # Search and retrieve Single Nucleotide Polymorphism data from openSNP
  "gistr", # a light interface to GitHub's gists for R.
  "gtrendsR", # R Functions to Perform and Display Google Trends Queries
  
  # Interfaces to the cloud / loud services
  "googlesheets", # Google Spreadsheets R API
  "rdrop2", # Programmatic Interface to the 'Dropbox' API
  "Rmonkey", # A Survey Monkey R Client

  # robust   
  "rms",
  "robustbase", # lm and glm without relying on distributional assumptions
  
  "roxygen2", # intra source documentation -hadleyverse
  
  # databases -----------
  "RPostgreSQL", # interface to postgresql
  "MonetDBLite", # in-process database engine including dplyr backend - ultra-fast column-based storage 
  "RSQLite", # in-process database engine including dplyr backend - rock-solid, row-based storage 
  "RSQLite.extfuns",
  
  "stringr", # hadley whickhams string processing package

  "swirl" # interactive R tutorial
)

install.packages(union(x, y))

## github package
z <- c("google/CausalImpact", # Estimating causal effects in time series, http://google.github.io/CausalImpact/, https://jjmullz.shinyapps.io/causal-impact/
       "haozhu233/ezsummary", # Summary stats tables making use od dplyr
       "trinker/wakefield" # wakefield is designed to quickly generate random data sets.
)

install_github(z)