This repository contains the Docker build environment for compiling the Brisbane Birds Atlas.
To download the image, execute the following command in the terminal:
docker pull "brisbanebirdteam/build-env:latest"
This image contains R (version 3.4.4), TinyTex, Pandoc (version 2.2.1-1), and assorted Debian packages for geospatial analysis. It also contains R packages for manipulating data and building the atlas website (obtained from the Microsoft R Application Network snapshot taken on 16th May 2018).
| Package | Version | Description |
|---|---|---|
| assertthat | 0.2.0 | Easy Pre and Post Assertions |
| backports | 1.1.2 | Reimplementations of Functions Introduced Since R-3.0.0 |
| base64enc | 0.1-3 | Tools for base64 encoding |
| BH | 1.66.0-1 | Boost C++ Header Files |
| bindr | 0.1.1 | Parametrized Active Bindings |
| bindrcpp | 0.2.2 | An ‘Rcpp’ Interface to Active Bindings |
| bit | 1.1-13 | A Class for Vectors of 1-Bit Booleans |
| bit64 | 0.9-7 | A S3 Class for Vectors of 64bit Integers |
| bookdown | 0.7 | Authoring Books and Technical Documents with R Markdown |
| boxr | 0.3.4 | Interface for the ‘Box.com API’ |
| cellranger | 1.1.0 | Translate Spreadsheet Cell Ranges to Rows and Columns |
| classInt | 0.2-3 | Choose Univariate Class Intervals |
| cli | 1.0.0 | Helpers for Developing Command Line Interfaces |
| clipr | 0.4.0 | Read and Write from the System Clipboard |
| clisymbols | 1.2.0 | Unicode Symbols at the R Prompt |
| colorspace | 1.3-2 | Color Space Manipulation |
| crayon | 1.3.4 | Colored Terminal Output |
| crosstalk | 1.0.0 | Inter-Widget Interactivity for HTML Widgets |
| curl | 3.2 | A Modern and Flexible Web Client for R |
| data.table | 1.11.2 | Extension of data.frame |
| DBI | 1.0.0 | R Database Interface |
| desc | 1.2.0 | Manipulate DESCRIPTION Files |
| devtools | 1.13.5 | Tools to Make Developing R Packages Easier |
| dichromat | 2.0-0 | Color Schemes for Dichromats |
| digest | 0.6.15 | Create Compact Hash Digests of R Objects |
| docopt | 0.4.5 | Command-Line Interface Specification Language |
| doParallel | 1.0.11 | Foreach Parallel Adaptor for the ‘parallel’ Package |
| dplyr | 0.7.4 | A Grammar of Data Manipulation |
| e1071 | 1.6-8 | Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien |
| enc | 0.2.0 | Portable Tools for ‘UTF-8’ Character Data |
| evaluate | 0.10.1 | Parsing and Evaluation Tools that Provide More Details than the Default |
| FNN | 1.1 | Fast Nearest Neighbor Search Algorithms and Applications |
| forcats | 0.3.0 | Tools for Working with Categorical Variables (Factors) |
| foreach | 1.4.4 | Provides Foreach Looping Construct for R |
| fs | 1.2.2 | Cross-Platform File System Operations Based on ‘libuv’ |
| ggplot2 | 2.2.1.9000 | Create Elegant Data Visualisations Using the Grammar of Graphics |
| gh | 1.0.1 | ‘GitHub’ ‘API’ |
| git2r | 0.21.0 | Provides Access to Git Repositories |
| glue | 1.2.0 | Interpreted String Literals |
| gridExtra | 2.3 | Miscellaneous Functions for “Grid” Graphics |
| gtable | 0.2.0 | Arrange ‘Grobs’ in Tables |
| haven | 1.1.1 | Import and Export ‘SPSS’, ‘Stata’ and ‘SAS’ Files |
| hexbin | 1.27.2 | Hexagonal Binning Routines |
| highr | 0.6 | Syntax Highlighting for R Source Code |
| hms | 0.4.2 | Pretty Time of Day |
| htmltools | 0.3.6 | Tools for HTML |
| htmlwidgets | 1.2 | HTML Widgets for R |
