Technical citations 本站技術引用

Open-source techniques

This site bio.odb.ntu.edu.tw/query is powered by R, Shiny-server
- Running under: Ubuntu 14.04.5 LTS
- R version 3.4.3 (2017-11-30) R Core Team (2018)
- The interactive R session to connect PostgresSQL database is bridged on OpenCpu API Ooms (2019)
List of R packages used:
- data.table Dowle and Srinivasan (2019)
  DT Xie, Cheng, and Tan (2018)
  future Bengtsson (2019c)
  GGally Schloerke et al. (2018)
  geojsonsf Cooley (2019)
  htmltools RStudio and Inc. (2017)
  leafem Appelhans (2019)
  leaflet Cheng, Karambelkar, and Xie (2018)
  leaflet.extras Karambelkar and Schloerke (2018)
  magrittr Bache and Wickham (2014)
  mapedit Appelhans, Russell, and Busetto (2019)
  mapview Appelhans et al. (2018)
  odbapi cywhale (2018)
  plotly Sievert et al. (2019)
  promises Cheng (2018)
  purrr Henry and Wickham (2019)
  R.cache Bengtsson (2018)
  raster Hijmans (2019)
  RColorBrewer Neuwirth (2014)
  Rcpp Eddelbuettel, Francois, Allaire, et al. (2019)
  RcppArmadillo Eddelbuettel, Francois, Bates, et al. (2019)
  rnaturalearth South (2019)
  robis Provoost and Bosch (2019)
  RPostgres Wickham, Ooms, and Müller (2018)
  sendmailR Mersmann (2014)
  shiny Chang et al. (2019)
  shinyAce Nijs et al. (2019)
  shinyjs Attali (2018)
  shinysky AnalytixWare (2014)
  shinyTree Trestle Technology, LLC and Allen (2018)
  sp Pebesma and Bivand (2018)
  sf Pebesma (2019)
  taxize Chamberlain et al. (2019)

Open API: now integrates with BioQuery GUI, and besides aboving, uses addtional R packages, including:
- configr Li (2018)
  doFuture Bengtsson (2019a)
  foreach Revolution Analytics and Weston (n.d.)
  furrr Vaughan and Dancho (2018)
  future.apply Bengtsson (2019b)
  GGally Schloerke et al. (2018)
  gginnards Aphalo (2019)
  ggrepel Slowikowski (2018)
  gridExtra Auguie (2017)
  gstat Pebesma and Graeler (2019)
  htmlwidgets Vaidyanathan et al. (2018)
  iNEXT Hsieh, Ma, and Chao (2019)
  jsonlite Ooms, Temple Lang, and Hilaiel (2018)
  stringr Wickham (2019)
  vegan Oksanen et al. (2019)
Manual for this site is generated by knitr Xie (2019) and rmarkdown Allaire et al. (2019)

REFERENCES

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AnalytixWare. 2014. Shinysky: A Set of Shiny Ui Components/Widgets. https://github.com/AnalytixWare/ShinySky.

Aphalo, Pedro J. 2019. Gginnards: Explore the Innards of ’Ggplot2’ Objects. https://CRAN.R-project.org/package=gginnards.

Appelhans, Tim. 2019. Leafem: ’Leaflet’ Extensions for ’Mapview’. https://CRAN.R-project.org/package=leafem.

Appelhans, Tim, Florian Detsch, Christoph Reudenbach, and Stefan Woellauer. 2018. Mapview: Interactive Viewing of Spatial Data in R. https://CRAN.R-project.org/package=mapview.

Appelhans, Tim, Kenton Russell, and Lorenzo Busetto. 2019. Mapedit: Interactive Editing of Spatial Data in R. https://CRAN.R-project.org/package=mapedit.

Attali, Dean. 2018. Shinyjs: Easily Improve the User Experience of Your Shiny Apps in Seconds. https://CRAN.R-project.org/package=shinyjs.

Auguie, Baptiste. 2017. GridExtra: Miscellaneous Functions for "Grid" Graphics. https://CRAN.R-project.org/package=gridExtra.

Bache, Stefan Milton, and Hadley Wickham. 2014. Magrittr: A Forward-Pipe Operator for R. https://CRAN.R-project.org/package=magrittr.

Bengtsson, Henrik. 2018. R.cache: Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed up Computations. https://CRAN.R-project.org/package=R.cache.

———. 2019a. DoFuture: A Universal Foreach Parallel Adapter Using the Future Api of the ’Future’ Package. https://CRAN.R-project.org/package=doFuture.

———. 2019b. Future.apply: Apply Function to Elements in Parallel Using Futures. https://CRAN.R-project.org/package=future.apply.

———. 2019c. Future: Unified Parallel and Distributed Processing in R for Everyone. https://CRAN.R-project.org/package=future.

Chamberlain, Scott, Eduard Szoecs, Zachary Foster, and Zebulun Arendsee. 2019. Taxize: Taxonomic Information from Around the Web. https://CRAN.R-project.org/package=taxize.

Chang, Winston, Joe Cheng, JJ Allaire, Yihui Xie, and Jonathan McPherson. 2019. Shiny: Web Application Framework for R. https://CRAN.R-project.org/package=shiny.

Cheng, Joe. 2018. Promises: Abstractions for Promise-Based Asynchronous Programming. https://CRAN.R-project.org/package=promises.

Cheng, Joe, Bhaskar Karambelkar, and Yihui Xie. 2018. Leaflet: Create Interactive Web Maps with the Javascript ’Leaflet’ Library. https://CRAN.R-project.org/package=leaflet.

Cooley, David. 2019. Geojsonsf: GeoJSON to Simple Feature Converter. https://CRAN.R-project.org/package=geojsonsf.

cywhale. 2018. Odbapi: API for Access Database in Odb, Iontu, Taiwan.

