In luismurao/ntbox: From Getting Biodiversity Data to Evaluating Species Distribution Models in a Friendly GUI Environment

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 4,
  fig.height = 4
)
library(dplyr)
options(rmarkdown.html_vignette.check_title = FALSE)

library(ntbox)
library(dplyr)

Geographic data

In this example we will dowonland ocrrence data for Leopardus wiedii from the Global Biodiversity Information Facility (https://www.gbif.org) and explore what is the provenance and date of collecting these points. Then we will remove sptial duplicates.

Searching the data

dAll_a <- ntbox::search_gbif_data(genus = "Leopardus",
                                  species = "wiedii",
                                  occlim = 5000,
                                  leafletplot = TRUE)

cat("Total number of occurrence data found:",nrow(dAll_a))

Data curation

In this example we filter those records starting in 1950.

dAll_b <- ntbox::clean_dup(dAll_a,longitude = "longitude","latitude",
                           threshold = 0)
cat("Total number of occurrence data affter cleanining spatial duplicates:",
    nrow(dAll_b))

dAll_c <- dAll_b %>% dplyr::filter(year>=1950)
cat("Total number of occurrence data for periods >=1950:",
    nrow(dAll_c))

m <- leaflet::leaflet(dAll_c)
m <- m %>% leaflet::addTiles()
m <- m %>% leaflet::addCircleMarkers(lng = ~longitude, 
                                     lat = ~latitude, 
                                     popup = ~leaflet_info, 
                                     fillOpacity = 0.25, 
                                     radius = 7,col="green")
m

Remove wired occurrences. Click on the pop-up to display gbif information (available when the downloaded data comes from search_gbif function), the points that are outside the distribution are the one on San Francisco (this comes from a collection; rowID=632), the record on Florida (rowID=508,489), and the ones that in the sea (544,595).

# Indixes of the wired data (can change depending the date of the gbif query)
to_rmIDs <- c(636,493,512,544,595)
to_rm <- which(dAll_c$ntboxID %in% to_rmIDs)
dAll <- dAll_c[-to_rm,]
m <- leaflet::leaflet(dAll)
m <- m %>% leaflet::addTiles()
m <- m %>% leaflet::addCircleMarkers(lng = ~longitude, 
                                     lat = ~latitude, 
                                     popup = ~leaflet_info, 
                                     fillOpacity = 0.25, 
                                     radius = 7,col="green")
m

luismurao/ntbox documentation built on May 9, 2024, 8:24 p.m.