Dockerfile of writing paper by R Markdown
This Dockerfile was developed for the Japanesese R users (So, it contains settings of Japanese environment). English version of this dockerfile is [here]((https://hub.docker.com/r/ykunisato/paper-r).
これは,RstudioでR Markdownを用いて論文執筆を行う際に便利なパッケージやアドインを含めたDockerファイルのリポジトリです。このDockerファイルでは,アカデミアのためのRSTUDIOにて紹介されているパッケージは大体用意できます。各種パッケージやアドインの詳細は,アカデミアのためのRSTUDIOを参照ください。
本Dockerファイルは,rocker/verseをベースにし,antoine-sachet/rocker-MLに記載されている方法を使ってrstanをインストールし,いくつかR Markdown関連のパッケージを追加しています。また,日本語環境の設定は,rocker-jp/verseを参考にしています。
作成者は専修大学人間科学部心理学科の国里愛彦です ([email protected])。エラーや追加してほしいパッケージなどがありましたら,気軽にご連絡ください。
Keywords: 心理学, 認知科学, 分析・執筆,rstudio, rstan, rmarkdown
使用法
Docker Desktopがインストールされていて,ある程度の通信速度があれば,数分で使用可能です。
1.Docker Desktop ( https://www.docker.com/products/docker-desktop )をインストールする。
2.ターミナル(Macの場合。Winはコマンドプロンプト?)を開く
3.ターミナルに以下を打ち込んで、コンテナーをrunする(runの前にPullが自動的なされます)。パスワードとコンテナ名はご自身の好きなように設定ください。
docker run -e PASSWORD=パスワード -p 8787:8787 -v $PWD:/home/rstudio -d --name コンテナ名 ykunisato/paper-r-jp
4.ブラウザを開いて,urlバー(アドレスバー)に,http://localhost:8787/ とタイプする
5.ブラウザ上にRstudioが出てくるので,IDにrstudio,パスに上記で設定したパスワードをいれる。
Docker間の依存関係について
国里(ykunisato)が管理しているRStudio用Dockerコンテナとその依存関係は以下になります。
- ykunisato/paper-r : 心理学系使いそうなRパッケージを入れたコンテナ(rocker/verseをベースに作成)
- ykunisato/paper-r-jp : ykunisato/paper-rをベースに日本語環境化したコンテナ(本コンテナ)
- ykunisato/ccp-lab-r : ykunisato/paper-rをベースに認知モデリング,心理学的ネットワーク分析,ネットワークメタ分析で使用するパッケージを追加したコンテナ
- ykunisato/ccp-lab-r-jp : ykunisato/ccp-lab-rをベースに日本語環境化したコンテナ
事前にインストールされている追加のRパッケージ
論文のテンプレート系パッケージ
- rticles : Article Formats for R Markdown
- papaja : Prepare reproducible APA journal articles with R Markdown
図表作成用パッケージ
- papaja : Prepare reproducible APA journal articles with R Markdown
- stargazer : Well-Formatted Regression and Summary Statistics Tables
- pixiedust : Tables so Beautifully Fine-Tuned You Will Believe It's Magic
- ggsci : Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'
解析結果の報告用パッケージ
- sigr : Succinct and Correct Statistical Summaries for Reports
- psycho : Efficient and Publishing-Oriented Workflow for Psychological Science
心理学などで使用しそうな解析パッケージ
- BayesFactor : Computation of Bayes Factors for Common Designs
- blavaan : Bayesian Latent Variable Analysis
- brms : Bayesian Regression Models using 'Stan'
- lme4 : Linear Mixed-Effects Models using 'Eigen' and S4
- psych : Procedures for Psychological, Psychometric, and Personality Research
- rstan : R Interface to Stan
- tidyverse : Easily Install and Load the 'Tidyverse'
RStudioの便利なアドイン
- citr : 'RStudio' Add-in to Insert Markdown Citations (BibTeX)
- gramr : The Grammar of Grammar
- wordcountaddin : Word counts and readability statistics in R markdown documents
Google Compute Engine関係
- googleComputeEngineR : R Interface with Google Compute Engine
- googleCloudStorageR : Interface with Google Cloud Storage API
- future : Unified Parallel and Distributed Processing in R for Everyone
その他
- abind : Combine Multidimensional Arrays
- acepack : ACE and AVAS for Selecting Multiple Regression Transformations