Dowle, Matt, and Arun Srinivasan. 2019. Data.table: Extension of ‘Data.frame‘. https://CRAN.R-project.org/package=data.table.

Eddelbuettel, Dirk, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou, Nathan Russell, Douglas Bates, and John Chambers. 2019. Rcpp: Seamless R and C++ Integration. https://CRAN.R-project.org/package=Rcpp.

Eddelbuettel, Dirk, Romain Francois, Doug Bates, and Binxiang Ni. 2019. RcppArmadillo: ’Rcpp’ Integration for the ’Armadillo’ Templated Linear Algebra Library. https://CRAN.R-project.org/package=RcppArmadillo.

Henry, Lionel, and Hadley Wickham. 2019. Purrr: Functional Programming Tools. https://CRAN.R-project.org/package=purrr.

Hijmans, Robert J. 2019. Raster: Geographic Data Analysis and Modeling. https://CRAN.R-project.org/package=raster.

Hsieh, T. C., K. H. Ma, and Anne Chao. 2019. INEXT: Interpolation and Extrapolation for Species Diversity. https://CRAN.R-project.org/package=iNEXT.

Karambelkar, Bhaskar, and Barret Schloerke. 2018. Leaflet.extras: Extra Functionality for ’Leaflet’ Package. https://CRAN.R-project.org/package=leaflet.extras.

Li, Jianfeng. 2018. Configr: An Implementation of Parsing and Writing Configuration File (Json/Ini/Yaml/Toml). https://CRAN.R-project.org/package=configr.

Mersmann, Olaf. 2014. SendmailR: Send Email Using R. https://CRAN.R-project.org/package=sendmailR.

Neuwirth, Erich. 2014. RColorBrewer: ColorBrewer Palettes. https://CRAN.R-project.org/package=RColorBrewer.

Nijs, Vincent, Forest Fang, Trestle Technology, LLC, and Jeff Allen. 2019. ShinyAce: Ace Editor Bindings for Shiny. https://CRAN.R-project.org/package=shinyAce.

Oksanen, Jari, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, et al. 2019. Vegan: Community Ecology Package. https://CRAN.R-project.org/package=vegan.

Ooms, Jeroen. 2019. Opencpu: Producing and Reproducing Results. https://CRAN.R-project.org/package=opencpu.

Ooms, Jeroen, Duncan Temple Lang, and Lloyd Hilaiel. 2018. Jsonlite: A Robust, High Performance Json Parser and Generator for R. https://CRAN.R-project.org/package=jsonlite.

Pebesma, Edzer. 2019. Sf: Simple Features for R. https://CRAN.R-project.org/package=sf.

Pebesma, Edzer, and Roger Bivand. 2018. Sp: Classes and Methods for Spatial Data. https://CRAN.R-project.org/package=sp.

Pebesma, Edzer, and Benedikt Graeler. 2019. Gstat: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction and Simulation. https://CRAN.R-project.org/package=gstat.

Provoost, Pieter, and Samuel Bosch. 2019. Robis: Ocean Biogeographic Information System (Obis) Client. https://CRAN.R-project.org/package=robis.

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Revolution Analytics, and Steve Weston. n.d. Foreach: Provides Foreach Looping Construct for R.

RStudio, and Inc. 2017. Htmltools: Tools for Html. https://CRAN.R-project.org/package=htmltools.

Schloerke, Barret, Jason Crowley, Di Cook, Francois Briatte, Moritz Marbach, Edwin Thoen, Amos Elberg, and Joseph Larmarange. 2018. GGally: Extension to ’Ggplot2’. https://CRAN.R-project.org/package=GGally.

Sievert, Carson, Chris Parmer, Toby Hocking, Scott Chamberlain, Karthik Ram, Marianne Corvellec, and Pedro Despouy. 2019. Plotly: Create Interactive Web Graphics via ’Plotly.js’. https://CRAN.R-project.org/package=plotly.

Slowikowski, Kamil. 2018. Ggrepel: Automatically Position Non-Overlapping Text Labels with ’Ggplot2’. https://CRAN.R-project.org/package=ggrepel.

South, Andy. 2019. Rnaturalearth: World Map Data from Natural Earth. https://github.com/ropenscilabs/rnaturalearth.

Trestle Technology, LLC, and Jeff Allen. 2018. ShinyTree: JsTree Bindings for Shiny. https://CRAN.R-project.org/package=shinyTree.

Vaidyanathan, Ramnath, Yihui Xie, JJ Allaire, Joe Cheng, and Kenton Russell. 2018. Htmlwidgets: HTML Widgets for R. https://CRAN.R-project.org/package=htmlwidgets.

Vaughan, Davis, and Matt Dancho. 2018. Furrr: Apply Mapping Functions in Parallel Using Futures. https://CRAN.R-project.org/package=furrr.

Wickham, Hadley. 2019. Stringr: Simple, Consistent Wrappers for Common String Operations. https://CRAN.R-project.org/package=stringr.

Wickham, Hadley, Jeroen Ooms, and Kirill Müller. 2018. RPostgres: ’Rcpp’ Interface to ’Postgresql’. https://CRAN.R-project.org/package=RPostgres.

Xie, Yihui. 2019. Knitr: A General-Purpose Package for Dynamic Report Generation in R. https://CRAN.R-project.org/package=knitr.

Xie, Yihui, Joe Cheng, and Xianying Tan. 2018. DT: A Wrapper of the Javascript Library ’Datatables’. https://CRAN.R-project.org/package=DT.

Technical citations 本站技術引用

cywhale

2019-07-12

Open-source techniques

REFERENCES