oceanhackweek / ohw20-proj-species-marine-protected-areas

ohw20-proj-species-marine-protected-areas

Using OBIS data and species distribution modeling

To start with, check out the notebook on pulling OBIS data here

• in ohw20-tutorials/08-R-tutorials/08-OBIS-access.ipynb
• in the same directory, check out the R-markdown version, robis.Rmd

Some interesting resources:

• es50 biodiversity measurement
  • https://data-blog.gbif.org/post/exploring-es50-for-gbif/
  • https://github.com/jhnwllr/es50

Potential projects:

• Linking an OBIS taxon download with OBPG satellite measurements
• Connecting es50 diversity with oceanographic features

Quick git instructions

• https://oceanhackweek.github.io/ohw-resources/prep/git/#git-steps-and-workflows

ohw20-proj-species-marine-protected-areas's Issues

RShiny: Visualize MPAs on the MPA tab

• Load a default MPA country (like Cuba)
• Add tooltip interactivity (to view metadata of each MPA)
• Add filtering capability
• Add selection capability (be able to select multiple MPAs by filtering or clicking/dragging)

Internal Server Error (HTTP 500)

One MPA in Cuba is still giving an internal server error.

To recreate this error:

1. Run lines 1-99 in the script 'CalculatingES50.R'
2. Make i = 88 (instead of running through all the MPAs)
3. Run lines 103-105
   hull = st_convex_hull(ES50_df$geom[[i]]) #find the convex hull for the polygon
text = st_as_text(hull) #convert it to text
SpeciesOccurence = occurrence(geometry = text) #query OBIS for species within that polygon

RShiny: Interactively fetch OBIS data

• Demo load and OBIS table and display it
• User input similar to https://mapper.obis.org/, e.g. species name
• Display OBIS record as a table

Combining OBIS and MPA visualization

• Color MPAs by number of OBIS entries
• Fetch OBIS entries based on selection of MPAs
• Statistics of fetched OBIS entries