- arrayhelpers : Convenience Functions for Arrays
- askpass : Safe Password Entry for R, Git, and SSH
- assertthat : Easy Pre and Post Assertions
- backports : Reimplementations of Functions Introduced Since R-3.0.0
- base64enc : Tools for base64 encoding
- bayesplot : Plotting for Bayesian Models
- BDgraph : Bayesian Structure Learning in Graphical Models using Birth-Death MCMC
- BH : Boost C++ Header Files
- bibtex : Bibtex Parser
- BiocManager : Access the Bioconductor Project Package Repository
- bit : A Class for Vectors of 1-Bit Booleans
- bit64 : A S3 Class for Vectors of 64bit Integers :
- bitops : Bitwise Operations
- blob : A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS')
- bookdown : Authoring Books and Technical Documents with R Markdown
- brew : Templating Framework for Report Generation
- bridgesampling : Bridge Sampling for Marginal Likelihoods and Bayes Factors
- Brobdingnag : Very Large Numbers in R
- broom : Convert Statistical Analysis Objects into Tidy Tibbles
- callr : Call R from R
- car : Companion to Applied Regression
- carData : Companion to Applied Regression Data Sets
- caret : Classification and Regression Training
- caTools : Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
- cellranger : Translate Spreadsheet Cell Ranges to Rows and Columns
- checkmate : Fast and Versatile Argument Checks
- cli : Helpers for Developing Command Line Interfaces
- clipr : Read and Write from the System Clipboard
- clisymbols : Unicode Symbols at the R Prompt
- coda : Output Analysis and Diagnostics for MCMC
- colorspace : A Toolbox for Manipulating and Assessing Colors and Palettes
- colourpicker : A Colour Picker Tool for Shiny and for Selecting Colours in Plots
- commonmark : High Performance CommonMark and Github Markdown Rendering in R
- CompQuadForm : Distribution Function of Quadratic Forms in Normal Variables
- contfrac : Continued Fractions
- corpcor : Efficient Estimation of Covariance and (Partial) Correlation
- covr : Test Coverage for Packages
- crayon : Colored Terminal Output
- crosstalk : Inter-Widget Interactivity for HTML Widgets
- curl : A Modern and Flexible Web Client for R
- d3Network : Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R
- data.table : Extension of 'data.frame'
- DBI : R Database Interface
- dbplyr : A 'dplyr' Back End for Databases
- desc : Manipulate DESCRIPTION Files
- DescTools : Tools for Descriptive Statistics
- deSolve : Solvers for Initial Value Problems of Differential Equations ('ODE','DAE', 'DDE')
- devtools : Tools to Make Developing R Packages Easier
- digest : Create Compact Hash Digests of R Objects
- docopt : Command-Line Interface Specification Language
- dplyr : A Grammar of Data Manipulation
- DT : A Wrapper of the JavaScript Library 'DataTables'
- dtplyr : Data Table Back-End for 'dplyr'
- dygraphs : Interface to 'Dygraphs' Interactive Time Series Charting Library
- e1071 : Misc Functions of the Department of Statistics, Probability Theory Group(Formerly: E1071), TU Wien
- ellipsis : Tools for Working with ...
