R interface (rBExIS)

The package that you need:

  • install.packages(“httr”)
  • install.packages(“XML”)
  • install.packages(“jsonlite”)
  • install_github(“BEXIS2/rBExIS”, subdir = “rBExIS”)
  • library(httr)
  • library(jsonlite)
  • library(XML)
  • library(rBExIS)
  • bexis.options() # info of the url and token number

bexis.options(base_url = “https://jexis.uni-jena.de”)
token_id<-”XXXXXXXXXX” •bexis.options(token = “token_id”)

#get list of all dataset ids
bexis_dataset_ids <- bexis.get.datasets()

#get data from bexis from dataset with id = xy
bexis_data90 <- bexis.get.dataset_by(id = 90)

! The NA value in the database will be read as the maximum double value 1.797693e+307 in R ( .Machine$double.xmax/10) if you use rBEXIS package.

For example, here is the code to correct the the biomass “NA” data from 2020:

a<-.Machine$double.xmax/100
d2020$biomass[d2020$biomass >a]<-NA