This repository contains the code and data of contemporary (1980s - 2017) diatom datasets of tropical South America (TSADB). The database includes diatom (unicelular siliceous algae) data and associated environmental variables of waterbody sites (streams, wetlands, lakes), covering an altitudinal gradient from 220 to 5,070 m a.s.l. between 8°N–30°S and 58–79°W.
Datasets are available as Excel Data Tables on Dryad and Zenodo as R files, while here the aim is to provide a shiny app to interactively visualize and explore the database in R for promoting biodiversity, biogeographic and paleolimnological studies in tropical South America.
A table with geographical coordinates of lakes is available (file biogeographySites.csv) in the data folder.
read.csv("data/biogeographySites.csv", stringsAsFactors = FALSE)
world <- map_data("world")
southamerica <- ggplot() +
geom_polygon(data = world, aes(x=long, y = lat, group = group), fill="lightgrey") +
geom_point(data=sites_map, aes(x=Long.DD.W, y=Lat.DD.S, col=Habitat), shape=20, size=4)+
coord_map("albers", parameters = c(-100, -100), ylim=c(-40,15), xlim=c(-82,-40)) +
xlab("Longitude") + ylab("Latitude") +
theme_bw()
The database is also available for visualisation through the R Markdown diatom-biogeography-southamerica.Rmd file
To explore the database, run the database_shiny.R file in the R scripts folder. The output generates the following files for each study region:
- Region table with basic site's information (e.g. year, site name, saple type)
- Map: Geographical distribution of sites
- Environment-table: variables for the physical habitat, water chemistry, and geo-climatic context
- Environment-boxplots: Boxplots for selected environmental variables
- Taxa: Site-by-species data matrix
- Ecological groups: Relative proportion of diatom ecological groups (freshwater planktic, oligosaline planktic, tychoplanktic, benthic, epiphytic, and saline)
Check out the contributor guide on how to share your data for the Tropical South American Database.