- elliptic : Weierstrass and Jacobi Elliptic Functions
- emmeans : Estimated Marginal Means, aka Least-Squares Means
- estimability : Tools for Assessing Estimability of Linear Predictions
- evaluate : Parsing and Evaluation Tools that Provide More Details than the Default
- expm : Matrix Exponential, Log, 'etc'
- fansi : ANSI Control Sequence Aware String Functions
- fdrtool : Estimation of (Local) False Discovery Rates and Higher Criticism
- feather : R Bindings to the Feather 'API'
- foghorn : Summarize CRAN Check Results in the Terminal
- forcats : Tools for Working with Categorical Variables (Factors)
- foreach : Provides Foreach Looping Construct for R
- formatR : Format R Code Automatically
- Formula : Extended Model Formulas
- fs : Cross-Platform File System Operations Based on 'libuv'
- future : Unified Parallel and Distributed Processing in R for Everyone
- generics : Common S3 Generics not Provided by Base R Methods Related to Model Fitting
- GGally : Extension to 'ggplot2'
- ggcorrplot : Visualization of a Correlation Matrix using 'ggplot2'
- ggm : Functions for graphical Markov models
- ggmcmc : Tools for Analyzing MCMC Simulations from Bayesian Inference
- ggplot2 : Create Elegant Data Visualisations Using the Grammar of Graphics
- ggridges : Ridgeline Plots in 'ggplot2'
- ggstance : Horizontal 'ggplot2' Components
- gh : 'GitHub' 'API'
- git2r : Provides Access to Git Repositories
- glasso : Graphical Lasso: Estimation of Gaussian Graphical Models
- glmnet : Lasso and Elastic-Net Regularized Generalized Linear Models
- globals : Identify Global Objects in R Expressions
- glue : Interpreted String Literals
- gmailr : Access the Gmail RESTful API
- gower : Gower's Distance
- gridExtra : Miscellaneous Functions for "Grid" Graphics
- gtable : Arrange 'Grobs' in Tables
- gtools : Various R Programming Tools
- haven : Import and Export 'SPSS', 'Stata' and 'SAS' Files
- HDInterval : Highest (Posterior) Density Intervals
- highlight : Syntax Highlighter
- highr : Syntax Highlighting for R Source Code
- Hmisc : Harrell Miscellaneous
- hms : Pretty Time of Day
- htmlTable : Advanced Tables for Markdown/HTML
- htmltools : Tools for HTML
- htmlwidgets : HTML Widgets for R
- httpuv : HTTP and WebSocket Server Library
- httr : Tools for Working with URLs and HTTP
- huge : High-Dimensional Undirected Graph Estimation
- hunspell : High-Performance Stemmer, Tokenizer, and Spell Checker
- hypergeo : The Gauss Hypergeometric Function
- igraph : Network Analysis and Visualization
- ini : Read and Write '.ini' Files
- inline : Functions to Inline C, C++, Fortran Function Calls from R
- ipred : Improved Predictors
- iterators : Provides Iterator Construct for R
- jpeg : Read and write JPEG images
- jsonlite : A Robust, High Performance JSON Parser and Generator for R
- knitr : A General-Purpose Package for Dynamic Report Generation in R
- koRpus : An R Package for Text Analysis
- koRpus.lang.en : Language Support for 'koRpus' Package: English
- labeling : Axis Labeling
- labelVector : Label Attributes for Atomic Vectors
- Lahman : Sean 'Lahman' Baseball Database
- LaplacesDemon : Complete Environment for Bayesian Inference
- later : Utilities for Delaying Function Execution
- latticeExtra : Extra Graphical Utilities Based on Lattice
- lava : Latent Variable Models
- lavaan : Latent Variable Analysis
- lazyeval : Lazy (Non-Standard) Evaluation
- lintr : A 'Linter' for R Code
- listenv : Environments Behaving (Almost) as Lists
- littler : R at the Command-Line via 'r'
- lmerTest : Tests in Linear Mixed Effects Models
- loo : Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models
- ltm : Latent Trait Models under IRT
- lubridate : Make Dealing with Dates a Little Easier
- magrittr : A Forward-Pipe Operator for R
- manipulate : Interactive Plots for RStudio
- maptools : Tools for Handling Spatial Objects
- markdown : 'Markdown' Rendering for R
