SA: South American plant species distribution data

In rspatial/disdat: Data for Comparing Species Distribution Modeling Methods

South American plant species distribution data

Description

Species occurrence data for 30 vascular plant species (all from the Bignoniaceae family) from Continental Brazil, Ecuador, Colombia, Bolivia, and Peru, South America (SA), and associated environmental data. Full details of the dataset are provided in the reference below. There are four data sets with training (po and bg) and test (pa, env) data:

po (training data) includes site names, species names, coordinates, occurrence ("1" for all, since all are presence records), group (plant), and site values for 11 environmental variables (below).

bg (training data) has 10000 sites selected at random across the study region. It is structured identically to po, with "0" for occurrence (not implying absence, but denoting background in a way suited to most modelling methods) and NA for group.

env (testing data) includes group, site names, coordinates, and site values for 11 environmental variables (below), at 152 sites. This file is suited to making predictions.

pa (testing data) includes group, site names, coordinates, and presence-absence records, one column per species. The sites are identical to the sites in env. This file is suited to evaluating the predictions made to env.

Raster (gridded) data for all environmental variables are available - see the reference below for details.

The coordinate reference system of the x and y coordinates is longitude, latitude, with the WGS84 datum (EPSG:4326).

The vignette provided with this package provides an example of how to fit and evaluate a model with these data.

Environmental variables (extracted from WorldClim):

Code	Description	Units	Type
sabio1	Annual mean temperature	degrees C * 10	Continuous
sabio2	Mean Diurnal Range (Mean of monthly (max temp - min temp))	degrees C * 10	Continuous
sabio4	Temperature Seasonality (standard deviation *100)	dimensionless	Continuous
sabio5	Max Temperature of Warmest Month	degrees C * 10	Continuous
sabio6	Min Temperature of Coldest Month	degrees C * 10	Continuous
sabio7	Temperature Annual Range	degrees C * 10	Continuous
sabio8	Mean Temperature of Wettest Quarter	mm	Continuous
sabio12	Annual Precipitation	mm	Continuous
sabio15	Precipitation Seasonality (Coefficient of Variation)	mm	Continuous
sabio17	Precipitation of Driest Quarter	mm	Continuous
sabio18	Precipitation of Warmest Quarter	mm	Continuous

Source

Environmental data prepared by Bette Loiselle, Lucia Lohmann and Catherine Graham. Species supplied by Bette Loiselle and Lucia Lohmann. PO data from the Missouri Botanical Gardens database and Lucia Lohmann; PA data collected by Al Gentry.

See the reference below for further details on source, accuracy, cleaning, and particular characteristics of these datasets.

References

Elith, J., Graham, C.H., Valavi, R., Abegg, M., Bruce, C., Ferrier, S., Ford, A., Guisan, A., Hijmans, R.J., Huettmann, F., Lohmann, L.G., Loiselle, B.A., Moritz, C., Overton, J.McC., Peterson, A.T., Phillips, S., Richardson, K., Williams, S., Wiser, S.K., Wohlgemuth, T. & Zimmermann, N.E., (2020). Presence-only and presence-absence data for comparing species distribution modeling methods. Biodiversity Informatics 15:69-80.

Examples

sa_po <- disPo("SA")
sa_bg <- disBg("SA")

sa_pa <- disPa("SA")
sa_env <- disEnv("SA")

x <- disData("SA")
sapply(x, head)

disCRS("SA")

rspatial/disdat documentation built on Feb. 14, 2023, 4:27 a.m.