| httpuv | 1.4.3 | HTTP and WebSocket Server Library |
| httr | 1.3.1 | Tools for Working with URLs and HTTP |
| ini | 0.3.0 | Read and Write ‘.ini’ Files |
| iterators | 1.0.9 | Provides Iterator Construct for R |
| jsonlite | 1.5 | A Robust, High Performance JSON Parser and Generator for R |
| kableExtra | 0.8.0 | Construct Complex Table with ‘kable’ and Pipe Syntax |
| knitr | 1.20 | A General-Purpose Package for Dynamic Report Generation in R |
| labeling | 0.3 | Axis Labeling |
| later | 0.7.2 | Utilities for Delaying Function Execution |
| lazyeval | 0.2.1 | Lazy (Non-Standard) Evaluation |
| leaflet | 2.0.0 | Create Interactive Web Maps with the JavaScript ‘Leaflet’ Library |
| littler | 0.3.3 | R at the Command-Line via ‘r’ |
| lubridate | 1.7.4 | Make Dealing with Dates a Little Easier |
| lwgeom | 0.1-4 | Bindings to Selected ‘liblwgeom’ Functions for Simple Features |
| magrittr | 1.5 | A Forward-Pipe Operator for R |
| markdown | 0.8 | ‘Markdown’ Rendering for R |
| memoise | 1.1.0 | Memoisation of Functions |
| mime | 0.5 | Map Filenames to MIME Types |
| munsell | 0.4.3 | Utilities for Using Munsell Colours |
| openssl | 1.0.1 | Toolkit for Encryption, Signatures and Certificates Based on OpenSSL |
| openxlsx | 4.0.17 | Read, Write and Edit XLSX Files |
| patchwork | 0.0.1 | The Composer of ggplots |
| piggyback | 0.0.0.9900 | Managing Larger Data on a GitHub Repository |
| pillar | 1.2.2 | Coloured Formatting for Columns |
| pkgconfig | 2.0.1 | Private Configuration for ‘R’ Packages |
| plogr | 0.2.0 | The ‘plog’ C++ Logging Library |
| plotly | 4.7.1 | Create Interactive Web Graphics via ‘plotly.js’ |
| plyr | 1.8.4 | Tools for Splitting, Applying and Combining Data |
| png | 0.1-7 | Read and write PNG images |
| promises | 1.0.1 | Abstractions for Promise-Based Asynchronous Programming |
| purrr | 0.2.4 | Functional Programming Tools |
| R6 | 2.2.2 | Classes with Reference Semantics |
| raster | 2.6-7 | Geographic Data Analysis and Modeling |
| RColorBrewer | 1.1-2 | ColorBrewer Palettes |
| Rcpp | 0.12.16 | Seamless R and C++ Integration |
| RcppTOML | 0.1.3 | ‘Rcpp’ Bindings to Parser for Tom’s Obvious Markup Language |
| readr | 1.1.1 | Read Rectangular Text Data |
| readxl | 1.1.0 | Read Excel Files |
| rematch | 1.0.1 | Match Regular Expressions with a Nicer ‘API’ |
| rematch2 | 2.0.1 | Tidy Output from Regular Expression Matching |
| remotes | 1.1.1 | R Package Installation from Remote Repositories, Including ‘GitHub’ |
| reshape2 | 1.4.3 | Flexibly Reshape Data: A Reboot of the Reshape Package |
| rgdal | 1.2-20 | Bindings for the ‘Geospatial’ Data Abstraction Library |
| rgeos | 0.3-26 | Interface to Geometry Engine - Open Source (‘GEOS’) |
| rio | 0.5.10 | A Swiss-Army Knife for Data I/O |
| rlang | 0.2.0 | Functions for Base Types and Core R and ‘Tidyverse’ Features |
| rmarkdown | 1.9 | Dynamic Documents for R |
| rnaturalearth | 0.1.0 | World Map Data from Natural Earth |
| rnaturalearthhires | 0.1.0 | High Resolution World Vector Map Data from Natural Earth used in rnaturalearth |
| RPostgreSQL | 0.6-2 | R Interface to the ‘PostgreSQL’ Database System |
| rprojroot | 1.3-2 | Finding Files in Project Subdirectories |
| rstudioapi | 0.7 | Safely Access the RStudio API |
| rvest | 0.3.2 | Easily Harvest (Scrape) Web Pages |
| scales | 0.5.0 | Scale Functions for Visualization |