- MatrixModels : Modelling with Sparse And Dense Matrices
- matrixStats : Functions that Apply to Rows and Columns of Matrices (and to Vectors)
- mcmc : Markov Chain Monte Carlo
- MCMCpack : Markov Chain Monte Carlo (MCMC) Package
- memoise : Memoisation of Functions
- microbenchmark : Accurate Timing Functions
- mime : Map Filenames to MIME Types
- miniUI : Shiny UI Widgets for Small Screens
- minqa : Derivative-free optimization algorithms by quadratic approximation
- mnormt : The Multivariate Normal and t Distributions
- mockery : Mocking Library for R
- ModelMetrics : Rapid Calculation of Model Metrics
- modelr : Modelling Functions that Work with the Pipe
- msm : Multi-State Markov and Hidden Markov Models in Continuous Time
- MuMIn : Multi-Model Inference
- munsell : Utilities for Using Munsell Colours
- mvtnorm : Multivariate Normal and t Distributions
- nFactors : Parallel Analysis and Non Graphical Solutions to the Cattell Scree Test
- nleqslv : Solve Systems of Nonlinear Equations
- nloptr : R Interface to NLopt
- nonnest2 : Tests of Non-Nested Models
- numDeriv : Accurate Numerical Derivatives
- nycflights13 : Flights that Departed NYC in 2013
- openssl : Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
- openxlsx : Read, Write and Edit XLSX Files
- packrat : A Dependency Management System for Projects and their R Package Dependencies
- parsedate : Recognize and Parse Dates in Various Formats, Including All ISO 8601 Formats
- pbapply : Adding Progress Bar to 'apply' Functions
- pbivnorm : Vectorized Bivariate Normal CDF
- pbkrtest Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison
- pillar : Coloured Formatting for Columns
- pingr : Check if a Remote Computer is Up
- pkgbuild : Find Tools Needed to Build R Packages
- pkgconfig : Private Configuration for 'R' Packages
- pkgdown : Make Static HTML Documentation for a Package
- pkgload : Simulate Package Installation and Attach
- pkgmaker : Development Utilities for R Packages
- PKI : Public Key Infrastucture for R Based on the X.509 Standard
- plogr : The 'plog' C++ Logging Library
- plyr : Tools for Splitting, Applying and Combining Data
- png : Read and write PNG images
- polycor : Polychoric and Polyserial Correlations
- ppcor : Partial and Semi-Partial (Part) Correlation
- praise : Praise Users
- prettyunits : Pretty, Human Readable Formatting of Quantities
- pROC : Display and Analyze ROC Curves
- processx : Execute and Control System Processes
- prodlim : Product-Limit Estimation for Censored Event History Analysis
- progress : Terminal Progress Bars
- projpred : Projection Predictive Feature Selection
- promises : Abstractions for Promise-Based Asynchronous Programming
- ps : List, Query, Manipulate System Processes
- purrr : Functional Programming Tools
- qgraph : Graph Plotting Methods, Psychometric Data Visualization and Graphical Model Estimation
- quantreg : Quantile Regression
- R6 : Encapsulated Classes with Reference Semantics
- rappdirs : Application Directories: Determine Where to Save Data, Caches, and Logs
- rcmdcheck : Run 'R CMD check' from 'R' and Capture Results
- RColorBrewer : ColorBrewer Palettes
- Rcpp : Seamless R and C++ Integration
- RcppArmadillo : 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
- RcppEigen : 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library
- RcppRoll : Efficient Rolling / Windowed Operations
- RCurl : General Network (HTTP/FTP/...) Client Interface for R
- readr : Read Rectangular Text Data
- readxl : Read Excel Files
- recipes : Preprocessing Tools to Create Design Matrices
- RefManageR : Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
- registry : Infrastructure for R Package Registries
- rematch : Match Regular Expressions with a Nicer 'API'
- rematch2 : Tidy Output from Regular Expression Matching
- remotes : R Package Installation from Remote Repositories, Including 'GitHub'
- reprex : Prepare Reproducible Example Code via the Clipboard
