/gbif_regional_statistics

regional statistics and graphs for GBIF

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GBIF regional statistics

Plots and statistics generated for GBIF regions.

How to make plots

Install R packages. You might need to install some other dependecies from CRAN too.

devtools::install_github("jhnwllr/gbifapi")
devtools::install_github("jhnwllr/gbifregionalstats", subdir="gbif_regional_statistics")
  1. Open /gbif_regional_statistics/gbifregionalstats/plot_gallery_notebook.rmd in Rstudio
  2. Run code chunk corresponding to plot that you want.

Running spark code to update data

  1. Find chunks in /gbif_regional_statistics/gbifregionalstats/plot_gallery_notebook.rmd with scala code.
  2. These need to run inside a spark2-shell instance on c4 or c5.
  3. csv files will be saved to /mnt/auto/misc/download.gbif.org/custom_download/jwaller/

Example settings for spark2-shell

spark2-shell --num-executors 40 --executor-cores 5 --driver-memory 8g --driver-cores 4 --executor-memory 32g

The csv files will be put in the public downloads folder, so they are accessible by the R scripts.

Plot Examples