BotanizeR quiz for memorizing the plant species • BotanizeR

BotanizeR is an R-package with Shiny app designed to help botany students and other people interested in plants to learn and distinguish plant diagnostic characters, memorize plant species, and train their identification skills. Students can browse a species list, images, plant characteristics, habitat descriptions and distribution information or play a quiz where images of a random species are shown and students have to guess the correct species. BotanizeR is highly flexible allowing lecturers to define their own species lists and to provide images and further useful information, or choose from linked online content from selected botanical online resources. A Quiz and Species overview pages can be made available via the package’s Shiny application or played within R directly.

1. Tutorials

Here, we provide tutorials on

2. Functions

An overview of all functions and data is given here.

3. Installation

library(devtools)
install_github("https://github.com/patrickweigelt/BotanizeR")

library(BotanizeR)

4. First steps

Shiny app

You can start the Shiny application with the function BotanizeR_shiny().

BotanizeR_shiny()

Running the console quiz

You can run the console version of the quiz using BotanizeR_quiz().

# Load species list for UK, Ireland and Germany based on floraweb.de and the 
# Online Atlas of the British and Irish flora 
# (https://www.brc.ac.uk/plantatlas/)
data(BotanizeR_species)

# Subset for about 700 species known from Sussex, UK
BotanizeR_Sussex <- 
  BotanizeR_species[which(BotanizeR_species$UK_Ireland_Sussex==1), ]

# Type in species name, or press enter for next hint or type "skip" and
# press enter for next species or type "exit" to end quiz and save results
BotanizeR_Sussex_practiced <- 
  BotanizeR_quiz(species_list = BotanizeR_Sussex,
                 image_floraweb = FALSE, image_ukplantatlas = TRUE, 
                 hints_ukplantatlas =  c('mapuk', 'familyuk', 'ecology', 
                                         'statusuk', 'trends', 'perennation',
                                         'lifeform', 'woodiness', 
                                         'clonality'), 
                 hints_floraweb = NULL, case_sensitive = FALSE)

# If you want to keep track of your progress, you can save the species list
# with updated scores locally and load it in the next session

5. Examples

To showcase the flexibililty of BotanizeR we present 4 use cases:

1) https://gift.uni-goettingen.de/shiny/BotanizeR/

This particular instance of the BotanizeR Shiny app exemplifies a few use cases. You can practice species from the Floras of Germany, Britain and Ireland based on information retrieved live from the websites of FloraWeb and the Online Atlas of the British and Irish flora. You can choose which of the Floras to practice species from, which species subset to use and which information from each of the websites to show.This instance of BotanizeR is based on the example data and default settings of the BotanizeR R package and can be customized and used for plant identification classes across central Europe.

2) https://gift.uni-goettingen.de/shiny/BotanizeR_winter/

In this more customized instance of BotanizeR you can practice 128 woody species from Germany based on images of various plant characteristics in winter state. The Setup page is disabled and the species have to be identified by images of bark, twig, and bud characteristics only. Only the German name, family and floristic status in Germany are drawn in addition from FloraWeb.

3) https://gift.uni-goettingen.de/shiny/BotanizeR_summer/

Here, you can practice 214 forest indicator species from Germany. In the settings tab, you can enable and disable images and hints from FloraWeb and the Online Atlas of the British and Irish flora as well as images from a local folder on the server including detailed images of plant characteristics like leaves, flowers, fruits, bark etc. You can also enable or disable additional hints drawn from the species list like the taxonomic group, family, German name, Ellenberg indicator values or flowering time.

4) https://gift.uni-goettingen.de/shiny/BotanizeR_Indonesia/

This instance of BotanizeR exemplifies two use cases from tropical regions. Here you can practice 113 common wayside plant species of lowland Jambi Province, Sumatra Rembold et al., 2017 or 107 common tree species from Lore Lindu National Park, Sulawesi Brambach et al., 2017. You can hoose which of the Floras to practice species from and which additional hints to show.

6. References and dependencies

Dependencies

BotanizeR depends on dplyr, htmltools, httr, imager, magick, rgbif, rgeos, sf, shiny, shinyBS, shinyFiles, shinythemes, shinyjs, slickR, sp and XML.

References

Bundesamt für Naturschutz (BfN): http://www.floraweb.de
Image authors: https://www.floraweb.de/ueberfloraweb/bildautoren.html

Online Atlas of the British and Irish flora: https://www.brc.ac.uk/plantatlas/
Image authors: https://www.brc.ac.uk/plantatlas/content/photos

Weigelt, P., Denelle, P., Brambach, F. & Kreft, H. (2021) A flexible R package with Shiny app to practice plant identification for online teaching and beyond. PLANTS, PEOPLE, PLANET, https://doi.org/10.1002/ppp3.10226.

BotanizeR