- reshape : Flexibly Reshape Data
- reshape2 : Flexibly Reshape Data: A Reboot of the Reshape Package
- rex : Friendly Regular Expressions
- rhub : Connect to 'R-hub'
- rio : A Swiss-Army Knife for Data I/O
- rJava : Low-Level R to Java Interface
- rjson : JSON for R
- rlang : Functions for Base Types and Core R and 'Tidyverse' Features
- rmarkdown : Dynamic Documents for R
- rmdshower : 'R' 'Markdown' Format for 'shower' Presentations
- RMySQL : Database Interface and 'MySQL' Driver for R
- rngtools : Utility Functions for Working with Random Number Generators
- roxygen2 : In-Line Documentation for R
- RPostgreSQL : R Interface to the 'PostgreSQL' Database System
- rprojroot : Finding Files in Project Subdirectories
- rsconnect : Deployment Interface for R Markdown Documents and Shiny Applications
- RSQLite : 'SQLite' Interface for R
- rstanarm : Bayesian Applied Regression Modeling via Stan
- rstantools : Tools for Developing R Packages Interfacing with 'Stan'
- rstudioapi : Safely Access the RStudio API
- rversions : Query 'R' Versions, Including 'r-release' and 'r-oldrel'
- rvest : Easily Harvest (Scrape) Web Pages
- sandwich : Robust Covariance Matrix Estimators
- scales : Scale Functions for Visualization
- selectr : Translate CSS Selectors to XPath Expressions
- servr : A Simple HTTP Server to Serve Static Files or Dynamic Documents
- sessioninfo : R Session Information
- shiny : Web Application Framework for R
- shinyjs : Easily Improve the User Experience of Your Shiny Apps in Seconds
- shinystan : Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models
- shinythemes : Themes for Shiny
- sourcetools : Tools for Reading, Tokenizing and Parsing R Code
- sp : Classes and Methods for Spatial Data
- SparseM : Sparse Linear Algebra
- spelling : Tools for Spell Checking in R
- SQUAREM : Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms
- StanHeaders : C++ Header Files for Stan
- stringdist : Approximate String Matching and String Distance Functions
- stringi : Character String Processing Facilities
- stringr : Simple, Consistent Wrappers for Common String Operations
- svUnit : SciViews GUI API - Unit testing
- sylly : Hyphenation and Syllable Counting for Text Analysis
- sylly.en : Language Support for 'sylly' Package: English
- sys : Powerful and Reliable Tools for Running System Commands in R
- testit : A Simple Package for Testing R Packages
- testthat : Unit Testing for R
- threejs : Interactive 3D Scatter Plots, Networks and Globes
- tibble : Simple Data Frames
- tidybayes : Tidy Data and 'Geoms' for Bayesian Models
- tidyr : Easily Tidy Data with 'spread()' and 'gather()' Functions
- tidyselect : Select from a Set of Strings
- timeDate : Rmetrics - Chronological and Calendar Objects
- tinytex : Helper Functions to Install and Maintain 'TeX Live', and Compile 'LaTeX'Documents
- tufte Tufte's Styles for R Markdown Documents
- usethis : Automate Package and Project Setup
- utf8 : Unicode Text Processing
- uuid : Tools for generating and handling of UUIDs
- V8 : Embedded JavaScript Engine for R
- viridis : Default Color Maps from 'matplotlib'
- viridisLite : Default Color Maps from 'matplotlib' (Lite Version)
- webshot : Take Screenshots of Web Pages
- whisker : {{mustache}} for R, logicless templating
- whoami : Username, Full Name, Email Address, 'GitHub' Username of the Current User
- withr : Run Code 'With' Temporarily Modified Global State
- wrapr : Wrap R Tools for Debugging and Parametric Programming
- xfun : Miscellaneous Functions by 'Yihui Xie'
- XML : Tools for Parsing and Generating XML Within R and S-Plus
- xml2 : Parse XML
- xopen : Open System Files, 'URLs', Anything
- xtable : Export Tables to LaTeX or HTML
- xts : eXtensible Time Series
- yaml : Methods to Convert R Data to YAML and Back
- zip : Cross-Platform 'zip' Compression
- zoo : S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)