| selectr | 0.4-1 | Translate CSS Selectors to XPath Expressions |
| sf | 0.6-2 | Simple Features for R |
| shiny | 1.0.5 | Web Application Framework for R |
| smoothr | 0.1.0 | Smooth and Tidy Spatial Features |
| sourcetools | 0.1.7 | Tools for Reading, Tokenizing and Parsing R Code |
| sp | 1.2-7 | Classes and Methods for Spatial Data |
| spData | 0.2.8.3 | Datasets for Spatial Analysis |
| stringi | 1.1.7 | Character String Processing Facilities |
| stringr | 1.3.0 | Simple, Consistent Wrappers for Common String Operations |
| styler | 1.0.1 | Non-Invasive Pretty Printing of R Code |
| tibble | 1.4.2 | Simple Data Frames |
| tidyr | 0.8.0 | Easily Tidy Data with ‘spread()’ and ‘gather()’ Functions |
| tidyselect | 0.2.4 | Select from a Set of Strings |
| tinytex | 0.8.1 | Helper Functions to Install and Maintain ‘TeX Live’, and Compile ‘LaTeX’ Documents |
| udunits2 | 0.13 | Udunits-2 Bindings for R |
| units | 0.5-1 | Measurement Units for R Vectors |
| usethis | 1.3.0 | Automate Package and Project Setup |
| utf8 | 1.1.3 | Unicode Text Processing |
| viridis | 0.5.1 | Default Color Maps from ‘matplotlib’ |
| viridisLite | 0.3.0 | Default Color Maps from ‘matplotlib’ (Lite Version) |
| whisker | 0.3-2 | {{mustache}} for R, logicless templating |
| withr | 2.1.2 | Run Code ‘With’ Temporarily Modified Global State |
| xfun | 0.3 | Miscellaneous Functions by ‘Yihui Xie’ |
| xml2 | 1.2.0 | Parse XML |
| xtable | 1.8-2 | Export Tables to LaTeX or HTML |
| yaml | 2.1.19 | Methods to Convert R Data to YAML and Back |
| base | 3.4.4 | The R Base Package |
| boot | 1.3-20 | Bootstrap Functions (Originally by Angelo Canty for S) |
| class | 7.3-14 | Functions for Classification |
| cluster | 2.0.6 | “Finding Groups in Data”: Cluster Analysis Extended Rousseeuw et al. |
| codetools | 0.2-15 | Code Analysis Tools for R |
| compiler | 3.4.4 | The R Compiler Package |
| datasets | 3.4.4 | The R Datasets Package |
| foreign | 0.8-69 | Read Data Stored by ‘Minitab’, ‘S’, ‘SAS’, ‘SPSS’, ‘Stata’, ‘Systat’, ‘Weka’, ‘dBase’, … |
| graphics | 3.4.4 | The R Graphics Package |
| grDevices | 3.4.4 | The R Graphics Devices and Support for Colours and Fonts |
| grid | 3.4.4 | The Grid Graphics Package |
| KernSmooth | 2.23-15 | Functions for Kernel Smoothing Supporting Wand & Jones (1995) |
| lattice | 0.20-35 | Trellis Graphics for R |
| MASS | 7.3-49 | Support Functions and Datasets for Venables and Ripley’s MASS |
| Matrix | 1.2-12 | Sparse and Dense Matrix Classes and Methods |
| methods | 3.4.4 | Formal Methods and Classes |
| mgcv | 1.8-23 | Mixed GAM Computation Vehicle with Automatic Smoothness Estimation |
| nlme | 3.1-131.1 | Linear and Nonlinear Mixed Effects Models |
| nnet | 7.3-12 | Feed-Forward Neural Networks and Multinomial Log-Linear Models |
| parallel | 3.4.4 | Support for Parallel computation in R |
| rpart | 4.1-13 | Recursive Partitioning and Regression Trees |
| spatial | 7.3-11 | Functions for Kriging and Point Pattern Analysis |
| splines | 3.4.4 | Regression Spline Functions and Classes |
| stats | 3.4.4 | The R Stats Package |
| stats4 | 3.4.4 | Statistical Functions using S4 Classes |
| survival | 2.41-3 | Survival Analysis |
| tcltk | 3.4.4 | Tcl/Tk Interface |
| tools | 3.4.4 | Tools for Package Development |
| utils | 3.4.4 | The R Utils Package |