Dockerfile of writing paper by R Markdown

This is a repository of Dockerfile including packages and add-ins that are useful for writing articles with R Markdown in Rstudio. This Dockerfile is based on rocker/verse. Installing rstan conducted by the method described in antoine-sachet / rocker-ML.

Maintainer is Yoshihiko Kunisato (ykunisato@psy.senshu-u.ac.jp)

Keywords: psychology, cognitive science, rstudio, rstan, rmarkdown

Usage

Install "Docker Desktop"
Open "terminal"(Mac) or Command Prompt(Win, I don't know Win. Sorry!)
Type the following code to pull a Docker container. Change the "password" and "name_of_container" as you like.

docker run -e PASSWORD=password -p 8787:8787 -v ~:/home/rstudio -d --name name_of_container ykunisato/paper-r

Open the web browser and type "http://localhost:8787/" in the URL bar.
You will see the Rstudio on the web browser. Type rstudio in ID column and password that you set in password column.

This Dockerfile add following R packages.

Templates for writing paper

rticles : Article Formats for R Markdown
papaja : Prepare reproducible APA journal articles with R Markdown

Publication-ready figure & table

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'

Reporting analyzed results

sigr : Succinct and Correct Statistical Summaries for Reports
psycho : Efficient and Publishing-Oriented Workflow for Psychological Science

Statistical analysis packages used in psychology

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'

Add-in of RStudio

citr : 'RStudio' Add-in to Insert Markdown Citations (BibTeX)
gramr : The Grammar of Grammar
wordcountaddin : Word counts and readability statistics in R markdown documents

Other packages

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
parSim : Parallel Simulation Studies
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)

satopan/paper-r