This app is built with Rhino. You can see a deployed version here: Biodata Discovery Board App Demo. Using the biodiversity data coming from the Global Biodiversity Information Facility, this Shiny app visualizes observed species on the map, draw a timeline with selected species observation, and allows the user to explore associated pictures.
This is an application built in Shiny. To run it, make sure you have R (>= 4.0.0) installed. For JavaScript and Sass development you'll also need Node.js (>= 16.0.0).
Run renv::restore(clean = TRUE) to synchronize the project library with the lockfile
when you initially clone the repo or switch branches.
To run the app, use Rscript -e 'shiny::runApp(launch.browser = TRUE)'.
git-lfs is required to fetch the example dataset
run git lfs pull
Then you'll find it here : inst/extdata/biodiversity_data_poland.db. This dataset is restricted to poland observations to save development time.
- You can download the whole dataset here.
- Then you will have to import occurence and multimedia csv files into an sqlite database
- Finally execute these few sqlite queries on your sqlite database :
-- Step 1 : Remove unecessary string in id column
UPDATE multimedia SET id = REPLACE(id, '@OBS', '')
UPDATE occurence SET id = REPLACE(id, '@OBS', '')
-- Step 2 : Remove unsused columns
CREATE TABLE occurence_tmp AS
SELECT column1, column2, /* other columns except the one you want to remove */
FROM occurence;
DROP TABLE occurence;
ALTER TABLE occurence_tmp RENAME TO occurence;
-- Step 3 : Convert taxonRank to integer
UPDATE occurence SET taxonRank = REPLACE(taxonRank, 'subspecies', '3');
UPDATE occurence SET taxonRank = REPLACE(taxonRank, 'multispecies', '2');
UPDATE occurence SET taxonRank = REPLACE(taxonRank, 'species', '1');
UPDATE occurence SET taxonRank = REPLACE(taxonRank, 'synonym', '4');
UPDATE occurence SET taxonRank = REPLACE(taxonRank, 'forma', '5');
UPDATE occurence SET taxonRank = REPLACE(taxonRank, 'hybrid', '6');
UPDATE occurence SET taxonRank = REPLACE(taxonRank, 'variety', '7');
-- Step 4 : Split occcurence table by kingdom
PRAGMA foreign_keys=off;
CREATE TABLE IF NOT EXISTS occurence_Fungi AS
SELECT * FROM occurence WHERE 1=0;
INSERT INTO occurence_Fungi
SELECT * FROM occurence WHERE kingdom = 'Fungi';
CREATE TABLE IF NOT EXISTS occurence_Animalia AS
SELECT * FROM occurence WHERE 1=0;
INSERT INTO occurence_Animalia
SELECT * FROM occurence WHERE kingdom = 'Animalia';
CREATE TABLE IF NOT EXISTS occurence_Plantae AS
SELECT * FROM occurence WHERE 1=0;
INSERT INTO occurence_Plantae
SELECT * FROM occurence WHERE kingdom = 'Plantae';
DROP TABLE occurence;
VACUUM;
-- Step 5 : Create species_family_match tables
CREATE TABLE IF NOT EXISTS species_family_match_Fungi AS
SELECT DISTINCT scientificName, family, taxonRank
FROM occurence_Fungi;
CREATE TABLE IF NOT EXISTS species_family_match_Plantae AS
SELECT DISTINCT scientificName, family, taxonRank
FROM occurence_Plantae;
CREATE TABLE IF NOT EXISTS species_family_match_Animalia AS
SELECT DISTINCT scientificName, family, taxonRank
FROM occurence_Animalia;
-- Step 6 : Create indexes
CREATE INDEX "idx_multimedia_id" ON "multimedia" (
"id"
);
CREATE INDEX "idx_occurence_Fungi_scientificName" ON "occurence_Fungi" (
"scientificName"
);
CREATE INDEX "idx_occurence_Plantae_scientificName" ON "occurence_Plantae" (
"scientificName"
);
CREATE INDEX "idx_occurence_Animalia_scientificName" ON "occurence_Animalia" (
"scientificName"
);
CREATE INDEX "idx_occurence_Plantae_taxonRank" ON "species_family_match_Plantae" (
"taxonRank"
);
CREATE INDEX "idx_occurence_Animalia_taxonRank" ON "species_family_match_Animalia" (
"taxonRank"
);
CREATE INDEX "idx_occurence_Fungi_taxonRank" ON "species_family_match_Fungi" (
"taxonRank"
);
PRAGMA foreign_keys=on;
-- Step 7 : Commit changes to make them permanent
COMMIT;
VACUUM;
- Edit config and .Renviron files to track your database in the app.